Starting phenix.real_space_refine on Thu Jul 2 08:37:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zt8_60453/07_2026/8zt8_60453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zt8_60453/07_2026/8zt8_60453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2026/8zt8_60453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2026/8zt8_60453.map" model { file = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2026/8zt8_60453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zt8_60453/07_2026/8zt8_60453.cif" } resolution = 2.34 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= 0.050 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 9 5.49 5 Mg 3 5.21 5 S 45 5.16 5 C 5118 2.51 5 N 1359 2.21 5 O 1459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 74 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 74 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 7996 At special positions: 0 Unit cell: (87.6, 85.41, 120.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 45 16.00 P 9 15.00 Mg 3 11.99 O 1459 8.00 N 1359 7.00 C 5118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " 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 NAG-ASN " NAG A 402 " - " ASN A 210 " " NAG A 403 " - " ASN A 153 " " NAG A 404 " - " ASN A 184 " " NAG B 503 " - " ASN B 210 " " NAG B 504 " - " ASN B 153 " " NAG B 505 " - " ASN B 184 " " NAG C 503 " - " ASN C 210 " " NAG C 504 " - " ASN C 153 " " NAG C 505 " - " ASN C 184 " Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 346.5 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 15 sheets defined 28.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 26 through 47 Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.566A pdb=" N TYR A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.521A pdb=" N GLU A 183 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 184 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE A 185 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.848A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.556A pdb=" N LEU A 246 " --> pdb=" O ASP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 355 removed outlier: 3.658A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 47 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.542A pdb=" N GLU B 183 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.264A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.895A pdb=" N LYS B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 355 removed outlier: 3.619A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.867A pdb=" N ASN C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.661A pdb=" N LYS C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.571A pdb=" N LEU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 355 removed outlier: 3.628A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.934A pdb=" N SER A 59 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 323 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS A 261 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N PHE A 326 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 70 removed outlier: 3.731A pdb=" N THR A 186 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 105 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 105 current: chain 'A' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 279 current: chain 'A' and resid 302 through 320 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 57 current: chain 'B' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 279 current: chain 'B' and resid 302 through 326 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 62 through 70 removed outlier: 4.101A pdb=" N THR B 186 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 200 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.098A pdb=" N ASN B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N PHE B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR B 146 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N TRP B 164 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ILE B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 56 through 59 removed outlier: 3.537A pdb=" N LYS C 325 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 59 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA C 323 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N CYS C 261 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N PHE C 326 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.929A pdb=" N THR C 186 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 