Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 06:02:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/07_2023/7paf_13268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/07_2023/7paf_13268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/07_2023/7paf_13268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/07_2023/7paf_13268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/07_2023/7paf_13268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/07_2023/7paf_13268_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 892 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 C 3992 2.51 5 N 926 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 44": "OD1" <-> "OD2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 6005 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 2 Chain: "A" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2116 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 2 Chain: "D" Number of atoms: 2151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2151 Unusual residues: {'PGT': 1} Classifications: {'peptide': 278, 'undetermined': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271, None: 1} Not linked: pdbres="ILE D 290 " pdbres="PGT D 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Time building chain proxies: 3.24, per 1000 atoms: 0.54 Number of scatterers: 6005 At special positions: 0 Unit cell: (102.726, 78.142, 93.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 1 15.00 O 1062 8.00 N 926 7.00 C 3992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " 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: 2.36 Conformation dependent library (CDL) restraints added in 991.6 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 6 sheets defined 58.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'A' and resid 7 through 30 removed outlier: 4.048A pdb=" N LEU A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 58 removed outlier: 4.149A pdb=" N PHE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.555A pdb=" N LEU A 80 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 101 through 119 Proline residue: A 110 - end of helix removed outlier: 4.056A pdb=" N SER A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 removed outlier: 4.632A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 179 removed outlier: 3.516A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A 171 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 206 removed outlier: 3.531A pdb=" N LEU A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 216 through 265 Proline residue: A 245 - end of helix removed outlier: 3.582A pdb=" N ALA A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'D' and resid 7 through 30 removed outlier: 4.077A pdb=" N LEU D 11 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 58 removed outlier: 4.148A pdb=" N PHE D 49 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.556A pdb=" N LEU D 80 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 101 through 119 Proline residue: D 110 - end of helix removed outlier: 4.050A pdb=" N SER D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 removed outlier: 4.632A pdb=" N GLY D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 179 removed outlier: 3.516A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D 171 " --> pdb=" O TRP D 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 206 removed outlier: 3.543A pdb=" N LEU D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 214 Processing helix chain 'D' and resid 216 through 243 Processing helix chain 'D' and resid 248 through 265 removed outlier: 3.697A pdb=" N ASN D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 Processing sheet with id= A, first strand: chain 'B' and resid 6 through 11 Processing sheet with id= B, first strand: chain 'B' and resid 14 through 17 Processing sheet with id= C, first strand: chain 'B' and resid 99 through 103 removed outlier: 3.754A pdb=" N ALA B 101 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 37 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG B 42 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLY B 51 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 6 through 11 Processing sheet with id= E, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= F, first strand: chain 'C' and resid 99 through 103 removed outlier: 3.748A pdb=" N ALA C 101 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 37 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG C 42 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N GLY C 51 " --> pdb=" O ARG C 42 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1050 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: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 900 1.32 - 1.44: 1772 1.44 - 1.56: 3428 1.56 - 1.68: 2 1.68 - 1.81: 40 Bond restraints: 6142 Sorted by residual: bond pdb=" C11 PGT D 301 " pdb=" O3 PGT D 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C31 PGT D 301 " pdb=" O2 PGT D 301 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C LYS D 247 " pdb=" O LYS D 247 " ideal model delta sigma weight residual 1.232 1.197 0.035 1.38e-02 5.25e+03 6.50e+00 bond pdb=" C LYS A 247 " pdb=" O LYS A 247 " ideal model delta sigma weight residual 1.232 1.198 0.035 1.38e-02 5.25e+03 6.35e+00 bond pdb=" CA PRO A 245 " pdb=" CB PRO A 245 " ideal model delta sigma weight residual 1.533 1.505 0.028 1.42e-02 4.96e+03 3.98e+00 ... (remaining 6137 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.12: 