Starting phenix.real_space_refine on Wed Sep 17 10:01:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zt8_60453/09_2025/8zt8_60453.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zt8_60453/09_2025/8zt8_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_60453/09_2025/8zt8_60453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zt8_60453/09_2025/8zt8_60453.map" model { file = "/net/cci-nas-00/data/ceres_data/8zt8_60453/09_2025/8zt8_60453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zt8_60453/09_2025/8zt8_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 76 Unusual residues: {' CA': 2, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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, 75 Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 2.05, per 1000 atoms: 0.26 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: 0.57 Conformation dependent library (CDL) restraints added in 326.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.03 Time building geometry restraints manager: 0.72 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: 1.670 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: 0.030 Process input model: 8.210 Find NCS groups from input model: 0.130 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 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 aren 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 covalent geometry : bond 0.00424 ( 8190) covalent geometry : angle 0.76432 (11121) SS BOND : bond 0.00206 ( 9) SS BOND : angle 0.76840 ( 18) hydrogen bonds : bond 0.22888 ( 244) hydrogen bonds : angle 7.39474 ( 669) link_NAG-ASN : bond 0.00836 ( 9) link_NAG-ASN : angle 3.15802 ( 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 : 0.321 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: 0.5935 time to fit residues: 151.8116 Evaluate side-chains 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.117225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089040 restraints weight = 11960.554| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.55 r_work: 0.3101 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8208 Z= 0.215 Angle : 0.689 10.422 11166 Z= 0.350 Chirality : 0.050 0.330 1242 Planarity : 0.005 0.038 1398 Dihedral : 9.338 84.447 1347 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.19 % Allowed : 14.42 % Favored : 82.39 % 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 aren not related in a simple way. whole: 0.23 (0.27), residues: 984 helix: 0.85 (0.34), residues: 285 sheet: 1.35 (0.31), residues: 252 loop : -1.03 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 244 TYR 0.031 0.002 TYR C 90 PHE 0.042 0.002 PHE B 33 TRP 0.011 0.001 TRP B 47 HIS 0.007 0.002 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 8190) covalent geometry : angle 0.65728 (11121) SS BOND : bond 0.00426 ( 9) SS BOND : angle 2.23924 ( 18) hydrogen bonds : bond 0.03856 ( 244) hydrogen bonds : angle 4.94235 ( 669) link_NAG-ASN : bond 0.00987 ( 9) link_NAG-ASN : angle 3.90761 ( 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 140 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.8382 (mp0) cc_final: 0.8153 (mm-30) REVERT: B 138 GLU cc_start: 0.8417 (pm20) cc_final: 0.8202 (mp0) REVERT: B 265 TRP cc_start: 0.8623 (m100) cc_final: 0.7817 (m-10) REVERT: C 172 LYS cc_start: 0.8522 (tppt) cc_final: 0.8316 (tppt) REVERT: C 258 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8444 (t70) REVERT: C 275 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8319 (mt0) REVERT: C 322 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8140 (ptmm) outliers start: 27 outliers final: 11 residues processed: 129 average time/residue: 0.5413 time to fit residues: 74.1554 Evaluate side-chains 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 38 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 0.0970 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.118833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090993 restraints weight = 11902.406| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.52 r_work: 0.3173 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8208 Z= 0.109 Angle : 0.565 12.485 11166 Z= 0.277 Chirality : 0.048 0.428 1242 Planarity : 0.004 0.034 1398 Dihedral : 8.881 87.086 1347 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.25 % Allowed : 15.96 % Favored : 81.80 % 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 aren not related in a simple way. whole: 0.56 (0.28), residues: 984 helix: 1.07 (0.34), residues: 285 sheet: 1.40 (0.32), residues: 264 loop : -0.74 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.019 0.001 TYR C 90 PHE 0.023 0.001 PHE B 33 TRP 0.007 0.001 TRP C 164 HIS 0.002 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8190) covalent geometry : angle 0.52690 (11121) SS BOND : bond 0.00283 ( 9) SS BOND : angle 1.63806 ( 18) hydrogen bonds : bond 0.03024 ( 244) hydrogen bonds : angle 4.68919 ( 669) link_NAG-ASN : bond 0.00744 ( 9) link_NAG-ASN : angle 4.01239 ( 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 111 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8500 (ttt-90) REVERT: B 265 TRP cc_start: 0.8603 (m100) cc_final: 0.7766 (m-10) REVERT: C 172 LYS cc_start: 0.8460 (tppt) cc_final: 0.8254 (tppt) REVERT: C 275 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8271 (mt0) REVERT: C 322 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8047 (ptmm) outliers start: 19 outliers final: 8 residues processed: 104 average time/residue: 