200 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 76 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 105 current: chain 'C' and resid 273 through 279 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 279 current: chain 'C' and resid 302 through 320 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.114A pdb=" N ASN C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 669 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: 0.90 Time building geometry restraints manager: 0.89 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: 2522 1.34 - 1.46: 1965 1.46 - 1.58: 3631 1.58 - 1.70: 15 1.70 - 1.82: 57 Bond restraints: 8190 Sorted by residual: bond pdb=" C4 ATP C 502 " pdb=" C5 ATP C 502 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 bond pdb=" C4 ATP B 502 " pdb=" C5 ATP B 502 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 bond pdb=" C5 ATP A 401 " pdb=" C6 ATP A 401 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C5 ATP C 502 " pdb=" C6 ATP C 502 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.87e+01 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 11036 3.37 - 6.74: 66 6.74 - 10.11: 13 10.11 - 13.49: 0 13.49 - 16.86: 6 Bond angle restraints: 11121 Sorted by residual: angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 123.01 16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 123.03 16.84 1.00e+00 1.00e+00 2.83e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 123.86 16.01 1.00e+00 1.00e+00 2.56e+02 angle pdb=" PA ATP A 401 " pdb=" O3A ATP A 401 " pdb=" PB ATP A 401 " ideal model delta sigma weight residual 136.83 122.42 14.41 1.00e+00 1.00e+00 2.08e+02 angle pdb=" PA ATP C 502 " pdb=" O3A ATP C 502 " pdb=" PB ATP C 502 " ideal model delta sigma weight residual 136.83 122.83 14.00 1.00e+00 1.00e+00 1.96e+02 ... (remaining 11116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 4696 15.46 - 30.92: 177 30.92 - 46.38: 42 46.38 - 61.84: 27 61.84 - 77.30: 5 Dihedral angle restraints: 4947 sinusoidal: 2157 harmonic: 2790 Sorted by residual: dihedral pdb=" C VAL B 44 " pdb=" N VAL B 44 " pdb=" CA VAL B 44 " pdb=" CB VAL B 44 " ideal model delta harmonic sigma weight residual -122.00 -130.50 8.50 0 2.50e+00 1.60e-01 1.16e+01 dihedral pdb=" C VAL C 40 " pdb=" N VAL C 40 " pdb=" CA VAL C 40 " pdb=" CB VAL C 40 " ideal model delta harmonic sigma weight residual -122.00 -130.21 8.21 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" C VAL B 39 " pdb=" N VAL B 39 " pdb=" CA VAL B 39 " pdb=" CB VAL B 39 " ideal model delta harmonic sigma weight residual -122.00 -129.98 7.98 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1017 0.055 - 0.110: 172 0.110 - 0.165: 38 0.165 - 0.220: 8 0.220 - 0.275: 7 Chirality restraints: 1242 Sorted by residual: chirality pdb=" C1 NAG C 505 " pdb=" ND2 ASN C 184 " pdb=" C2 NAG C 505 " pdb=" O5 NAG C 505 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C1 NAG B 505 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 505 " pdb=" O5 NAG B 505 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1239 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 92 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO A 93 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 92 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 93 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 92 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO B 93 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.016 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 177 2.68 - 3.24: 7357 3.24 - 3.79: 12669 3.79 - 4.35: 16931 4.35 - 4.90: 28137 Nonbonded interactions: 65271 Sorted by model distance: nonbonded pdb=" O3G ATP B 502 " pdb="MG MG C 501 " model vdw 2.127 2.170 nonbonded pdb="MG MG A 405 " pdb=" O3G ATP C 502 " model vdw 2.210 2.170 nonbonded pdb=" O3G ATP A 401 " pdb="MG MG B 501 " model vdw 2.237 2.170 nonbonded pdb=" OD1 ASP C 170 " pdb="MG MG C 501 " model vdw 2.307 2.170 nonbonded pdb=" OG SER B 63 " pdb=" OD1 ASN B 191 " model vdw 2.313 3.040 ... (remaining 65266 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 355 or resid 403 through 404)) selection = (chain 'B' and (resid 26 through 355 or resid 503 through 504)) selection = (chain 'C' and (resid 26 through 355 or resid 503 through 504)) } 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: 2.180 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.850 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 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:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 