Starting phenix.real_space_refine on Tue Feb 13 16:36:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/02_2024/7paf_13268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/02_2024/7paf_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_13268/02_2024/7paf_13268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/02_2024/7paf_13268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/02_2024/7paf_13268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7paf_13268/02_2024/7paf_13268_updated.pdb" } resolution = 3.75 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= 0.013 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-dev-5238/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: 3.84, per 1000 atoms: 0.64 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.44 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: 1.61 Time building geometry restraints manager: 2.19 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: 3203 17.31 - 34.61: 253 34.61 - 51.92: 33 51.92 - 69.23: 9 69.23 - 86.53: 4 Dihedral angle restraints: 3502 sinusoidal: 1266 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 3499 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 11.830 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.140 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- 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 : 13.225 86.535 2072 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 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 17 HIS 0.005 0.001 HIS A 43 PHE 0.009 0.001 PHE D 225 TYR 0.012 0.001 TYR A 255 ARG 0.002 0.000 ARG A 191 *********************** 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 : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LEU cc_start: 0.6788 (mt) cc_final: 0.6427 (mm) REVERT: D 184 GLU cc_start: 0.7670 (pm20) cc_final: 0.7376 (pm20) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1683 time to fit residues: 37.7580 Evaluate side-chains 120 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.1988 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= 0.261 Angle : 0.663 8.507 8354 Z= 0.343 Chirality : 0.042 0.133 1000 Planarity : 0.005 0.059 1002 Dihedral : 6.857 59.045 860 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.95 % Favored : 95.79 % Rotamer: Outliers : 2.53 % Allowed : 18.99 % Favored : 78.48 % 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: -1.25 (0.30), residues: 760 helix: -0.34 (0.24), residues: 454 sheet: 0.03 (0.47), residues: 114 loop : -2.26 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 107 HIS 0.007 0.001 HIS A 43 PHE 0.016 0.002 PHE A 196 TYR 0.015 0.002 TYR D 109 ARG 0.003 0.001 ARG A 71 *********************** 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: 16 poor density : 126 time to evaluate : 0.705 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: B 63 TYR cc_start: 0.7984 (m-80) cc_final: 0.7660 (m-80) REVERT: C 8 LEU cc_start: 0.6871 (mt) cc_final: 0.6646 (mm) outliers start: 16 outliers final: 14 residues processed: 134 average time/residue: 0.1533 time to fit residues: 28.6073 Evaluate side-chains 127 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL 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: 0.9980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7645 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6142 Z= 0.260 Angle : 0.633 6.915 8354 Z= 0.331 Chirality : 0.040 0.128 1000 Planarity : 0.004 0.047 1002 Dihedral : 6.865 58.561 860 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.00 % Rotamer: Outliers : 4.75 % Allowed : 20.89 % Favored : 74.37 % 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: -0.75 (0.31), residues: 760 helix: 0.04 (0.25), residues: 456 sheet: 0.35 (0.49), residues: 114 loop : -2.12 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 107 HIS 0.007 0.001 HIS A 43 PHE 0.014 0.001 PHE A 225 TYR 0.014 0.002 TYR D 109 ARG 0.003 0.000 ARG D 71 *********************** 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 158 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.056 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: B 63 TYR cc_start: 0.8008 (m-80) cc_final: 0.7658 (m-80) REVERT: C 8 LEU cc_start: 0.6883 (mt) cc_final: 0.6632 (mm) REVERT: D 261 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8238 (tp) outliers start: 30 outliers final: 16 residues processed: 146 average time/residue: 0.1612 time to fit residues: 32.1654 Evaluate side-chains 129 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6142 Z= 0.233 Angle : 0.644 9.017 8354 Z= 0.336 Chirality : 0.041 0.146 1000 Planarity : 0.004 0.041 1002 Dihedral : 6.862 58.102 860 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.43 % Allowed : 23.10 % Favored : 72.47 % 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: -0.41 (0.31), residues: 760 helix: 0.33 (0.25), residues: 454 sheet: 0.45 (0.49), residues: 114 loop : -2.00 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 40 HIS 0.004 0.001 HIS D 43 PHE 0.011 0.001 PHE D 225 TYR 0.015 0.001 TYR A 287 ARG 0.003 0.001 ARG A 63 *********************** 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 137 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6721 (mpp) cc_final: 0.6245 (mtt) REVERT: C 8 LEU cc_start: 0.6884 (mt) cc_final: 0.6600 (mm) REVERT: D 43 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7630 (t-170) outliers start: 28 outliers final: 14 residues processed: 122 average time/residue: 0.1516 time to fit residues: 25.9847 Evaluate side-chains 121 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 0.1980 chunk 30 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.0170 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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: 0.7604 moved from start: 0.2966 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= 0.218 Angle : 0.636 9.565 8354 Z= 0.328 Chirality : 0.040 0.131 1000 Planarity : 0.003 0.038 1002 Dihedral : 6.872 57.605 860 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.91 % Allowed : 22.63 % Favored : 72.47 % 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: -0.18 (0.31), residues: 760 helix: 0.51 (0.26), residues: 452 sheet: 0.42 (0.45), residues: 124 loop : -1.93 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 17 HIS 0.004 0.001 HIS D 43 PHE 0.009 0.001 PHE A 225 TYR 0.013 0.001 TYR D 109 ARG 0.003 0.000 ARG D 63 *********************** 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 143 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 MET cc_start: 0.3921 (ptm) cc_final: 0.3648 (ptm) REVERT: A 43 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7700 (t-170) REVERT: A 87 MET cc_start: 0.6652 (mpp) cc_final: 0.6134 (mtt) REVERT: C 8 LEU cc_start: 0.6848 (mt) cc_final: 0.6593 (mm) REVERT: C 108 MET cc_start: 0.4035 (ptm) cc_final: 0.3791 (ptm) REVERT: D 43 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7581 (t-170) outliers start: 31 outliers final: 21 residues processed: 134 average time/residue: 0.1340 time to fit residues: 25.1738 Evaluate side-chains 131 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6142 Z= 0.181 Angle : 0.641 12.215 8354 Z= 0.320 Chirality : 0.039 0.135 1000 Planarity : 0.003 0.034 1002 Dihedral : 6.784 59.759 860 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.32 % Allowed : 24.53 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.32), residues: 760 helix: 0.75 (0.26), residues: 450 sheet: 0.54 (0.45), residues: 124 loop : -1.99 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 17 HIS 0.002 0.001 HIS D 43 PHE 0.033 0.001 PHE B 72 TYR 0.013 0.001 TYR C 99 ARG 0.002 0.000 ARG A 63 *********************** 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 142 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6687 (mpp) cc_final: 0.6027 (mtt) REVERT: C 8 LEU cc_start: 0.6859 (mt) cc_final: 0.6581 (mm) outliers start: 21 outliers final: 17 residues processed: 133 average time/residue: 0.1404 time to fit residues: 26.0839 Evaluate side-chains 128 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 92 TYR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 206 SER 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: 0.5980 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6142 Z= 0.277 Angle : 0.697 11.879 8354 Z= 0.351 Chirality : 0.042 0.176 1000 Planarity : 0.003 0.036 1002 Dihedral : 7.062 59.148 860 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.80 % Allowed : 25.32 % Favored : 70.89 % 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: -0.19 (0.31), residues: 760 helix: 0.52 (0.25), residues: 450 sheet: 0.39 (0.45), residues: 124 loop : -1.92 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 17 HIS 0.006 0.001 HIS D 43 PHE 0.018 0.002 PHE C 72 TYR 0.016 0.002 TYR D 109 ARG 0.003 0.000 ARG D 191 *********************** 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 136 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 MET cc_start: 0.3899 (ptm) cc_final: 0.3657 (ptm) REVERT: A 43 HIS cc_start: 0.8100 (OUTLIER) cc_final: 0.7752 (t-170) REVERT: A 87 MET cc_start: 0.6764 (mpp) cc_final: 0.6088 (mtt) REVERT: A 230 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7499 (mmt) REVERT: C 8 LEU cc_start: 0.6871 (mt) cc_final: 0.6558 (mm) REVERT: C 108 MET cc_start: 0.3945 (ptm) cc_final: 0.3715 (ptm) REVERT: D 43 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7634 (t-170) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 0.1395 time to fit residues: 24.1550 Evaluate side-chains 128 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 206 SER 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: 2.9990 