Starting phenix.real_space_refine on Fri Mar 15 17:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlv_14790/03_2024/7zlv_14790.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlv_14790/03_2024/7zlv_14790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlv_14790/03_2024/7zlv_14790.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlv_14790/03_2024/7zlv_14790.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlv_14790/03_2024/7zlv_14790.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlv_14790/03_2024/7zlv_14790.pdb" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 39 5.16 5 C 7794 2.51 5 N 2040 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "i PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 230": "OE1" <-> "OE2" Residue "i GLU 250": "OE1" <-> "OE2" Residue "h PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 230": "OE1" <-> "OE2" Residue "h GLU 250": "OE1" <-> "OE2" Residue "j PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 230": "OE1" <-> "OE2" Residue "j GLU 250": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12234 Number of models: 1 Model: "" Number of chains: 3 Chain: "i" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Chain: "h" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Chain: "j" Number of atoms: 4078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4078 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 1 Time building chain proxies: 6.47, per 1000 atoms: 0.53 Number of scatterers: 12234 At special positions: 0 Unit cell: (78.358, 74.305, 274.253, 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 39 16.00 O 2361 8.00 N 2040 7.00 C 7794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.4 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 39 sheets defined 2.8% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'i' and resid 83 through 90 Processing helix chain 'i' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL i 262 " --> pdb=" O SER i 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG i 263 " --> pdb=" O ALA i 259 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 90 Processing helix chain 'h' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL h 262 " --> pdb=" O SER h 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG h 263 " --> pdb=" O ALA h 259 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 90 Processing helix chain 'j' and resid 258 through 264 removed outlier: 3.863A pdb=" N VAL j 262 " --> pdb=" O SER j 258 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG j 263 " --> pdb=" O ALA j 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'i' and resid 12 through 17 Processing sheet with id=AA2, first strand: chain 'i' and resid 47 through 53 removed outlier: 7.175A pdb=" N TYR i 78 " --> pdb=" O ILE i 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'i' and resid 47 through 53 removed outlier: 3.904A pdb=" N GLN i 99 " --> pdb=" O VAL i 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 109 through 115 removed outlier: 3.669A pdb=" N VAL i 128 " --> pdb=" O PHE i 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE i 167 " --> pdb=" O VAL i 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'i' and resid 154 through 159 removed outlier: 7.272A pdb=" N ILE i 141 " --> pdb=" O TYR i 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL i 158 " --> pdb=" O CYS i 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS i 139 " --> pdb=" O VAL i 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR i 140 " --> pdb=" O SER i 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 154 through 159 removed outlier: 7.272A pdb=" N ILE i 141 " --> pdb=" O TYR i 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL i 158 " --> pdb=" O CYS i 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS i 139 " --> pdb=" O VAL i 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR i 140 " --> pdb=" O SER i 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR i 175 " --> pdb=" O PHE i 203 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE i 203 " --> pdb=" O TYR i 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 182 through 184 