0.078 8208 Z= 0.327 Angle : 0.779 16.858 11166 Z= 0.568 Chirality : 0.051 0.275 1242 Planarity : 0.003 0.030 1398 Dihedral : 9.783 77.302 3144 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.25 % Allowed : 2.96 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.44 (0.26), residues: 984 helix: 1.11 (0.33), residues: 267 sheet: 0.90 (0.32), residues: 258 loop : -1.95 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.012 0.001 TYR A 55 PHE 0.011 0.001 PHE B 49 TRP 0.010 0.001 TRP C 47 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.33 ( 8190) covalent geometry : angle 0.76432 / 0.57 (11121) SS BOND : bond 0.00206 / 0.12 ( 9) SS BOND : angle 0.76840 / 0.52 ( 18) hydrogen bonds : bond 0.22888 / 15.62 ( 244) hydrogen bonds : angle 7.39474 / 5.35 ( 669) link_NAG-ASN : bond 0.00836 / 0.48 ( 9) link_NAG-ASN : angle 3.15802 / 2.16 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 ILE cc_start: 0.7691 (mt) cc_final: 0.7470 (mt) outliers start: 19 outliers final: 0 residues processed: 243 average time/residue: 0.5916 time to fit residues: 151.8811 Evaluate side-chains 116 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 180 HIS A 191 ASN A 220 HIS A 290 ASN B 56 GLN B 83 GLN B 191 ASN B 220 HIS C 191 ASN C 220 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089198 restraints weight = 12045.268| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.53 r_work: 0.3122 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8208 Z= 0.211 Angle : 0.686 10.432 11166 Z= 0.348 Chirality : 0.050 0.339 1242 Planarity : 0.005 0.032 1398 Dihedral : 9.273 84.928 1347 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.19 % Allowed : 14.54 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.27), residues: 984 helix: 0.87 (0.34), residues: 285 sheet: 1.34 (0.31), residues: 252 loop : -1.08 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.030 0.002 TYR C 90 PHE 0.043 0.002 PHE B 33 TRP 0.010 0.001 TRP B 47 HIS 0.007 0.002 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 8190) covalent geometry : angle 0.65367 / 0.34 (11121) SS BOND : bond 0.00339 / 0.18 ( 9) SS BOND : angle 2.48758 / 1.84 ( 18) hydrogen bonds : bond 0.04154 / 2.81 ( 244) hydrogen bonds : angle 4.99928 / 3.65 ( 669) link_NAG-ASN : bond 0.01663 / 0.96 ( 9) link_NAG-ASN : angle 3.80489 / 2.61 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8385 (mp0) cc_final: 0.8174 (mm-30) REVERT: B 138 GLU cc_start: 0.8415 (pm20) cc_final: 0.8186 (mp0) REVERT: B 172 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (ptpp) REVERT: B 265 TRP cc_start: 0.8629 (m100) cc_final: 0.7842 (m-10) REVERT: C 172 LYS cc_start: 0.8512 (tppt) cc_final: 0.8303 (tppt) REVERT: C 258 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8426 (t70) REVERT: C 275 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8300 (mt0) REVERT: C 322 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8155 (ptmm) outliers start: 27 outliers final: 11 residues processed: 127 average time/residue: 0.5595 time to fit residues: 75.4142 Evaluate side-chains 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087314 restraints weight = 11983.186| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.52 r_work: 0.3095 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8208 Z= 0.140 Angle : 0.593 11.808 11166 Z= 0.293 Chirality : 0.050 0.435 1242 Planarity : 0.004 0.034 1398 Dihedral : 9.058 86.826 1347 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.07 % Allowed : 15.48 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.55 (0.28), residues: 984 helix: 1.04 (0.34), residues: 285 sheet: 1.30 (0.31), residues: 267 loop : -0.69 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.020 0.001 TYR C 90 PHE 0.025 0.001 PHE B 33 TRP 0.007 0.001 TRP C 164 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8190) covalent geometry : angle 0.55272 / 0.28 (11121) SS BOND : bond 0.00397 / 0.20 ( 9) SS BOND : angle 1.82493 / 1.37 ( 18) hydrogen bonds : bond 0.03298 / 2.16 ( 244) hydrogen bonds : angle 4.70589 / 3.41 ( 669) link_NAG-ASN : bond 0.00693 / 0.38 ( 9) link_NAG-ASN : angle 4.18386 / 2.95 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8757 (pp) REVERT: A 197 ARG cc_start: 0.8876 (ttm-80) cc_final: 0.8556 (ttt-90) REVERT: B 172 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8580 (ptpp) REVERT: B 265 TRP cc_start: 0.8653 (m100) cc_final: 0.7850 (m-10) REVERT: C 275 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8222 (mt0) REVERT: C 322 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8047 (ptmm) outliers start: 26 outliers final: 11 residues processed: 112 average time/residue: 0.5228 time to fit residues: 62.5486 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 81 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.076870 restraints weight = 11430.674| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.58 r_work: 0.2845 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8208 Z= 0.160 Angle : 0.676 12.281 11166 Z= 0.323 Chirality : 0.051 0.532 1242 Planarity : 0.004 0.038 1398 Dihedral : 11.232 95.904 1347 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.84 % Allowed : 16.19 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.67 (0.28), residues: 984 helix: 1.12 (0.34), residues: 285 sheet: 1.35 (0.32), residues: 267 loop : -0.59 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 244 TYR 0.018 0.001 TYR C 90 PHE 0.024 0.002 PHE C 92 TRP 0.007 0.001 TRP A 47 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 8190) covalent geometry : angle 0.64545 / 0.31 (11121) SS BOND : bond 0.00324 / 0.18 ( 9) SS BOND : angle 2.38784 / 1.78 ( 18) hydrogen bonds : bond 0.03138 / 2.03 ( 244) hydrogen bonds : angle 4.52287 / 3.29 ( 669) link_NAG-ASN : bond 0.01752 / 1.19 ( 9) link_NAG-ASN : angle 3.67257 / 2.15 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8580 (ttt-90) REVERT: B 172 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8493 (ptpp) REVERT: B 265 TRP cc_start: 0.8635 (m100) cc_final: 0.7806 (m-10) REVERT: C 258 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8256 (t70) REVERT: C 275 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8097 (mt0) REVERT: C 322 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8015 (ptmm) outliers start: 24 outliers final: 12 residues processed: 109 average time/residue: 0.5539 time to fit residues: 64.2564 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 258 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 0.0370 chunk 12 optimal weight: 4.9990 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.074174 restraints weight = 11425.715| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.59 r_work: 0.2795 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 8208 Z= 0.171 Angle : 0.669 11.460 11166 Z= 0.328 Chirality : 0.047 0.278 1242 Planarity : 0.004 0.040 1398 Dihedral : 10.542 88.821 1347 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.66 % Allowed : 15.48 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.72 (0.28), residues: 984 helix: 1.18 (0.34), residues: 285 sheet: 1.23 (0.30), residues: 297 loop : -0.60 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 244 TYR 0.018 0.001 TYR C 90 PHE 0.027 0.001 PHE A 92 TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 8190) covalent geometry : angle 0.63674 / 0.32 (11121) SS BOND : bond 0.00373 / 0.20 ( 9) SS BOND : angle 3.62910 / 2.30 ( 18) hydrogen bonds : bond 0.03133 / 2.06 ( 244) hydrogen bonds : angle 4.50875 / 3.28 ( 669) link_NAG-ASN : bond 0.00691 / 0.44 ( 9) link_NAG-ASN : angle 3.07096 / 2.00 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8909 (ttm-80) cc_final: 0.8631 (ttt-90) REVERT: B 172 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8459 (ptpp) REVERT: B 265 TRP cc_start: 0.8666 (m100) cc_final: 0.7778 (m-10) REVERT: C 172 LYS cc_start: 0.8718 (ttpp) cc_final: 0.7999 (tptp) REVERT: C 258 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8297 (t70) REVERT: C 260 GLU cc_start: 0.7708 (mp0) cc_final: 0.7350 (mp0) REVERT: C 275 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8082 (mt0) outliers start: 31 outliers final: 15 residues processed: 113 average time/residue: 0.5483 time to fit residues: 66.0147 Evaluate side-chains 100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 172 LYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.070497 restraints weight = 11498.789| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.57 r_work: 0.2722 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8208 Z= 0.232 Angle : 0.724 11.239 11166 Z= 0.356 Chirality : 0.050 0.298 1242 Planarity : 0.004 0.045 1398 Dihedral : 10.443 78.488 1347 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.84 % Allowed : 17.97 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.86 (0.28), residues: 984 helix: 1.52 (0.35), residues: 267 sheet: 1.14 (0.29), residues: 312 loop : -0.50 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 244 TYR 0.018 0.002 TYR C 90 PHE 0.036 0.002 PHE C 92 TRP 0.011 0.001 TRP C 259 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 ( 8190) covalent