113 107.12 - 113.85: 3542 113.85 - 120.57: 2508 120.57 - 127.30: 2136 127.30 - 134.03: 55 Bond angle restraints: 8354 Sorted by residual: angle pdb=" N ALA A 246 " pdb=" CA ALA A 246 " pdb=" C ALA A 246 " ideal model delta sigma weight residual 111.28 117.52 -6.24 1.09e+00 8.42e-01 3.28e+01 angle pdb=" N ALA D 246 " pdb=" CA ALA D 246 " pdb=" C ALA D 246 " ideal model delta sigma weight residual 111.36 117.49 -6.13 1.09e+00 8.42e-01 3.16e+01 angle pdb=" C PRO A 245 " pdb=" N ALA A 246 " pdb=" CA ALA A 246 " ideal model delta sigma weight residual 120.28 126.45 -6.17 1.34e+00 5.57e-01 2.12e+01 angle pdb=" C GLN A 244 " pdb=" N PRO A 245 " pdb=" CA PRO A 245 " ideal model delta sigma weight residual 119.84 115.64 4.20 1.25e+00 6.40e-01 1.13e+01 angle pdb=" N GLN D 244 " pdb=" CA GLN D 244 " pdb=" C GLN D 244 " ideal model delta sigma weight residual 109.81 117.23 -7.42 2.21e+00 2.05e-01 1.13e+01 ... (remaining 8349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3198 17.31 - 34.61: 246 34.61 - 51.92: 33 51.92 - 69.23: 6 69.23 - 86.53: 4 Dihedral angle restraints: 3487 sinusoidal: 1251 harmonic: 2236 Sorted by residual: dihedral pdb=" CA ILE D 125 " pdb=" C ILE D 125 " pdb=" N SER D 126 " pdb=" CA SER D 126 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE A 125 " pdb=" C ILE A 125 " pdb=" N SER A 126 " pdb=" CA SER A 126 " ideal model delta harmonic sigma weight residual 180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB GLU A 179 " pdb=" CG GLU A 179 " pdb=" CD GLU A 179 " pdb=" OE1 GLU A 179 " ideal model delta sinusoidal sigma weight residual 0.00 83.63 -83.63 1 3.00e+01 1.11e-03 9.48e+00 ... (remaining 3484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 856 0.056 - 0.111: 129 0.111 - 0.167: 11 0.167 - 0.223: 0 0.223 - 0.278: 4 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA GLN A 244 " pdb=" N GLN A 244 " pdb=" C GLN A 244 " pdb=" CB GLN A 244 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA GLN D 244 " pdb=" N GLN D 244 " pdb=" C GLN D 244 " pdb=" CB GLN D 244 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 PGT D 301 " pdb=" C4 PGT D 301 " pdb=" C6 PGT D 301 " pdb=" O5 PGT D 301 " both_signs ideal model delta sigma weight residual False -2.30 -2.56 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 997 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 244 " -0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO A 245 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 244 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 245 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 258 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C TRP D 258 " -0.019 2.00e-02 2.50e+03 pdb=" O TRP D 258 " 0.007 2.00e-02 2.50e+03 pdb=" N THR D 259 " 0.006 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1328 2.78 - 3.31: 6042 3.31 - 3.84: 9854 3.84 - 4.37: 11027 4.37 - 4.90: 19555 Nonbonded interactions: 47806 Sorted by model distance: nonbonded pdb=" OD2 ASP C 104 " pdb=" OH TYR C 118 " model vdw 2.247 2.440 nonbonded pdb=" OD2 ASP B 104 " pdb=" OH TYR B 118 " model vdw 2.252 2.440 nonbonded pdb=" OD1 ASN D 128 " pdb=" N THR D 129 " model vdw 2.342 2.520 nonbonded pdb=" OD1 ASN A 128 " pdb=" N THR A 129 " model vdw 2.342 2.520 nonbonded pdb=" OG SER D 13 " pdb=" OD1 ASN D 252 " model vdw 2.388 2.440 ... (remaining 47801 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 'D' and resid 6 through 290) } ncs_group { reference = chain 'B' selection = chain 'C' } 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 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 12.210 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.640 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 0.004 0.127 6142 Z= 0.254 Angle : 0.681 9.715 8354 Z= 0.373 Chirality : 0.043 0.278 1000 Planarity : 0.003 0.072 1002 Dihedral : 12.963 86.535 2057 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.26), residues: 760 helix: -1.55 (0.21), residues: 450 sheet: -0.63 (0.45), residues: 114 loop : -2.66 (0.38), residues: 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1976 time to fit residues: 44.6368 Evaluate side-chains 119 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN A 90 ASN A 192 GLN C 86 GLN D 90 ASN D 192 GLN D 244 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6142 Z= 0.260 Angle : 0.665 8.828 8354 Z= 0.344 Chirality : 0.042 0.132 1000 Planarity : 0.005 0.061 1002 Dihedral : 5.838 48.513 845 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 760 helix: -0.36 (0.24), residues: 454 sheet: 0.04 (0.47), residues: 114 loop : -2.27 (0.41), residues: 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1437 time to fit residues: 26.8716 Evaluate side-chains 127 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0678 time to fit residues: 2.6676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.0670 chunk 61 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN D 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6142 Z= 0.219 Angle : 0.619 8.125 8354 Z= 0.321 Chirality : 0.040 0.128 1000 Planarity : 0.004 0.046 1002 Dihedral : 5.889 52.810 845 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.13 % Favored : 94.74 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.31), residues: 760 helix: 0.14 (0.25), residues: 454 sheet: 0.41 (0.49), residues: 114 loop : -2.14 (0.42), residues: 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 138 average time/residue: 0.1575 time to fit residues: 