Starting phenix.real_space_refine on Thu Mar 13 13:57:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhq_60112/03_2025/8zhq_60112.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhq_60112/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zhq_60112/03_2025/8zhq_60112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhq_60112/03_2025/8zhq_60112.map" model { file = "/net/cci-nas-00/data/ceres_data/8zhq_60112/03_2025/8zhq_60112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhq_60112/03_2025/8zhq_60112.cif" } resolution = 2.37 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= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.00, per 1000 atoms: 0.67 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.17 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: 2.64 Time building geometry restraints manager: 2.74 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: 0.010 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.770 Find NCS groups from input model: 0.140 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:15.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- 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 9112 Z= 0.248 Angle : 0.644 8.795 12373 Z= 0.331 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 (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: -1.02 (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 TRP 0.015 0.001 TRP E 141 HIS 0.004 0.001 HIS E 56 PHE 0.015 0.001 PHE E 130 TYR 0.012 0.001 TYR E 83 ARG 0.010 0.001 ARG E 74 *********************** 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 : 1.353 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: 1.3286 time to fit residues: 190.0653 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 : 1.268 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082289 restraints weight = 13234.120| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.68 r_work: 0.2967 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9112 Z= 0.200 Angle : 0.635 12.586 12373 Z= 0.317 Chirality : 0.046 0.332 1381 Planarity : 0.005 0.061 1585 Dihedral : 13.719 102.870 1410 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.96 % Allowed : 17.31 % 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 (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: -0.89 (0.25), residues: 1150 helix: 1.23 (0.54), residues: 100 sheet: 0.01 (0.30), residues: 320 loop : -1.18 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.004 0.001 HIS E 56 PHE 0.013 0.001 PHE E 130 TYR 0.012 0.001 TYR E 83 ARG 0.006 0.001 ARG E 74 *********************** 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 164 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 1.027 Fit side-chains REVERT: A 3 GLU cc_start: 0.8111 (tp30) cc_final: 0.7906 (tp30) REVERT: B 190 LYS cc_start: 0.8540 (mptt) cc_final: 0.8299 (mmmt) REVERT: C 72 ASP cc_start: 0.8332 (t0) cc_final: 0.7966 (t70) REVERT: D 19 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7985 (tttp) REVERT: D 65 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8699 (mmtt) REVERT: D 67 GLN cc_start: 0.8564 (mp10) cc_final: 0.8268 (mt0) REVERT: D 100 TYR cc_start: 0.9018 (t80) cc_final: 0.8811 (t80) outliers start: 49 outliers final: 28 residues processed: 151 average time/residue: 1.3265 time to fit residues: 212.9509 Evaluate side-chains 139 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 105 LYS 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 93 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 6 optimal weight: 0.0030 chunk 94 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 E 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.082342 restraints weight = 13542.563| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.77 r_work: 0.2967 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9112 Z= 0.186 Angle : 0.599 7.601 12373 Z= 0.303 Chirality : 0.045 0.263 1381 Planarity : 0.005 0.051 1585 Dihedral : 11.838 97.417 1396 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 5.26 % Allowed : 17.91 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.84 (0.25), residues: 1150 helix: 1.31 (0.54), residues: 100 sheet: 0.04 (0.30), residues: 320 loop : -1.15 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.003 0.001 HIS C 206 PHE 0.012 0.001 PHE E 130 TYR 0.012 0.001 TYR D 100 ARG 0.005 0.001 ARG E 74 *********************** 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 163 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 111 time to evaluate : 1.071 Fit side-chains REVERT: A 3 GLU cc_start: 0.8106 (tp30) cc_final: 0.7872 (tp30) REVERT: A 82 GLU cc_start: 0.9060 (tt0) cc_final: 0.8835 (mt-10) REVERT: B 190 LYS cc_start: 0.8506 (mptt) cc_final: 0.8274 (mmmt) REVERT: C 72 ASP cc_start: 0.8357 (t0) cc_final: 0.7977 (t70) REVERT: D 19 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7946 (ttpp) REVERT: D 65 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8590 (mmtt) REVERT: D 67 GLN cc_start: 0.8497 (mp10) cc_final: 0.8252 (mt0) REVERT: D 82 GLN cc_start: 0.8229 (pt0) cc_final: 0.7209 (mp10) REVERT: D 100 TYR cc_start: 0.8935 (t80) cc_final: 0.8727 (t80) outliers start: 52 outliers final: 26 residues processed: 150 average time/residue: 1.4078 time to fit residues: 224.5644 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 : 0.861 ------------------------------------------------------------------------------- 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 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 THR 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 19 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 93 ILE 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 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 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 51 ASN A 170 GLN C 113 ASN D 39 GLN D 82 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 = 0.4020 r_free = 0.4020 target = 0.142008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.082390 restraints weight = 13313.100| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.69 r_work: 0.2973 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9112 Z= 0.215 Angle : 0.610 8.369 12373 Z= 0.308 Chirality : 0.045 0.286 1381 Planarity : 0.005 0.050 1585 Dihedral : 11.130 92.123 1392 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 4.96 % Allowed : 18.02 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.83 (0.25), residues: 1150 helix: 1.07 (0.55), residues: 100 sheet: 0.11 (0.30), residues: 318 loop : -1.13 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.004 0.001 HIS E 56 PHE 0.014 0.001 PHE E 130 TYR 0.012 0.001 TYR E 83 ARG 0.006 0.001 ARG E 74 *********************** 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 162 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.943 Fit side-chains REVERT: A 3 GLU cc_start: 0.8183 (tp30) cc_final: 0.7958 (tp30) REVERT: A 82 GLU cc_start: 0.9084 (tt0) cc_final: 0.8878 (mt-10) REVERT: B 190 LYS cc_start: 0.8478 (mptt) cc_final: 0.8232 (mmmt) REVERT: C 72 ASP cc_start: 0.8345 (t0) cc_final: 0.7976 (t70) REVERT: D 43 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8754 (mmmm) REVERT: D 65 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8706 (mmtt) REVERT: D 82 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7712 (pm20) outliers start: 49 outliers final: 25 residues processed: 149 average time/residue: 1.3149 time to fit residues: 208.7806 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 139 ILE 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 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 93 ILE 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 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 41 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN C 113 ASN C 203 ASN D 39 GLN D 82 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 = 0.4030 r_free = 0.4030 target = 0.142977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084049 restraints weight = 13595.034| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.71 r_work: 0.2978 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9112 Z= 0.207 Angle : 0.610 8.844 12373 Z= 0.307 Chirality : 0.045 0.287 1381 Planarity : 0.005 0.049 1585 Dihedral : 10.531 88.765 1388 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.45 % Allowed : 18.62 % 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 (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: -0.84 (0.25), residues: 1150 helix: 0.94 (0.54), residues: 106 sheet: 0.08 (0.30), residues: 318 loop : -1.12 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 163 HIS 0.004 0.001 HIS E 56 PHE 0.013 0.001 PHE E 130 TYR 0.020 0.001 TYR D 100 ARG 0.007 0.001 ARG B 108 *********************** 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 155 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.954 Fit side-chains REVERT: A 3 GLU cc_start: 0.8169 (tp30) cc_final: 0.7954 (tp30) REVERT: A 82 GLU cc_start: 0.9065 (tt0) cc_final: 0.8814 (mt-10) REVERT: B 190 LYS cc_start: 0.8485 (mptt) cc_final: 0.8218 (mmmt) REVERT: C 72 ASP cc_start: 0.8440 (t0) cc_final: 0.8064 (t0) REVERT: D 65 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8571 (mmtt) REVERT: D 67 GLN cc_start: 0.8497 (mp10) cc_final: 0.8191 (mt0) REVERT: D 82 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7431 (mp10) outliers start: 44 outliers final: 24 residues processed: 143 average time/residue: 1.3090 time to fit residues: 200.4579 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 139 ILE 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 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 65 LYS Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 93 ILE 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 302 LYS 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 5 