Processing sheet with id=AA8, first strand: chain 'i' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN i 217 " --> pdb=" O ASP i 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP i 239 " --> pdb=" O ASN i 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS i 221 " --> pdb=" O ARG i 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'i' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE i 251 " --> pdb=" O VAL i 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'i' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE i 251 " --> pdb=" O VAL i 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'i' and resid 333 through 335 Processing sheet with id=AB3, first strand: chain 'i' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY i 431 " --> pdb=" O LYS i 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS i 440 " --> pdb=" O GLY i 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 676 through 679 removed outlier: 3.828A pdb=" N HIS i 686 " --> pdb=" O LYS i 677 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 12 through 17 Processing sheet with id=AB6, first strand: chain 'h' and resid 47 through 53 removed outlier: 7.175A pdb=" N TYR h 78 " --> pdb=" O ILE h 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'h' and resid 47 through 53 removed outlier: 3.904A pdb=" N GLN h 99 " --> pdb=" O VAL h 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'h' and resid 109 through 115 removed outlier: 3.670A pdb=" N VAL h 128 " --> pdb=" O PHE h 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE h 167 " --> pdb=" O VAL h 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'h' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE h 141 " --> pdb=" O TYR h 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL h 158 " --> pdb=" O CYS h 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS h 139 " --> pdb=" O VAL h 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 140 " --> pdb=" O SER h 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE h 141 " --> pdb=" O TYR h 156 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL h 158 " --> pdb=" O CYS h 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS h 139 " --> pdb=" O VAL h 158 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 140 " --> pdb=" O SER h 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR h 175 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE h 203 " --> pdb=" O TYR h 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 182 through 184 Processing sheet with id=AC3, first strand: chain 'h' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN h 217 " --> pdb=" O ASP h 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP h 239 " --> pdb=" O ASN h 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS h 221 " --> pdb=" O ARG h 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE h 251 " --> pdb=" O VAL h 274 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'h' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE h 251 " --> pdb=" O VAL h 274 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 333 through 335 Processing sheet with id=AC7, first strand: chain 'h' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY h 431 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS h 440 " --> pdb=" O GLY h 431 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 676 through 679 removed outlier: 3.829A pdb=" N HIS h 686 " --> pdb=" O LYS h 677 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'j' and resid 12 through 17 Processing sheet with id=AD1, first strand: chain 'j' and resid 47 through 53 removed outlier: 7.175A pdb=" N TYR j 78 " --> pdb=" O ILE j 35 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'j' and resid 47 through 53 removed outlier: 3.903A pdb=" N GLN j 99 " --> pdb=" O VAL j 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'j' and resid 109 through 115 removed outlier: 3.670A pdb=" N VAL j 128 " --> pdb=" O PHE j 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE j 167 " --> pdb=" O VAL j 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE j 141 " --> pdb=" O TYR j 156 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL j 158 " --> pdb=" O CYS j 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS j 139 " --> pdb=" O VAL j 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR j 140 " --> pdb=" O SER j 180 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'j' and resid 154 through 159 removed outlier: 7.273A pdb=" N ILE j 141 " --> pdb=" O TYR j 156 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL j 158 " --> pdb=" O CYS j 139 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS j 139 " --> pdb=" O VAL j 158 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR j 140 " --> pdb=" O SER j 180 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR j 175 " --> pdb=" O PHE j 203 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE j 203 " --> pdb=" O TYR j 175 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'j' and resid 182 through 184 Processing sheet with id=AD7, first strand: chain 'j' and resid 216 through 223 removed outlier: 4.366A pdb=" N ASN j 217 " --> pdb=" O ASP j 239 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP j 239 " --> pdb=" O ASN j 217 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS j 221 " --> pdb=" O ARG j 235 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'j' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE j 251 " --> pdb=" O VAL j 274 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'j' and resid 270 through 274 removed outlier: 4.103A pdb=" N PHE j 251 " --> pdb=" O VAL j 274 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'j' and resid 333 through 335 Processing sheet with id=AE2, first strand: chain 'j' and resid 413 through 415 removed outlier: 4.025A pdb=" N GLY j 431 " --> pdb=" O LYS j 440 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS j 440 " --> pdb=" O GLY j 431 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 676 through 679 removed outlier: 3.828A pdb=" N HIS j 686 " --> pdb=" O LYS j 677 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 945 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: 4.20 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3966 1.34 - 1.46: 2810 1.46 - 1.58: 5647 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 12495 Sorted by residual: bond pdb=" N MET j 1 " pdb=" CA MET j 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET h 1 " pdb=" CA MET h 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N MET i 1 " pdb=" CA MET i 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N VAL i 639 " pdb=" CA VAL i 639 " ideal model delta sigma weight residual 1.459 1.472 -0.014 1.22e-02 6.72e+03 1.25e+00 bond pdb=" N VAL j 639 " pdb=" CA VAL j 639 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.22e-02 6.72e+03 1.22e+00 ... (remaining 12490 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.76: 348 106.76 - 113.59: 6919 113.59 - 120.42: 4270 120.42 - 127.25: 5335 127.25 - 134.08: 129 Bond angle restraints: 17001 Sorted by residual: angle pdb=" N PRO h 439 " pdb=" CA PRO h 439 " pdb=" C PRO h 439 " ideal model delta sigma weight residual 111.03 114.57 -3.54 1.54e+00 4.22e-01 5.28e+00 angle pdb=" N PRO i 439 " pdb=" CA PRO i 439 " pdb=" C PRO i 439 " ideal model delta sigma weight residual 111.03 114.54 -3.51 1.54e+00 4.22e-01 5.20e+00 angle pdb=" N PRO j 439 " pdb=" CA PRO j 439 " pdb=" C PRO j 439 " ideal model delta sigma weight residual 111.03 114.53 -3.50 1.54e+00 4.22e-01 5.18e+00 angle pdb=" N ASN j 682 " pdb=" CA ASN j 682 " pdb=" C ASN j 682 " ideal model delta sigma weight residual 110.61 113.26 -2.65 1.25e+00 6.40e-01 4.48e+00 angle pdb=" N ALA i 641 " pdb=" CA ALA i 641 " pdb=" C ALA i 641 " ideal model delta sigma weight residual 107.73 111.11 -3.38 1.61e+00 3.86e-01 4.41e+00 ... (remaining 16996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6690 17.55 - 35.10: 594 35.10 - 52.66: 87 52.66 - 70.21: 6 70.21 - 87.76: 12 Dihedral angle restraints: 7389 sinusoidal: 2829 harmonic: 4560 Sorted by residual: dihedral pdb=" CA THR h 321 " pdb=" C THR h 321 " pdb=" N PRO h 322 " pdb=" CA PRO h 322 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA THR i 321 " pdb=" C THR i 321 " pdb=" N PRO i 322 " pdb=" CA