Starting phenix.real_space_refine on Wed Sep 17 13:46:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhq_60112/09_2025/8zhq_60112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhq_60112/09_2025/8zhq_60112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zhq_60112/09_2025/8zhq_60112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhq_60112/09_2025/8zhq_60112.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zhq_60112/09_2025/8zhq_60112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhq_60112/09_2025/8zhq_60112.map" } resolution = 2.37 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 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5577 2.51 5 N 1505 2.21 5 O 1774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8904 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1580 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "B" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1621 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain: "C" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1591 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain breaks: 1 Chain: "D" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1567 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2464 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.26 Number of scatterers: 8904 At special positions: 0 Unit cell: (67.89, 100.74, 185.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1774 8.00 N 1505 7.00 C 5577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 49 " distance=2.03 Simple disulfide: pdb=" SG CYS E 143 " - pdb=" SG CYS E 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS E 327 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 258 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS E 274 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS E 287 " - pdb=" SG CYS E 292 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-4 " NAG G 2 " - " MAN G 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG D 301 " - " ASN D 28 " " NAG F 1 " - " ASN E 33 " " NAG G 1 " - " ASN E 63 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 416.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 22 sheets defined 12.2% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.635A pdb=" N GLU A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.854A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 182 through 189 Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.629A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.918A pdb=" N ASN D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 54 through 65 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 87 through 92 removed outlier: 4.005A pdb=" N ARG E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TRP E 92 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 92' Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 267 through 278 removed outlier: 3.797A pdb=" N GLY E 278 " --> pdb=" O CYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.623A pdb=" N TRP A 34 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.602A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.338A pdb=" N LEU B 11 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS B 107 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 13 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.387A pdb=" N VAL B 133 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU B 179 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.996A pdb=" N TYR C 33 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.751A pdb=" N LEU C 108 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 127 through 129 removed outlier: 5.976A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 129 removed outlier: 5.976A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.507A pdb=" N ASN C 205 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.795A pdb=" N THR D 119 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP D 33 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.795A pdb=" N THR D 119 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS D 96 " --> pdb=" O TRP D 112 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP D 112 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG D 98 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 106 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 70 through 71 removed outlier: 6.668A pdb=" N TYR E 70 " --> pdb=" O LEU E 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.631A pdb=" N SER E 81 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE E 129 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE E 175 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU E 131 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS E 110 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N GLY E 142 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 147 through 149 Processing sheet with id=AC1, first strand: chain 'E' and resid 177 through 180 removed outlier: 6.656A pdb=" N MET E 334 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 208 " --> pdb=" O MET E 334 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR E 336 " --> pdb=" O CYS E 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 177 through 180 removed outlier: 4.007A pdb=" N ALA E 228 " --> pdb=" O MET E 240 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 244 through 248 Processing sheet with id=AC4, first strand: chain 'E' and resid 256 through 259 removed outlier: 6.906A pdb=" N ARG E 281 " --> pdb=" O CYS E 305 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N LEU E 307 " --> pdb=" O ARG E 281 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 663 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: 1.50 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2863 1.34 - 1.46: 2187 1.46 - 1.58: 3997 1.58 - 1.70: 2 1.70 - 1.82: 63 Bond restraints: 9112 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C1 MAN G 3 " pdb=" C2 MAN G 3 " ideal model delta sigma weight residual 1.526 1.596 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C1 MAN G 3 " pdb=" O5 MAN G 3 " ideal model delta sigma weight residual 1.399 1.451 -0.052 2.00e-02 2.50e+03 6.89e+00 bond pdb=" CB PRO D 176 " pdb=" CG PRO D 176 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.54e+00 bond pdb=" C1 NAG D 301 " pdb=" O5 NAG D 301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 ... (remaining 9107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12064 1.76 - 3.52: 248 3.52 - 5.28: 46 5.28 - 7.04: 11 7.04 - 8.79: 4 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C PRO D 156 " pdb=" N GLU D 157 " pdb=" CA GLU D 157 " ideal model delta sigma weight residual 122.28 116.79 5.49 1.02e+00 9.61e-01 2.90e+01 angle pdb=" CB LYS D 13 " pdb=" CG LYS D 13 " pdb=" CD LYS D 13 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CA PRO D 176 " pdb=" N PRO D 176 " pdb=" CD PRO D 176 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" CA ARG E 91 " pdb=" CB ARG E 91 " pdb=" CG ARG E 91 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N GLU D 157 " pdb=" CA GLU D 157 " pdb=" C GLU D 157 " ideal model delta sigma weight residual 110.73 115.38 -4.65 1.55e+00 4.16e-01 9.00e+00 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 5059 23.38 - 46.77: 374 46.77 - 70.15: 69 70.15 - 93.53: 11 93.53 - 116.92: 25 Dihedral angle restraints: 5538 sinusoidal: 2208 harmonic: 3330 Sorted by residual: dihedral pdb=" CB CYS E 266 " pdb=" SG CYS E 266 " pdb=" SG CYS E 303 " pdb=" CB CYS E 303 " ideal model delta sinusoidal sigma weight residual -86.00 -131.28 45.28 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 59.92 33.08 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" C1 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O5 NAG F 1 " pdb=" C4 NAG F 1 " ideal model delta sinusoidal sigma weight residual -64.11 52.81 -116.92 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1379 0.158 - 0.316: 1 0.316 - 0.474: 0 0.474 - 0.631: 0 0.631 - 0.789: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 33 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN E 63 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" C1 NAG D 301 " pdb=" ND2 ASN D 28 " pdb=" C2 NAG D 301 " pdb=" O5 NAG D 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1378 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 207 " 0.052 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO C 208 