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.0170 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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: 0.7579 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6142 Z= 0.200 Angle : 0.664 11.792 8354 Z= 0.332 Chirality : 0.040 0.172 1000 Planarity : 0.003 0.033 1002 Dihedral : 6.968 58.325 860 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.32 % Allowed : 25.79 % Favored : 70.89 % 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: -0.04 (0.31), residues: 760 helix: 0.64 (0.26), residues: 448 sheet: 0.47 (0.44), residues: 124 loop : -1.86 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 17 HIS 0.003 0.001 HIS D 43 PHE 0.021 0.001 PHE B 72 TYR 0.013 0.001 TYR D 109 ARG 0.002 0.000 ARG A 63 *********************** 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 139 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 MET cc_start: 0.3751 (ptm) cc_final: 0.3477 (ptm) REVERT: A 87 MET cc_start: 0.6700 (mpp) cc_final: 0.6158 (mtt) REVERT: C 8 LEU cc_start: 0.6827 (mt) cc_final: 0.6559 (mm) REVERT: C 108 MET cc_start: 0.3819 (ptm) cc_final: 0.3563 (ptm) REVERT: D 43 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7513 (t-170) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.1377 time to fit residues: 24.5618 Evaluate side-chains 132 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 72 optimal weight: 0.0270 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- 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: 0.7598 moved from start: 0.3452 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= 0.226 Angle : 0.684 12.193 8354 Z= 0.341 Chirality : 0.041 0.167 1000 Planarity : 0.003 0.034 1002 Dihedral : 7.013 58.134 860 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.48 % Allowed : 26.58 % Favored : 69.94 % 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: 0.59 (0.25), residues: 454 sheet: 0.71 (0.47), residues: 114 loop : -1.71 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 17 HIS 0.004 0.001 HIS D 43 PHE 0.015 0.001 PHE C 72 TYR 0.014 0.001 TYR D 109 ARG 0.003 0.000 ARG C 23 *********************** 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 141 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7850 (t70) REVERT: A 87 MET cc_start: 0.6733 (mpp) cc_final: 0.5961 (mtt) REVERT: C 8 LEU cc_start: 0.6824 (mt) cc_final: 0.6541 (mm) REVERT: D 43 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7576 (t-170) REVERT: D 87 MET cc_start: 0.6827 (mpp) cc_final: 0.6089 (mtt) outliers start: 22 outliers final: 19 residues processed: 130 average time/residue: 0.1373 time to fit residues: 24.7880 Evaluate side-chains 134 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.3551 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= 0.228 Angle : 0.698 12.356 8354 Z= 0.346 Chirality : 0.041 0.168 1000 Planarity : 0.003 0.033 1002 Dihedral : 6.960 57.598 860 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.32 % Allowed : 27.53 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 760 helix: 0.60 (0.25), residues: 454 sheet: 0.85 (0.48), residues: 110 loop : -1.68 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 17 HIS 0.004 0.001 HIS D 43 PHE 0.011 0.001 PHE D 225 TYR 0.014 0.001 TYR D 109 ARG 0.002 0.000 ARG D 63 ********************** 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 141 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.6754 (mpp) cc_final: 0.5934 (mtt) REVERT: C 8 LEU cc_start: 0.6808 (mt) cc_final: 0.6506 (mm) REVERT: D 43 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7631 (t-170) REVERT: D 87 MET cc_start: 0.6674 (mpp) cc_final: 0.6164 (mtt) outliers start: 21 outliers final: 19 residues processed: 130 average time/residue: 0.1553 time to fit residues: 27.3247 Evaluate side-chains 138 residues out of total 632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.191656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.164676 restraints weight = 8738.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.163520 restraints weight = 13629.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.164093 restraints weight = 11914.835| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6142 Z= 0.242 Angle : 0.699 12.632 8354 Z= 0.348 Chirality : 0.041 0.167 1000 Planarity : 0.003 0.034 1002 Dihedral : 6.929 58.144 860 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.48 % Allowed : 27.37 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 760 helix: 0.58 (0.25), residues: 454 sheet: 0.77 (0.47), residues: 110 loop : -1.61 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 107 HIS 0.005 0.001 HIS D 43 PHE 0.014 0.001 PHE D 54 TYR 0.014 0.001 TYR B 63 ARG 0.004 0.000 ARG D 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1551.97 seconds wall clock time: 28 minutes 59.26 seconds (1739.26 seconds total)