PRO i 322 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA THR j 321 " pdb=" C THR j 321 " pdb=" N PRO j 322 " pdb=" CA PRO j 322 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 7386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1157 0.032 - 0.065: 444 0.065 - 0.097: 148 0.097 - 0.130: 148 0.130 - 0.162: 29 Chirality restraints: 1926 Sorted by residual: chirality pdb=" CA ILE j 414 " pdb=" N ILE j 414 " pdb=" C ILE j 414 " pdb=" CB ILE j 414 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ILE i 414 " pdb=" N ILE i 414 " pdb=" C ILE i 414 " pdb=" CB ILE i 414 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA ILE h 414 " pdb=" N ILE h 414 " pdb=" C ILE h 414 " pdb=" CB ILE h 414 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.48e-01 ... (remaining 1923 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR h 321 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.08e+00 pdb=" N PRO h 322 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO h 322 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO h 322 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR i 321 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO i 322 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO i 322 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO i 322 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR j 321 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO j 322 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO j 322 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO j 322 " -0.041 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 118 2.43 - 3.05: 8777 3.05 - 3.67: 18272 3.67 - 4.28: 26892 4.28 - 4.90: 44598 Nonbonded interactions: 98657 Sorted by model distance: nonbonded pdb=" O LEU h 651 " pdb=" NE ARG j 662 " model vdw 1.813 2.520 nonbonded pdb=" NE ARG i 662 " pdb=" O LEU j 651 " model vdw 1.877 2.520 nonbonded pdb=" O LEU i 651 " pdb=" NE ARG h 662 " model vdw 1.905 2.520 nonbonded pdb=" O VAL i 645 " pdb=" O ALA h 641 " model vdw 1.935 3.040 nonbonded pdb=" O VAL h 645 " pdb=" O ALA j 641 " model vdw 1.979 3.040 ... (remaining 98652 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 'h' selection = chain 'i' selection = chain 'j' } 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=0.00 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: 5.560 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: 13.320 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.510 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 : 0.003 0.032 12495 Z= 0.172 Angle : 0.596 4.650 17001 Z= 0.338 Chirality : 0.050 0.162 1926 Planarity : 0.006 0.110 2184 Dihedral : 13.596 87.761 4479 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.52 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.19), residues: 1569 helix: -1.46 (1.01), residues: 39 sheet: -1.44 (0.26), residues: 381 loop : -3.06 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP j 300 HIS 0.004 0.001 HIS j 630 PHE 0.008 0.001 PHE h 101 TYR 0.011 0.001 TYR j 71 ARG 0.005 0.001 ARG h 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 633 MET cc_start: 0.1901 (mmt) cc_final: -0.0124 (mtt) REVERT: i 676 MET cc_start: -0.0860 (pmm) cc_final: -0.1637 (pmm) REVERT: h 433 ASP cc_start: 0.4555 (t0) cc_final: 0.4339 (t0) REVERT: h 633 MET cc_start: 0.1119 (mmt) cc_final: 0.0243 (mtt) REVERT: h 676 MET cc_start: -0.0972 (pmm) cc_final: -0.1362 (pmm) REVERT: j 108 ARG cc_start: 0.6533 (mmp-170) cc_final: 0.6220 (mmm160) REVERT: j 433 ASP cc_start: 0.4134 (t0) cc_final: 0.3834 (t0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2116 time to fit residues: 45.3006 Evaluate side-chains 98 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 217 ASN ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12495 Z= 0.310 Angle : 0.721 8.291 17001 Z= 0.385 Chirality : 0.054 0.190 1926 Planarity : 0.006 0.105 2184 Dihedral : 6.934 33.219 1704 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.15 % Favored : 88.66 % Rotamer: Outliers : 0.08 % Allowed : 9.22 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.18), residues: 1569 helix: -1.95 (0.90), residues: 