29.6763 Evaluate side-chains 116 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0577 time to fit residues: 1.0958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6142 Z= 0.256 Angle : 0.656 9.085 8354 Z= 0.340 Chirality : 0.041 0.139 1000 Planarity : 0.004 0.043 1002 Dihedral : 6.033 56.534 845 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.31), residues: 760 helix: 0.31 (0.25), residues: 454 sheet: 0.51 (0.49), residues: 114 loop : -2.00 (0.43), residues: 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 116 average time/residue: 0.1448 time to fit residues: 23.6212 Evaluate side-chains 112 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.683 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0678 time to fit residues: 1.7270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6142 Z= 0.243 Angle : 0.650 9.489 8354 Z= 0.334 Chirality : 0.040 0.128 1000 Planarity : 0.003 0.037 1002 Dihedral : 6.099 58.098 845 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.31), residues: 760 helix: 0.39 (0.25), residues: 454 sheet: 0.49 (0.45), residues: 124 loop : -1.93 (0.45), residues: 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 120 average time/residue: 0.1482 time to fit residues: 24.9613 Evaluate side-chains 109 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0584 time to fit residues: 1.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6142 Z= 0.208 Angle : 0.651 9.977 8354 Z= 0.327 Chirality : 0.040 0.141 1000 Planarity : 0.003 0.035 1002 Dihedral : 6.047 53.836 845 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.31), residues: 760 helix: 0.57 (0.26), residues: 450 sheet: 0.67 (0.45), residues: 124 loop : -2.02 (0.44), residues: 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 122 average time/residue: 0.1451 time to fit residues: 24.9909 Evaluate side-chains 111 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0577 time to fit residues: 1.1057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 88 ASN ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 6142 Z= 0.243 Angle : 0.677 12.042 8354 Z= 0.339 Chirality : 0.041 0.157 1000 Planarity : 0.003 0.036 1002 Dihedral : 6.141 55.527 845 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 1.42 % 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: -0.13 (0.31), residues: 760 helix: 0.52 (0.25), residues: 450 sheet: 0.77 (0.46), residues: 116 loop : -1.95 (0.43), residues: 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 113 average time/residue: 0.1506 time to fit residues: 23.6340 Evaluate side-chains 102 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0619 time to fit residues: 1.0223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6142 Z= 0.219 Angle : 0.678 10.457 8354 Z= 0.343 Chirality : 0.041 0.170 1000 Planarity : 0.003 0.035 1002 Dihedral : 6.121 59.696 845 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.42 % 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: 0.00 (0.31), residues: 760 helix: 0.66 (0.26), residues: 448 sheet: 0.81 (0.46), residues: 116 loop : -1.92 (0.43), residues: 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 113 average time/residue: 0.1488 time to fit residues: 23.5146 Evaluate side-chains 111 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0685 time to fit residues: 1.3883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.0570 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 6142 Z= 0.245 Angle : 0.694 10.842 8354 Z= 0.350 Chirality : 0.042 0.178 1000 Planarity : 0.003 0.034 1002 Dihedral : 6.022 53.397 845 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.31), residues: 760 helix: 0.61 (0.26), residues: 452 sheet: 0.77 (0.47), residues: 116 loop : -1.83 (0.44), residues: 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 117 average time/residue: 0.1573 time to fit residues: 25.2851 Evaluate side-chains 112 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0749 time to fit residues: 1.1368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.0040 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 6142 Z= 0.238 Angle : 0.707 12.487 8354 Z= 0.354 Chirality : 0.042 0.179 1000 Planarity : 0.003 0.034 1002 Dihedral : 5.983 52.713 845 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.31), residues: 760 helix: 0.65 (0.26), residues: 452 sheet: 0.93 (0.47), residues: 112 loop : -1.78 (0.44), residues: 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 119 average time/residue: 0.1658 time to fit residues: 26.6004 Evaluate side-chains 113 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0827 time to fit residues: 1.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.189424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.160258 restraints weight = 8483.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.159122 restraints weight = 12306.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.159956 restraints weight = 10458.228| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 6142 Z= 0.271 Angle : 0.730 12.890 8354 Z= 0.366 Chirality : 0.043 0.193 1000 Planarity : 0.003 0.034 1002 Dihedral : 6.036 53.115 845 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.31), residues: 760 helix: 0.55 (0.25), residues: 454 sheet: 0.87 (0.47), residues: 112 loop : -1.71 (0.44), residues: 194 =============================================================================== Job complete usr+sys time: 1483.11 seconds wall clock time: 27 minutes 36.63 seconds (1656.63 seconds total)