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 68 ASN C 113 ASN 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 = 0.3963 r_free = 0.3963 target = 0.139361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.077104 restraints weight = 13303.221| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.97 r_work: 0.2805 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9112 Z= 0.386 Angle : 0.687 10.149 12373 Z= 0.342 Chirality : 0.049 0.370 1381 Planarity : 0.005 0.050 1585 Dihedral : 10.553 86.687 1387 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.45 % Allowed : 18.52 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.95 (0.25), residues: 1150 helix: 0.71 (0.52), residues: 106 sheet: -0.01 (0.30), residues: 313 loop : -1.16 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 163 HIS 0.006 0.001 HIS E 56 PHE 0.018 0.002 PHE E 130 TYR 0.016 0.002 TYR C 104 ARG 0.006 0.001 ARG E 322 *********************** 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 151 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.916 Fit side-chains REVERT: A 3 GLU cc_start: 0.8215 (tp30) cc_final: 0.7790 (tp30) REVERT: B 190 LYS cc_start: 0.8491 (mptt) cc_final: 0.8243 (mmmt) REVERT: C 72 ASP cc_start: 0.8340 (t0) cc_final: 0.7940 (t0) REVERT: D 65 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8641 (mmtt) REVERT: D 67 GLN cc_start: 0.8530 (mp10) cc_final: 0.8253 (mt0) REVERT: D 82 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7227 (mp10) outliers start: 44 outliers final: 23 residues processed: 142 average time/residue: 1.2904 time to fit residues: 194.9678 Evaluate side-chains 132 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 139 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 C 113 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.141729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.081350 restraints weight = 13489.022| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.74 r_work: 0.2950 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9112 Z= 0.207 Angle : 0.626 9.257 12373 Z= 0.312 Chirality : 0.046 0.301 1381 Planarity : 0.004 0.049 1585 Dihedral : 10.167 85.346 1386 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.34 % Allowed : 19.84 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.90 (0.25), residues: 1150 helix: 0.85 (0.53), residues: 106 sheet: 0.00 (0.30), residues: 318 loop : -1.14 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 163 HIS 0.003 0.001 HIS E 56 PHE 0.013 0.001 PHE E 130 TYR 0.015 0.001 TYR D 100 ARG 0.009 0.001 ARG E 322 *********************** 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 145 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.191 Fit side-chains REVERT: A 3 GLU cc_start: 0.8207 (tp30) cc_final: 0.7993 (tp30) REVERT: A 20 ILE cc_start: 0.9077 (mt) cc_final: 0.8861 (mp) REVERT: B 190 LYS cc_start: 0.8463 (mptt) cc_final: 0.8198 (mmmt) REVERT: C 72 ASP cc_start: 0.8463 (t0) cc_final: 0.8074 (t0) REVERT: D 65 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8658 (mmtt) outliers start: 33 outliers final: 19 residues processed: 135 average time/residue: 1.3400 time to fit residues: 192.6805 Evaluate side-chains 131 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 139 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 53 THR 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 216 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 65 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 49 optimal weight: 0.0040 chunk 12 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 109 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076907 restraints weight = 13565.652| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.94 r_work: 0.2799 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9112 Z= 0.377 Angle : 0.711 9.882 12373 Z= 0.353 Chirality : 0.050 0.396 1381 Planarity : 0.005 0.050 1585 Dihedral : 9.984 82.630 1383 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.34 % Allowed : 20.04 % 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 (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: -0.96 (0.25), residues: 1150 helix: 1.15 (0.53), residues: 94 sheet: 0.02 (0.30), residues: 311 loop : -1.22 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 163 HIS 0.006 0.001 HIS E 56 PHE 0.018 0.002 PHE E 130 TYR 0.016 0.002 TYR C 104 ARG 0.010 0.001 ARG E 74 *********************** 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 143 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.921 Fit side-chains REVERT: A 3 GLU cc_start: 0.8259 (tp30) cc_final: 0.7835 (tp30) REVERT: A 60 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7474 (ptt90) REVERT: B 190 LYS cc_start: 0.8473 (mptt) cc_final: 0.8209 (mmmt) REVERT: D 65 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8571 (mmtt) REVERT: D 67 GLN cc_start: 0.8519 (mp10) cc_final: 0.8112 (mt0) REVERT: E 215 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8347 (mp10) outliers start: 33 outliers final: 23 residues processed: 136 average time/residue: 1.4915 time to fit residues: 214.9456 Evaluate side-chains 128 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 60 ARG Chi-restraints excluded: chain A residue 88 ASN 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 53 THR 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 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 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 215 GLN 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 106 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 0.0030 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 C 113 ASN D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.141557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.081417 restraints weight = 13519.933| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.74 r_work: 0.2947 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9112 Z= 0.211 Angle : 0.652 9.384 12373 Z= 0.325 Chirality : 0.046 0.311 1381 Planarity : 0.005 0.050 1585 Dihedral : 9.617 81.516 1383 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.14 % Allowed : 20.14 % 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 (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: -0.86 (0.25), residues: 1150 helix: 1.41 (0.55), residues: 94 sheet: 0.07 (0.30), residues: 302 loop : -1.15 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 163 HIS 0.003 0.001 HIS C 206 PHE 0.013 0.001 PHE E 130 TYR 0.017 0.001 TYR D 154 ARG 0.009 0.001 ARG E 74 *********************** 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 134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.041 Fit side-chains REVERT: B 190 LYS cc_start: 0.8480 (mptt) cc_final: 0.8202 (mmmt) REVERT: C 72 ASP cc_start: 0.8406 (t0) cc_final: 0.7940 (t70) REVERT: D 65 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8582 (mmtt) REVERT: D 67 GLN cc_start: 0.8503 (mp10) cc_final: 0.8015 (mt0) outliers start: 31 outliers final: 21 residues processed: 126 average time/residue: 1.3541 time to fit residues: 181.0956 Evaluate side-chains 124 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 53 THR 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 65 LYS Chi-restraints excluded: chain D residue 82 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.139939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078321 restraints weight = 13406.039| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.94 r_work: 0.2830 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9112 Z= 0.297 Angle : 0.693 9.429 12373 Z= 0.346 Chirality : 0.048 0.352 1381 Planarity : 0.005 0.068 1585 Dihedral : 9.400 79.278 1383 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.94 % Allowed : 20.55 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: -0.89 (0.25), residues: 1150 helix: 1.32 (0.54), residues: 94 sheet: 0.05 (0.30), residues: 302 loop : -1.16 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 163 HIS 0.006 0.001 HIS E 56 PHE 0.016 0.001 PHE E 130 TYR 0.019 0.001 TYR D 154 ARG 0.015 0.001 ARG E 322 ********************** 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: 29 poor density : 102 time to evaluate : 0.980 Fit side-chains REVERT: A 60 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7647 (ptt90) REVERT: C 72 ASP cc_start: 0.8222 (t0) cc_final: 0.7748 (t70) REVERT: D 65 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8565 (mmtt) REVERT: D 67 GLN cc_start: 0.8488 (mp10) cc_final: 0.8069 (mt0) outliers start: 29 outliers final: 20 residues processed: 124 average time/residue: 1.4545 time to fit residues: 192.1788 Evaluate side-chains 122 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 60 ARG Chi-restraints excluded: chain A residue 88 ASN 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 53 THR 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 65 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.142625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084218 restraints weight = 13687.204| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.68 r_work: 0.2980 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9112 Z= 0.213 Angle : 0.656 9.034 12373 Z= 0.328 Chirality : 0.046 0.308 1381 Planarity : 0.005 0.049 1585 Dihedral : 9.024 76.853 1383 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.83 % Allowed : 20.45 % 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 (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: -0.83 (0.25), residues: 1150 helix: 1.45 (0.55), residues: 94 sheet: 0.04 (0.30), residues: 309 loop : -1.11 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 163 HIS 0.005 0.001 HIS C 206 PHE 0.013 0.001 PHE E 130 TYR 0.016 0.001 TYR D 100 ARG 0.010 0.001 ARG E 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11524.10 seconds wall clock time: 200 minutes 18.65 seconds (12018.65 seconds total)