42 sheet: -1.35 (0.24), residues: 402 loop : -3.13 (0.15), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP j 429 HIS 0.007 0.002 HIS i 630 PHE 0.021 0.002 PHE j 261 TYR 0.012 0.002 TYR j 138 ARG 0.006 0.001 ARG i 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.583 Fit side-chains REVERT: i 433 ASP cc_start: 0.5351 (t0) cc_final: 0.5093 (t0) REVERT: h 108 ARG cc_start: 0.6596 (mmp-170) cc_final: 0.6206 (mmm160) REVERT: h 433 ASP cc_start: 0.5342 (t0) cc_final: 0.5063 (t0) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2312 time to fit residues: 44.4816 Evaluate side-chains 95 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 0.0770 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 217 ASN ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12495 Z= 0.296 Angle : 0.712 9.587 17001 Z= 0.379 Chirality : 0.053 0.236 1926 Planarity : 0.006 0.116 2184 Dihedral : 6.998 37.725 1704 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.28 % Favored : 88.53 % Rotamer: Outliers : 0.08 % Allowed : 6.50 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.18), residues: 1569 helix: -2.22 (0.84), residues: 42 sheet: -1.68 (0.22), residues: 474 loop : -3.01 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP j 429 HIS 0.010 0.002 HIS i 630 PHE 0.020 0.002 PHE j 261 TYR 0.013 0.002 TYR h 660 ARG 0.011 0.001 ARG j 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: i 162 MET cc_start: 0.6637 (tpp) cc_final: 0.6415 (tpp) REVERT: i 433 ASP cc_start: 0.5768 (t0) cc_final: 0.5482 (t0) REVERT: h 433 ASP cc_start: 0.5524 (t0) cc_final: 0.5307 (t0) REVERT: h 633 MET cc_start: 0.1831 (mmt) cc_final: 0.0907 (mtt) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2115 time to fit residues: 42.2929 Evaluate side-chains 91 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12495 Z= 0.269 Angle : 0.695 11.270 17001 Z= 0.366 Chirality : 0.052 0.232 1926 Planarity : 0.006 0.088 2184 Dihedral : 6.902 39.760 1704 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.47 % Favored : 88.34 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.18), residues: 1569 helix: -2.17 (0.84), residues: 42 sheet: -1.57 (0.22), residues: 474 loop : -2.96 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP j 350 HIS 0.008 0.002 HIS i 630 PHE 0.018 0.002 PHE h 261 TYR 0.013 0.002 TYR j 71 ARG 0.014 0.001 ARG j 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.273 Fit side-chains REVERT: i 433 ASP cc_start: 0.5734 (t0) cc_final: 0.5446 (t0) REVERT: i 676 MET cc_start: -0.1619 (pmm) cc_final: -0.2481 (pmm) REVERT: h 108 ARG cc_start: 0.6911 (mmp-170) cc_final: 0.6542 (mmm160) REVERT: h 633 MET cc_start: 0.1939 (mmt) cc_final: 0.0888 (mtt) REVERT: j 154 VAL cc_start: 0.7685 (m) cc_final: 0.7406 (p) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2086 time to fit residues: 39.2623 Evaluate side-chains 84 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 329 ASN ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12495 Z= 0.309 Angle : 0.728 14.534 17001 Z= 0.381 Chirality : 0.052 0.203 1926 Planarity : 0.005 0.081 2184 Dihedral : 7.075 44.439 1704 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.05 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.19), residues: 1569 helix: -2.28 (0.82), residues: 42 sheet: -1.65 (0.22), residues: 504 loop : -2.99 (0.16), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP j 350 HIS 0.010 0.002 HIS j 630 PHE 0.023 0.002 PHE j 261 TYR 0.016 0.002 TYR h 660 ARG 0.005 0.001 ARG h 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 108 ARG cc_start: 0.6797 (mmp-170) cc_final: 0.6442 (mmm160) REVERT: i 430 MET cc_start: 0.5063 (mpp) cc_final: 0.4816 (mpp) REVERT: i 433 ASP cc_start: 0.5903 (t0) cc_final: 0.5591 (t0) REVERT: i 627 MET cc_start: 0.1890 (ttp) cc_final: 0.1384 (pmm) REVERT: i 676 MET cc_start: -0.1753 (pmm) cc_final: -0.2449 (pmm) REVERT: h 233 ASP cc_start: 0.7782 (t70) cc_final: 0.7472 (t0) REVERT: h 430 MET cc_start: 0.5490 (mpp) cc_final: 0.5104 (mpp) REVERT: h 433 ASP cc_start: 0.5161 (t0) cc_final: 0.4908 (t0) REVERT: h 633 MET cc_start: 0.2080 (mmt) cc_final: -0.0575 (mtp) REVERT: j 154 VAL