0.5405 time to fit residues: 59.7349 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 318 LEU 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 318 LEU Chi-restraints excluded: chain C residue 347 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.112870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084301 restraints weight = 12130.001| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.52 r_work: 0.3055 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8208 Z= 0.180 Angle : 0.727 21.316 11166 Z= 0.341 Chirality : 0.050 0.419 1242 Planarity : 0.004 0.042 1398 Dihedral : 9.152 87.616 1347 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.25 % Allowed : 15.48 % 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 aren not related in a simple way. whole: 0.66 (0.28), residues: 984 helix: 1.16 (0.34), residues: 285 sheet: 1.32 (0.31), residues: 267 loop : -0.60 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 244 TYR 0.018 0.002 TYR C 90 PHE 0.026 0.002 PHE C 92 TRP 0.009 0.001 TRP A 47 HIS 0.004 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8190) covalent geometry : angle 0.61574 (11121) SS BOND : bond 0.00360 ( 9) SS BOND : angle 2.10227 ( 18) hydrogen bonds : bond 0.03307 ( 244) hydrogen bonds : angle 4.58357 ( 669) link_NAG-ASN : bond 0.00891 ( 9) link_NAG-ASN : angle 7.72813 ( 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 115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8921 (ttm-80) cc_final: 0.8583 (ttt-90) REVERT: B 265 TRP cc_start: 0.8722 (m100) cc_final: 0.7937 (m-10) REVERT: C 275 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8264 (mt0) REVERT: C 322 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8159 (ptmm) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 0.5703 time to fit residues: 66.8892 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 245 SER 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 337 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 114 GLN C 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.074105 restraints weight = 11437.305| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.58 r_work: 0.2792 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8208 Z= 0.194 Angle : 0.716 14.345 11166 Z= 0.346 Chirality : 0.049 0.344 1242 Planarity : 0.004 0.043 1398 Dihedral : 10.468 87.242 1347 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.66 % Allowed : 15.25 % Favored : 81.09 % 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 aren not related in a simple way. whole: 0.71 (0.28), residues: 984 helix: 1.18 (0.34), residues: 285 sheet: 1.21 (0.30), residues: 297 loop : -0.58 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 244 TYR 0.018 0.002 TYR C 90 PHE 0.028 0.002 PHE A 92 TRP 0.010 0.001 TRP B 164 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8190) covalent geometry : angle 0.66526 (11121) SS BOND : bond 0.00455 ( 9) SS BOND : angle 2.73844 ( 18) hydrogen bonds : bond 0.03325 ( 244) hydrogen bonds : angle 4.57395 ( 669) link_NAG-ASN : bond 0.00946 ( 9) link_NAG-ASN : angle 4.98778 ( 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 127 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8963 (ttm-80) cc_final: 0.8658 (ttt-90) REVERT: B 261 CYS cc_start: 0.8779 (p) cc_final: 0.8394 (m) REVERT: B 265 TRP cc_start: 0.8682 (m100) cc_final: 0.7780 (m-10) REVERT: C 275 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8097 (mt0) outliers start: 31 outliers final: 14 residues processed: 119 average time/residue: 0.5050 time to fit residues: 64.0003 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 : 0.318 ------------------------------------------------------------------------------- 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 172 LYS 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 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 337 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.4980 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 0.0370 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS 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 = 0.104689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.074583 restraints weight = 11486.936| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.59 r_work: 0.2803 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 8208 Z= 0.143 Angle : 0.643 10.673 11166 Z= 0.315 Chirality : 0.046 0.302 1242 Planarity : 0.004 0.046 1398 Dihedral : 10.069 82.079 1347 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.48 % Allowed : 17.26 % Favored : 80.26 % 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 aren not related in a simple way. whole: 0.74 (0.28), residues: 984 helix: 1.19 (0.34), residues: 285 sheet: 1.30 (0.30), residues: 294 loop : -0.60 (0.31), residues: 405 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 0.001 PHE A 92 TRP 0.007 0.001 TRP C 164 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8190) covalent geometry : angle 0.61245 (11121) SS BOND : bond 0.00345 ( 9) SS BOND : angle 2.84945 ( 18) hydrogen bonds : bond 0.03016 ( 244) hydrogen bonds : angle 4.49942 ( 669) link_NAG-ASN : bond 0.00817 ( 9) link_NAG-ASN : angle 3.31704 ( 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 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8948 (ttm-80) cc_final: 0.8626 (ttt-90) REVERT: B 265 TRP cc_start: 0.8676 (m100) cc_final: 0.7770 (m-10) REVERT: C 172 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8011 (tptp) REVERT: C 260 GLU