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 38 " 0.041 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 39 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO D 14 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " -0.031 5.00e-02 4.00e+02 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 521 2.72 - 3.27: 8817 3.27 - 3.81: 14970 3.81 - 4.36: 18808 4.36 - 4.90: 31257 Nonbonded interactions: 74373 Sorted by model distance: nonbonded pdb=" O ILE C 27 " pdb=" ND2 ASN C 76 " model vdw 2.181 3.120 nonbonded pdb=" O ASN A 131 " pdb=" OG SER A 193 " model vdw 2.208 3.040 nonbonded pdb=" N GLU B 143 " pdb=" OE1 GLU B 143 " model vdw 2.214 3.120 nonbonded pdb=" N GLN D 67 " pdb=" OE1 GLN D 67 " model vdw 2.228 3.120 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 172 " model vdw 2.236 3.040 ... (remaining 74368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 0.094 9130 Z= 0.168 Angle : 0.680 15.887 12415 Z= 0.339 Chirality : 0.049 0.789 1381 Planarity : 0.006 0.078 1585 Dihedral : 18.661 116.916 3378 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.44 % Allowed : 19.33 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.25), residues: 1150 helix: 0.89 (0.52), residues: 100 sheet: -0.12 (0.30), residues: 322 loop : -1.21 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 74 TYR 0.012 0.001 TYR E 83 PHE 0.015 0.001 PHE E 130 TRP 0.015 0.001 TRP E 141 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9112) covalent geometry : angle 0.64438 (12373) SS BOND : bond 0.00261 ( 12) SS BOND : angle 0.72095 ( 24) hydrogen bonds : bond 0.13393 ( 254) hydrogen bonds : angle 6.76483 ( 663) link_ALPHA1-4 : bond 0.01258 ( 1) link_ALPHA1-4 : angle 1.24273 ( 3) link_BETA1-4 : bond 0.01335 ( 2) link_BETA1-4 : angle 5.80367 ( 6) link_NAG-ASN : bond 0.00836 ( 3) link_NAG-ASN : angle 6.59895 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.298 Fit side-chains REVERT: D 67 GLN cc_start: 0.8686 (mp10) cc_final: 0.8306 (mt0) outliers start: 34 outliers final: 26 residues processed: 134 average time/residue: 0.6535 time to fit residues: 92.8879 Evaluate side-chains 130 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN B 137 ASN B 189 HIS C 113 ASN D 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.140826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079129 restraints weight = 13349.079| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.84 r_work: 0.2828 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9130 Z= 0.163 Angle : 0.672 12.552 12415 Z= 0.330 Chirality : 0.047 0.367 1381 Planarity : 0.005 0.061 1585 Dihedral : 13.917 103.273 1410 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 5.06 % Allowed : 17.21 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1150 helix: 1.17 (0.53), residues: 100 sheet: -0.01 (0.30), residues: 320 loop : -1.20 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 74 TYR 0.014 0.001 TYR E 83 PHE 0.014 0.001 PHE E 130 TRP 0.015 0.001 TRP E 141 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9112) covalent geometry : angle 0.65064 (12373) SS BOND : bond 0.00257 ( 12) SS BOND : angle 0.80463 ( 24) hydrogen bonds : bond 0.03530 ( 254) hydrogen bonds : angle 5.46100 ( 663) link_ALPHA1-4 : bond 0.01094 ( 1) link_ALPHA1-4 : angle 1.69262 ( 3) link_BETA1-4 : bond 0.01013 ( 2) link_BETA1-4 : angle 4.27247 ( 6) link_NAG-ASN : bond 0.00702 ( 3) link_NAG-ASN : angle 5.16712 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.342 Fit side-chains REVERT: A 3 GLU cc_start: 0.8114 (tp30) cc_final: 0.7891 (tp30) REVERT: B 190 LYS cc_start: 0.8573 (mptt) cc_final: 0.8342 (mmmt) REVERT: C 72 ASP cc_start: 0.8138 (t0) cc_final: 0.7777 (t70) REVERT: D 19 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7858 (tttp) REVERT: D 65 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8705 (mmtt) REVERT: D 67 GLN cc_start: 0.8580 (mp10) cc_final: 0.8270 (mt0) REVERT: D 100 TYR cc_start: 0.8878 (t80) cc_final: 0.8595 (t80) outliers start: 50 outliers final: 28 residues processed: 149 average time/residue: 0.6522 time to fit residues: 102.7152 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN B 137 ASN C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN E 68 GLN E 