cc_start: 0.7641 (m) cc_final: 0.7373 (p) REVERT: j 433 ASP cc_start: 0.5110 (t0) cc_final: 0.4893 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2188 time to fit residues: 40.2555 Evaluate side-chains 86 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 150 optimal weight: 0.0980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12495 Z= 0.241 Angle : 0.698 13.176 17001 Z= 0.363 Chirality : 0.052 0.196 1926 Planarity : 0.005 0.062 2184 Dihedral : 6.843 43.755 1704 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.26 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.19), residues: 1569 helix: -2.21 (0.82), residues: 42 sheet: -1.31 (0.23), residues: 474 loop : -2.97 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP j 429 HIS 0.007 0.002 HIS i 630 PHE 0.015 0.002 PHE h 261 TYR 0.017 0.002 TYR h 71 ARG 0.005 0.000 ARG h 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 433 ASP cc_start: 0.5781 (t0) cc_final: 0.5457 (t0) REVERT: i 627 MET cc_start: 0.1235 (ttp) cc_final: 0.0256 (pmm) REVERT: i 676 MET cc_start: -0.1701 (pmm) cc_final: -0.2330 (pmm) REVERT: h 233 ASP cc_start: 0.7667 (t70) cc_final: 0.7404 (t0) REVERT: h 627 MET cc_start: 0.0823 (mtt) cc_final: 0.0374 (mtt) REVERT: j 154 VAL cc_start: 0.7544 (m) cc_final: 0.7338 (p) REVERT: j 627 MET cc_start: 0.1969 (ptm) cc_final: 0.1246 (ptm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2127 time to fit residues: 42.7129 Evaluate side-chains 92 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 0.2980 chunk 110 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 630 HIS h 630 HIS ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 397 ASN ** j 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12495 Z= 0.205 Angle : 0.661 11.207 17001 Z= 0.346 Chirality : 0.051 0.202 1926 Planarity : 0.005 0.058 2184 Dihedral : 6.576 41.404 1704 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.43 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.19), residues: 1569 helix: -2.01 (0.83), residues: 42 sheet: -1.16 (0.24), residues: 474 loop : -2.91 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP j 429 HIS 0.002 0.001 HIS h 291 PHE 0.013 0.002 PHE i 401 TYR 0.017 0.002 TYR j 660 ARG 0.006 0.001 ARG i 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: i 103 MET cc_start: 0.3758 (ttp) cc_final: 0.3287 (ppp) REVERT: i 421 TRP cc_start: 0.6637 (t60) cc_final: 0.5713 (t60) REVERT: i 627 MET cc_start: 0.1706 (ttp) cc_final: 0.0676 (pmm) REVERT: i 676 MET cc_start: -0.1627 (pmm) cc_final: -0.2179 (pmm) REVERT: h 233 ASP cc_start: 0.7527 (t70) cc_final: 0.7315 (t0) REVERT: h 627 MET cc_start: 0.0857 (mtt) cc_final: 0.0353 (mtt) REVERT: h 633 MET cc_start: 0.2417 (mmt) cc_final: 0.2038 (mmt) REVERT: j 271 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8492 (mttm) REVERT: j 429 TRP cc_start: 0.3244 (t60) cc_final: 0.1719 (t60) REVERT: j 430 MET cc_start: 0.4839 (mpp) cc_final: 0.4497 (mpp) REVERT: j 627 MET cc_start: 0.2030 (ptm) cc_final: 0.1339 (ptm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2286 time to fit residues: 47.1446 Evaluate side-chains 94 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 409 GLN ** h 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12495 Z= 0.326 Angle : 0.744 15.658 17001 Z= 0.388 Chirality : 0.053 0.218 1926 Planarity : 0.006 0.145 2184 Dihedral : 7.044 46.255 1704 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.79 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.19), residues: 1569 helix: -2.29 (0.82), residues: 42 sheet: -1.45 (0.23), residues: 522 loop : -3.01 (0.17), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP j 429 HIS 0.005 0.001 HIS j 630 PHE 0.025 0.003 PHE h 261 TYR 0.018 0.002 TYR j 71 ARG 0.011 0.001 ARG j 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: i 421 TRP cc_start: 0.6504 (t60) cc_final: 0.5953 (t60) REVERT: i 627 MET cc_start: 0.2328 (ttp) cc_final: 0.0946 (pmm) REVERT: h 627 MET cc_start: 0.1784 (mtt) cc_final: 0.1368 (mtt) REVERT: h 633 MET cc_start: 0.2654 (mmt) cc_final: 0.2309 (mmt) REVERT: j 429 TRP cc_start: 0.4078 (t60) cc_final: 0.2294 (t60) REVERT: j 430 MET cc_start: 