geometry : angle 0.68963 / 0.35 (11121) SS BOND : bond 0.00497 / 0.26 ( 9) SS BOND : angle 3.35225 / 2.31 ( 18) hydrogen bonds : bond 0.03546 / 2.34 ( 244) hydrogen bonds : angle 4.53795 / 3.27 ( 669) link_NAG-ASN : bond 0.00869 / 0.54 ( 9) link_NAG-ASN : angle 3.66639 / 2.73 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8949 (ttm-80) cc_final: 0.8689 (ttt-90) REVERT: B 265 TRP cc_start: 0.8705 (m100) cc_final: 0.7812 (m-10) REVERT: C 260 GLU cc_start: 0.7651 (mp0) cc_final: 0.7302 (mp0) REVERT: C 275 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8030 (mt0) outliers start: 24 outliers final: 14 residues processed: 104 average time/residue: 0.5355 time to fit residues: 59.4794 Evaluate side-chains 94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.104317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.074051 restraints weight = 11345.314| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.57 r_work: 0.2793 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8208 Z= 0.127 Angle : 0.647 10.768 11166 Z= 0.313 Chirality : 0.045 0.251 1242 Planarity : 0.004 0.049 1398 Dihedral : 9.820 72.525 1347 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.89 % Allowed : 19.15 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.73 (0.28), residues: 984 helix: 1.22 (0.34), residues: 285 sheet: 1.23 (0.30), residues: 294 loop : -0.59 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 244 TYR 0.018 0.001 TYR B 90 PHE 0.023 0.001 PHE A 92 TRP 0.008 0.001 TRP A 164 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8190) covalent geometry : angle 0.60898 / 0.30 (11121) SS BOND : bond 0.00486 / 0.26 ( 9) SS BOND : angle 3.54765 / 2.45 ( 18) hydrogen bonds : bond 0.02812 / 1.83 ( 244) hydrogen bonds : angle 4.37378 / 3.17 ( 669) link_NAG-ASN : bond 0.00751 / 0.47 ( 9) link_NAG-ASN : angle 3.45728 / 2.69 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8687 (ttt-90) REVERT: B 261 CYS cc_start: 0.8712 (p) cc_final: 0.8387 (m) REVERT: B 265 TRP cc_start: 0.8687 (m100) cc_final: 0.7835 (m-10) REVERT: C 172 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8376 (tppp) REVERT: C 258 ASP cc_start: 0.8730 (t70) cc_final: 0.8263 (t70) REVERT: C 260 GLU cc_start: 0.7648 (mp0) cc_final: 0.7296 (mp0) REVERT: C 275 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8080 (mt0) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 0.5625 time to fit residues: 58.7325 Evaluate side-chains 91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 244 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.072544 restraints weight = 11385.167| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.58 r_work: 0.2765 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8208 Z= 0.159 Angle : 0.670 10.533 11166 Z= 0.326 Chirality : 0.047 0.272 1242 Planarity : 0.004 0.056 1398 Dihedral : 9.854 71.232 1347 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.65 % Allowed : 19.62 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.74 (0.28), residues: 984 helix: 1.19 (0.34), residues: 285 sheet: 1.25 (0.30), residues: 294 loop : -0.57 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.017 0.002 TYR B 90 PHE 0.027 0.001 PHE C 92 TRP 0.008 0.001 TRP C 85 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8190) covalent geometry : angle 0.63037 / 0.31 (11121) SS BOND : bond 0.00418 / 0.22 ( 9) SS BOND : angle 3.36451 / 2.30 ( 18) hydrogen bonds : bond 0.03001 / 1.97 ( 244) hydrogen bonds : angle 4.39343 / 3.17 ( 669) link_NAG-ASN : bond 0.01038 / 0.67 ( 9) link_NAG-ASN : angle 3.77382 / 3.01 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8700 (ttt-90) REVERT: B 221 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8642 (mtpp) REVERT: B 261 CYS cc_start: 0.8724 (p) cc_final: 0.8448 (m) REVERT: B 265 TRP cc_start: 0.8693 (m100) cc_final: 0.7809 (m-10) REVERT: C 258 ASP cc_start: 0.8778 (t70) cc_final: 0.8218 (t70) REVERT: C 260 GLU cc_start: 0.7617 (mp0) cc_final: 0.7229 (mp0) REVERT: C 275 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8038 (mt0) outliers start: 14 outliers final: 11 residues processed: 95 average time/residue: 0.5468 time to fit residues: 55.4684 Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 244 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 73 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.080970 restraints weight = 12031.062| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.51 r_work: 0.2959 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8208 Z= 0.141 Angle : 0.647 10.156 11166 Z= 0.314 Chirality : 