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.138712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077456 restraints weight = 13464.784| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.78 r_work: 0.2797 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9130 Z= 0.273 Angle : 0.699 8.876 12415 Z= 0.348 Chirality : 0.049 0.268 1381 Planarity : 0.005 0.056 1585 Dihedral : 12.456 98.479 1399 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.77 % Allowed : 17.31 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.25), residues: 1150 helix: 0.94 (0.52), residues: 100 sheet: 0.02 (0.30), residues: 326 loop : -1.28 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 322 TYR 0.016 0.002 TYR C 104 PHE 0.018 0.002 PHE E 130 TRP 0.017 0.002 TRP E 141 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 9112) covalent geometry : angle 0.68144 (12373) SS BOND : bond 0.00438 ( 12) SS BOND : angle 1.18497 ( 24) hydrogen bonds : bond 0.03936 ( 254) hydrogen bonds : angle 5.43061 ( 663) link_ALPHA1-4 : bond 0.01563 ( 1) link_ALPHA1-4 : angle 1.83640 ( 3) link_BETA1-4 : bond 0.00792 ( 2) link_BETA1-4 : angle 4.88800 ( 6) link_NAG-ASN : bond 0.00716 ( 3) link_NAG-ASN : angle 3.72868 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 103 time to evaluate : 0.320 Fit side-chains REVERT: A 3 GLU cc_start: 0.8174 (tp30) cc_final: 0.7751 (tp30) REVERT: A 82 GLU cc_start: 0.9084 (tt0) cc_final: 0.8836 (mt-10) REVERT: B 190 LYS cc_start: 0.8530 (mptt) cc_final: 0.8298 (mmmt) REVERT: C 72 ASP cc_start: 0.8302 (t0) cc_final: 0.7878 (t70) REVERT: D 19 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8021 (ttpp) REVERT: D 65 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8774 (mmtt) REVERT: D 67 GLN cc_start: 0.8544 (mp10) cc_final: 0.8246 (mt0) REVERT: E 91 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6955 (tpt170) outliers start: 57 outliers final: 31 residues processed: 146 average time/residue: 0.6437 time to fit residues: 99.6428 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 170 GLN B 137 ASN C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN D 82 GLN E 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078999 restraints weight = 13488.069| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.81 r_work: 0.2826 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9130 Z= 0.155 Angle : 0.639 8.079 12415 Z= 0.321 Chirality : 0.046 0.274 1381 Planarity : 0.005 0.052 1585 Dihedral : 11.650 93.389 1398 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.66 % Allowed : 18.42 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.25), residues: 1150 helix: 0.88 (0.54), residues: 100 sheet: -0.07 (0.30), residues: 320 loop : -1.20 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 24 TYR 0.013 0.001 TYR D 100 PHE 0.014 0.001 PHE E 130 TRP 0.015 0.001 TRP E 141 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9112) covalent geometry : angle 0.62730 (12373) SS BOND : bond 0.00260 ( 12) SS BOND : angle 0.84611 ( 24) hydrogen bonds : bond 0.03304 ( 254) hydrogen bonds : angle 5.27209 ( 663) link_ALPHA1-4 : bond 0.01317 ( 1) link_ALPHA1-4 : angle 1.72705 ( 3) link_BETA1-4 : bond 0.00996 ( 2) link_BETA1-4 : angle 4.40320 ( 6) link_NAG-ASN : bond 0.00333 ( 3) link_NAG-ASN : angle 2.55625 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.406 Fit side-chains REVERT: A 3 GLU cc_start: 0.8182 (tp30) cc_final: 0.7953 (tp30) REVERT: A 82 GLU cc_start: 0.9082 (tt0) cc_final: 0.8808 (mt-10) REVERT: B 108 ARG cc_start: 0.8279 (ptm-80) cc_final: 0.8028 (ptm-80) REVERT: B 190 LYS cc_start: 0.8536 (mptt) cc_final: 0.8302 (mmmt) REVERT: C 72 ASP cc_start: 0.8246 (t0) cc_final: 0.7895 (t0) REVERT: D 65 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8763 (mmtt) REVERT: D 82 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: D 100 TYR cc_start: 0.8811 (t80) cc_final: 0.8546 (t80) outliers start: 46 outliers final: 26 residues processed: 146 average time/residue: 0.6709 time to fit residues: 103.9498 Evaluate side-chains 139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 92 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN B 137 ASN C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.138992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076562 