0.5164 (mpp) cc_final: 0.4801 (mpp) REVERT: j 627 MET cc_start: 0.1916 (ptm) cc_final: 0.1476 (ptm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2088 time to fit residues: 39.9267 Evaluate side-chains 84 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.0370 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.4270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 397 ASN ** j 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12495 Z= 0.187 Angle : 0.645 11.196 17001 Z= 0.340 Chirality : 0.051 0.181 1926 Planarity : 0.005 0.070 2184 Dihedral : 6.449 41.430 1704 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.19), residues: 1569 helix: -1.86 (0.84), residues: 42 sheet: -1.18 (0.23), residues: 483 loop : -2.83 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP j 429 HIS 0.003 0.001 HIS j 291 PHE 0.011 0.001 PHE i 101 TYR 0.019 0.001 TYR j 71 ARG 0.008 0.001 ARG h 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: i 271 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8317 (mttm) REVERT: i 421 TRP cc_start: 0.6559 (t60) cc_final: 0.6091 (t60) REVERT: i 433 ASP cc_start: 0.6477 (t70) cc_final: 0.6218 (t0) REVERT: i 627 MET cc_start: 0.1767 (ttp) cc_final: 0.0960 (pmm) REVERT: h 421 TRP cc_start: 0.6234 (t60) cc_final: 0.5481 (t60) REVERT: h 627 MET cc_start: 0.1892 (mtt) cc_final: 0.1466 (mtt) REVERT: h 633 MET cc_start: 0.2591 (mmt) cc_final: 0.2192 (mmt) REVERT: j 430 MET cc_start: 0.4823 (mpp) cc_final: 0.4522 (mpp) REVERT: j 627 MET cc_start: 0.1911 (ptm) cc_final: 0.1460 (ptm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2181 time to fit residues: 42.6998 Evaluate side-chains 99 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 143 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 397 ASN ** j 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12495 Z= 0.192 Angle : 0.640 10.809 17001 Z= 0.337 Chirality : 0.051 0.181 1926 Planarity : 0.005 0.066 2184 Dihedral : 6.331 39.977 1704 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.43 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.19), residues: 1569 helix: -1.79 (0.85), residues: 42 sheet: -1.19 (0.23), residues: 486 loop : -2.74 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP j 429 HIS 0.003 0.001 HIS j 291 PHE 0.014 0.002 PHE h 401 TYR 0.017 0.001 TYR j 71 ARG 0.010 0.001 ARG j 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: i 271 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8361 (mttm) REVERT: i 421 TRP cc_start: 0.6486 (t60) cc_final: 0.6075 (t60) REVERT: i 627 MET cc_start: 0.2193 (ttp) cc_final: 0.1127 (pmm) REVERT: h 421 TRP cc_start: 0.6280 (t60) cc_final: 0.5704 (t60) REVERT: h 627 MET cc_start: 0.2002 (mtt) cc_final: 0.1111 (mtt) REVERT: j 108 ARG cc_start: 0.6716 (mmp-170) cc_final: 0.6448 (mmm160) REVERT: j 429 TRP cc_start: 0.3794 (t60) cc_final: 0.2341 (t60) REVERT: j 430 MET cc_start: 0.4549 (mpp) cc_final: 0.4128 (mpp) REVERT: j 627 MET cc_start: 0.1896 (ptm) cc_final: 0.1367 (ptm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2263 time to fit residues: 43.7497 Evaluate side-chains 95 residues out of total 1323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.103282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.085033 restraints weight = 46713.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086673 restraints weight = 28353.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.087788 restraints weight = 18721.105| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12495 Z= 0.196 Angle : 0.636 11.017 17001 Z= 0.335 Chirality : 0.050 0.174 1926 Planarity : 0.005 0.062 2184 Dihedral : 6.260 39.466 1704 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.37 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.19), residues: 1569 helix: -1.80 (0.85), residues: 42 sheet: -1.36 (0.23), residues: 516 loop : -2.71 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP j 429 HIS 0.003 0.001 HIS j 291 PHE 0.014 0.002 PHE i 401 TYR 0.017 0.001 TYR j 71 ARG 0.009 0.001 ARG j 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.49 seconds wall clock time: 43 minutes 14.01 seconds (2594.01 seconds total)