0.046 0.250 1242 Planarity : 0.004 0.061 1398 Dihedral : 9.639 68.677 1347 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.48 % Allowed : 18.79 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.75 (0.28), residues: 984 helix: 1.23 (0.34), residues: 285 sheet: 1.23 (0.30), residues: 294 loop : -0.56 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.017 0.001 TYR C 90 PHE 0.024 0.001 PHE A 92 TRP 0.007 0.001 TRP C 259 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8190) covalent geometry : angle 0.61121 / 0.30 (11121) SS BOND : bond 0.00331 / 0.18 ( 9) SS BOND : angle 3.09836 / 2.11 ( 18) hydrogen bonds : bond 0.02841 / 1.85 ( 244) hydrogen bonds : angle 4.32205 / 3.13 ( 669) link_NAG-ASN : bond 0.01060 / 0.66 ( 9) link_NAG-ASN : angle 3.57869 / 2.83 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8941 (ttm-80) cc_final: 0.8731 (ttt-90) REVERT: B 216 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8534 (pptt) REVERT: B 221 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8711 (mtpp) REVERT: B 261 CYS cc_start: 0.8650 (p) cc_final: 0.8377 (m) REVERT: B 265 TRP cc_start: 0.8779 (m100) cc_final: 0.7951 (m-10) REVERT: C 172 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8531 (tppp) REVERT: C 260 GLU cc_start: 0.7642 (mp0) cc_final: 0.7298 (mp0) REVERT: C 275 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8200 (mt0) outliers start: 21 outliers final: 15 residues processed: 99 average time/residue: 0.5411 time to fit residues: 57.1561 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 LYS Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 8.9990 chunk 14 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 114 GLN C 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.080274 restraints weight = 12147.836| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.52 r_work: 0.2960 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8208 Z= 0.149 Angle : 0.634 10.004 11166 Z= 0.314 Chirality : 0.046 0.251 1242 Planarity : 0.004 0.057 1398 Dihedral : 9.378 82.996 1347 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.65 % Allowed : 19.74 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.81 (0.28), residues: 984 helix: 1.23 (0.34), residues: 285 sheet: 1.30 (0.30), residues: 294 loop : -0.51 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.017 0.001 TYR C 90 PHE 0.029 0.001 PHE A 92 TRP 0.008 0.001 TRP C 259 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8190) covalent geometry : angle 0.60432 / 0.31 (11121) SS BOND : bond 0.00395 / 0.21 ( 9) SS BOND : angle 3.05191 / 2.09 ( 18) hydrogen bonds : bond 0.02902 / 1.90 ( 244) hydrogen bonds : angle 4.30430 / 3.11 ( 669) link_NAG-ASN : bond 0.00935 / 0.60 ( 9) link_NAG-ASN : angle 3.08251 / 2.53 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8567 (pptt) REVERT: B 221 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8739 (mtpp) REVERT: B 261 CYS cc_start: 0.8675 (p) cc_final: 0.8407 (m) REVERT: B 265 TRP cc_start: 0.8800 (m100) cc_final: 0.8000 (m-10) REVERT: C 172 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8607 (tppp) REVERT: C 260 GLU cc_start: 0.7605 (mp0) cc_final: 0.7347 (mp0) REVERT: C 275 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8236 (mt0) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.5382 time to fit residues: 55.1891 Evaluate side-chains 95 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082126 restraints weight = 12014.331| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.51 r_work: 0.2997 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8208 Z= 0.121 Angle : 0.614 9.873 11166 Z= 0.304 Chirality : 0.045 0.260 1242 Planarity : 0.004 0.060 1398 Dihedral : 9.197 89.988 1347 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.54 % Allowed : 20.21 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.83 (0.28), residues: 984 helix: 1.27 (0.34), residues: 285 sheet: 1.30 (0.30), residues: 294 loop : -0.52 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 244 TYR 0.017 0.001 TYR C 90 PHE 0.020 0.001 PHE A 92 TRP 0.008 0.001 TRP A 164 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 8190) covalent geometry : angle 0.58288 / 0.29 (11121) SS BOND : bond 0.00408 / 0.21 ( 9) SS BOND : angle 3.30953 / 2.17 ( 18) hydrogen bonds : bond 0.02640 / 1.73 ( 244) hydrogen bonds : angle 4.31039 / 3.12 ( 669) link_NAG-ASN : bond 0.00877 / 0.56 ( 9) link_NAG-ASN : angle 2.92243 / 2.45 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.42 seconds wall clock time: 62 minutes 30.69 seconds (3750.69 seconds total)