restraints weight = 13485.117| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.03 r_work: 0.2794 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9130 Z= 0.243 Angle : 0.691 8.698 12415 Z= 0.343 Chirality : 0.049 0.342 1381 Planarity : 0.005 0.055 1585 Dihedral : 11.309 89.952 1391 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.45 % Allowed : 18.83 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.25), residues: 1150 helix: 0.61 (0.52), residues: 106 sheet: -0.03 (0.30), residues: 327 loop : -1.25 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 74 TYR 0.016 0.002 TYR C 104 PHE 0.017 0.001 PHE E 130 TRP 0.016 0.001 TRP E 141 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 9112) covalent geometry : angle 0.67569 (12373) SS BOND : bond 0.00393 ( 12) SS BOND : angle 1.08562 ( 24) hydrogen bonds : bond 0.03649 ( 254) hydrogen bonds : angle 5.31495 ( 663) link_ALPHA1-4 : bond 0.01579 ( 1) link_ALPHA1-4 : angle 1.89264 ( 3) link_BETA1-4 : bond 0.00907 ( 2) link_BETA1-4 : angle 4.86253 ( 6) link_NAG-ASN : bond 0.00603 ( 3) link_NAG-ASN : angle 3.18842 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.267 Fit side-chains REVERT: A 3 GLU cc_start: 0.8208 (tp30) cc_final: 0.7783 (tp30) REVERT: A 82 GLU cc_start: 0.9080 (tt0) cc_final: 0.8838 (mt-10) REVERT: B 108 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.7978 (ptm-80) REVERT: B 190 LYS cc_start: 0.8481 (mptt) cc_final: 0.8240 (mmmt) REVERT: C 72 ASP cc_start: 0.8324 (t0) cc_final: 0.7957 (t0) REVERT: D 65 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8658 (mmtt) REVERT: D 67 GLN cc_start: 0.8543 (mp10) cc_final: 0.8274 (mt0) REVERT: D 82 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: D 100 TYR cc_start: 0.8837 (t80) cc_final: 0.8579 (t80) outliers start: 44 outliers final: 27 residues processed: 147 average time/residue: 0.6300 time to fit residues: 98.2969 Evaluate side-chains 141 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN C 113 ASN D 39 GLN D 82 GLN E 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.137057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075649 restraints weight = 13550.710| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.80 r_work: 0.2758 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 9130 Z= 0.379 Angle : 0.783 10.684 12415 Z= 0.386 Chirality : 0.053 0.460 1381 Planarity : 0.005 0.056 1585 Dihedral : 11.386 85.811 1390 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.66 % Allowed : 18.72 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.24), residues: 1150 helix: 0.61 (0.51), residues: 100 sheet: 0.05 (0.30), residues: 312 loop : -1.36 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 74 TYR 0.020 0.002 TYR C 104 PHE 0.023 0.002 PHE E 130 TRP 0.019 0.002 TRP E 141 HIS 0.007 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00889 ( 9112) covalent geometry : angle 0.76231 (12373) SS BOND : bond 0.00553 ( 12) SS BOND : angle 1.53179 ( 24) hydrogen bonds : bond 0.04203 ( 254) hydrogen bonds : angle 5.50696 ( 663) link_ALPHA1-4 : bond 0.01889 ( 1) link_ALPHA1-4 : angle 2.14964 ( 3) link_BETA1-4 : bond 0.01101 ( 2) link_BETA1-4 : angle 5.45502 ( 6) link_NAG-ASN : bond 0.01002 ( 3) link_NAG-ASN : angle 4.40727 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8272 (tp30) cc_final: 0.8011 (tp30) REVERT: B 108 ARG cc_start: 0.8192 (ptm-80) cc_final: 0.7916 (ptm-80) REVERT: B 190 LYS cc_start: 0.8421 (mptt) cc_final: 0.8179 (mmmt) REVERT: C 72 ASP cc_start: 0.8481 (t0) cc_final: 0.8072 (t0) REVERT: D 67 GLN cc_start: 0.8603 (mp10) cc_final: 0.8297 (mt0) REVERT: E 91 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7027 (tpt170) outliers start: 46 outliers final: 31 residues processed: 145 average time/residue: 0.6749 time to fit residues: 103.6391 Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 25 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 131 ASN A 170 GLN C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 82 GLN E 40 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.141635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.082533 restraints weight = 13798.546| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.70 r_work: 0.2953 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9130 Z= 0.131 Angle : 0.660 8.806 12415 Z= 0.328 Chirality : 0.046 0.302 1381 Planarity : 0.005 0.054 1585 Dihedral : 10.719 85.360 1390 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.74 % Allowed : 20.24 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.25), residues: 1150 helix: 0.71 (0.52), residues: 106 sheet: -0.03 (0.30), residues: 308 loop : -1.23 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 74 TYR 0.019 0.001 TYR D 154 PHE 0.013 0.001 PHE E 130 TRP 0.016 0.001 TRP D 163 HIS 0.004 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9112) covalent geometry : angle 0.64828 (12373) SS BOND : bond 0.00201 ( 12) SS BOND : angle 0.79099 ( 24) hydrogen bonds : bond 0.03084 ( 254) hydrogen bonds : angle 5.27149 ( 663) link_ALPHA1-4 : bond 0.01391 ( 1) link_ALPHA1-4 : angle 1.74538 ( 3) link_BETA1-4 : bond 0.01166 ( 2) link_BETA1-4 : angle 4.47483 ( 6) link_NAG-ASN : bond 0.00392 ( 3) link_NAG-ASN : angle 2.67560 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.308 Fit side-chains REVERT: B 190 LYS cc_start: 0.8428 (mptt) cc_final: 0.8160 (mmmt) REVERT: D 65 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8753 (mmtt) REVERT: D 67 GLN cc_start: 0.8576 (mp10) cc_final: 0.8311 (mt0) REVERT: D 82 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: D 184 LEU cc_start: 0.7626 (pp) cc_final: 0.7063 (pp) REVERT: D 185 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.4562 (t80) outliers start: 37 outliers final: 25 residues processed: 133 average time/residue: 0.6733 time to fit residues: 94.7143 Evaluate side-chains 129 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.0970 chunk 52 optimal weight: 0.0570 chunk 37 optimal weight: 8.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.141039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081233 restraints weight = 13389.360| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.70 r_work: 0.2948 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9130 Z= 0.129 Angle : 0.666 11.726 12415 Z= 0.330 Chirality : 0.046 0.301 1381 Planarity : 0.005 0.052 1585 Dihedral : 10.031 81.571 1388 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.54 % Allowed : 21.36 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.25), residues: 1150 helix: 1.00 (0.54), residues: 100 sheet: 0.01 (0.30), residues: 311 loop : -1.20 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 108 TYR 0.019 0.001 TYR D 154 PHE 0.012 0.001 PHE E 130 TRP 0.015 0.001 TRP E 141 HIS 0.003 0.001 HIS C 206 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9112) covalent geometry : angle 0.65413 (12373) SS BOND : bond 0.00208 ( 12) SS BOND : angle 0.80749 ( 24) hydrogen bonds : bond 0.03035 ( 254) hydrogen bonds : angle 5.14573 ( 663) link_ALPHA1-4 : bond 0.01212 ( 1) link_ALPHA1-4 : angle 1.95620 ( 3) link_BETA1-4 : bond 0.01257 ( 2) link_BETA1-4 : angle 4.68692 ( 6) link_NAG-ASN : bond 0.00363 ( 3) link_NAG-ASN : angle 2.30507 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.350 Fit side-chains REVERT: B 190 LYS cc_start: 0.8400 (mptt) cc_final: 0.8177 (mmmt) REVERT: C 72 ASP cc_start: 0.8436 (t0) cc_final: 0.7947 (t70) REVERT: C 211 THR cc_start: 0.8032 (m) cc_final: 0.7811 (m) REVERT: D 65 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8779 (mmtt) REVERT: D 82 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: D 185 TYR cc_start: 0.5369 (OUTLIER) cc_final: 0.5013 (t80) outliers start: 35 outliers final: 25 residues processed: 131 average time/residue: 0.6621 time to fit residues: 92.0035 Evaluate side-chains 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.141401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082288 restraints weight = 13699.755| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.73 r_work: 0.2953 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9130 Z= 0.157 Angle : 0.676 10.623 12415 Z= 0.334 Chirality : 0.047 0.331 1381 Planarity : 0.005 0.051 1585 Dihedral : 9.673 79.048 1387 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.83 % Allowed : 21.66 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.25), residues: 1150 helix: 0.97 (0.54), residues: 100 sheet: 0.00 (0.30), residues: 311 loop : -1.18 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 74 TYR 0.019 0.001 TYR D 154 PHE 0.014 0.001 PHE E 130 TRP 0.015 0.001 TRP D 163 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 9112) covalent geometry : angle 0.66281 (12373) SS BOND : bond 0.00267 ( 12) SS BOND : angle 0.90026 ( 24) hydrogen bonds : bond 0.03165 ( 254) hydrogen bonds : angle 5.12450 ( 663) link_ALPHA1-4 : bond 0.01248 ( 1) link_ALPHA1-4 : angle 2.15062 ( 3) link_BETA1-4 : bond 0.01148 ( 2) link_BETA1-4 : angle 4.80990 ( 6) link_NAG-ASN : bond 0.00420 ( 3) link_NAG-ASN : angle 2.56104 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8487 (t0) cc_final: 0.7986 (t70) REVERT: C 211 THR cc_start: 0.8077 (m) cc_final: 0.7875 (m) REVERT: D 67 GLN cc_start: 0.8507 (mp10) cc_final: 0.8231 (mt0) REVERT: D 82 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: D 185 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.5115 (t80) outliers start: 28 outliers final: 21 residues processed: 126 average time/residue: 0.6796 time to fit residues: 90.8876 Evaluate side-chains 124 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080205 restraints weight = 13450.442| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.72 r_work: 0.2844 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9130 Z= 0.165 Angle : 0.681 10.443 12415 Z= 0.337 Chirality : 0.047 0.342 1381 Planarity : 0.005 0.051 1585 Dihedral : 9.401 77.304 1385 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.04 % Allowed : 21.56 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.25), residues: 1150 helix: 0.96 (0.54), residues: 100 sheet: 0.04 (0.30), residues: 308 loop : -1.18 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 74 TYR 0.018 0.001 TYR D 154 PHE 0.015 0.001 PHE E 130 TRP 0.015 0.001 TRP D 163 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9112) covalent geometry : angle 0.66770 (12373) SS BOND : bond 0.00286 ( 12) SS BOND : angle 0.92073 ( 24) hydrogen bonds : bond 0.03238 ( 254) hydrogen bonds : angle 5.12089 ( 663) link_ALPHA1-4 : bond 0.01182 ( 1) link_ALPHA1-4 : angle 2.24824 ( 3) link_BETA1-4 : bond 0.01138 ( 2) link_BETA1-4 : angle 4.90856 ( 6) link_NAG-ASN : bond 0.00464 ( 3) link_NAG-ASN : angle 2.67222 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.360 Fit side-chains REVERT: B 190 LYS cc_start: 0.8438 (mptt) cc_final: 0.8162 (mmtt) REVERT: C 72 ASP cc_start: 0.8331 (t0) cc_final: 0.7843 (t0) REVERT: D 67 GLN cc_start: 0.8501 (mp10) cc_final: 0.8226 (mt0) REVERT: D 82 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7954 (pm20) REVERT: D 185 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.5183 (t80) outliers start: 30 outliers final: 23 residues processed: 123 average time/residue: 0.6725 time to fit residues: 87.7970 Evaluate side-chains 126 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.141910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.083016 restraints weight = 13576.772| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.72 r_work: 0.2968 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9130 Z= 0.142 Angle : 0.673 10.175 12415 Z= 0.334 Chirality : 0.047 0.323 1381 Planarity : 0.005 0.051 1585 Dihedral : 9.169 75.804 1385 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.04 % Allowed : 21.56 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.25), residues: 1150 helix: 1.46 (0.55), residues: 94 sheet: 0.05 (0.30), residues: 302 loop : -1.16 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 74 TYR 0.017 0.001 TYR D 154 PHE 0.014 0.001 PHE E 130 TRP 0.015 0.001 TRP D 163 HIS 0.004 0.001 HIS E 56 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9112) covalent geometry : angle 0.66045 (12373) SS BOND : bond 0.00240 ( 12) SS BOND : angle 0.82306 ( 24) hydrogen bonds : bond 0.03097 ( 254) hydrogen bonds : angle 5.09081 ( 663) link_ALPHA1-4 : bond 0.01134 ( 1) link_ALPHA1-4 : angle 2.22296 ( 3) link_BETA1-4 : bond 0.01309 ( 2) link_BETA1-4 : angle 4.90491 ( 6) link_NAG-ASN : bond 0.00419 ( 3) link_NAG-ASN : angle 2.48085 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5558.37 seconds wall clock time: 95 minutes 13.83 seconds (5713.83 seconds total)