cc_start: 0.7680 (mp0) cc_final: 0.7441 (mp0) REVERT: C 275 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8081 (mt0) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 0.5307 time to fit residues: 58.2376 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 267 VAL Chi-restraints excluded: chain B residue 275 GLN 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 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.073708 restraints weight = 11372.305| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.58 r_work: 0.2786 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8208 Z= 0.155 Angle : 0.638 10.180 11166 Z= 0.315 Chirality : 0.046 0.254 1242 Planarity : 0.004 0.051 1398 Dihedral : 9.739 78.334 1347 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 18.32 % Favored : 79.55 % 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 aren not related in a simple way. whole: 0.76 (0.28), residues: 984 helix: 1.20 (0.34), residues: 285 sheet: 1.30 (0.30), residues: 294 loop : -0.58 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 244 TYR 0.017 0.001 TYR C 90 PHE 0.026 0.001 PHE A 92 TRP 0.008 0.001 TRP C 259 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8190) covalent geometry : angle 0.61166 (11121) SS BOND : bond 0.00579 ( 9) SS BOND : angle 2.97948 ( 18) hydrogen bonds : bond 0.03016 ( 244) hydrogen bonds : angle 4.37861 ( 669) link_NAG-ASN : bond 0.01155 ( 9) link_NAG-ASN : angle 2.87768 ( 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 106 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8970 (ttm-80) cc_final: 0.8666 (ttt-90) REVERT: B 261 CYS cc_start: 0.8752 (p) cc_final: 0.8446 (m) REVERT: B 265 TRP cc_start: 0.8691 (m100) cc_final: 0.7838 (m-10) REVERT: C 275 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8066 (mt0) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.5088 time to fit residues: 54.2064 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 245 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 275 GLN 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 337 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 88 optimal weight: 0.0970 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.069985 restraints weight = 11491.868| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.58 r_work: 0.2712 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8208 Z= 0.230 Angle : 0.700 12.163 11166 Z= 0.351 Chirality : 0.049 0.296 1242 Planarity : 0.004 0.056 1398 Dihedral : 10.392 74.057 1347 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.60 % Allowed : 17.85 % Favored : 79.55 % 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 aren not related in a simple way. whole: 0.87 (0.28), residues: 984 helix: 1.56 (0.35), residues: 267 sheet: 1.10 (0.29), residues: 312 loop : -0.47 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 244 TYR 0.017 0.002 TYR C 90 PHE 0.035 0.002 PHE C 92 TRP 0.012 0.001 TRP C 259 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 8190) covalent geometry : angle 0.67691 (11121) SS BOND : bond 0.00566 ( 9) SS BOND : angle 3.06162 ( 18) hydrogen bonds : bond 0.03584 ( 244) hydrogen bonds : angle 4.48704 ( 669) link_NAG-ASN : bond 0.00905 ( 9) link_NAG-ASN : angle 2.80175 ( 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 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8974 (ttm-80) cc_final: 0.8705 (ttt-90) REVERT: A 322 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8455 (ptmm) REVERT: B 265 TRP cc_start: 0.8733 (m100) cc_final: 0.7839 (m-10) REVERT: C 260 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: C 275 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8012 (mt0) outliers start: 22 outliers final: 16 residues processed: 102 average time/residue: 0.4870 time to fit residues: 53.3176 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 275 GLN 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 244 ARG Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.070047 restraints weight = 11433.745| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.58 r_work: 0.2712 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8208 Z= 0.222 Angle : 1.044 59.198 11166 Z= 0.557 Chirality : 0.049 0.300 1242 Planarity : 0.004 0.060 1398 Dihedral : 10.555 73.541 1347 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 19.03 % Favored : 78.84 % 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 aren not related in a simple way. whole: 0.85 (0.28), residues: 984 helix: 1.56 (0.35), residues: 267 sheet: 1.09 (0.29), residues: 312 loop : -0.51 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 244 TYR 0.017 0.002 TYR C 90 PHE 0.037 0.002 PHE C 92 TRP 0.011 0.001 TRP C 259 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8190) covalent geometry : angle 1.01966 (11121) SS BOND : bond 0.00421 ( 9) SS BOND : angle 2.81629 ( 18) hydrogen bonds : bond 0.03464 ( 244) hydrogen bonds : angle 4.47055 ( 669) link_NAG-ASN : bond 0.02715 ( 9) link_NAG-ASN : angle 4.13581 ( 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 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8969 (ttm-80) cc_final: 0.8703 (ttt-90) REVERT: A 322 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8422 (ptmm) REVERT: B 216 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8429 (pptt) REVERT: B 265 TRP cc_start: 0.8725 (m100) cc_final: 0.7817 (m-10) REVERT: C 260 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: C 275 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8010 (mt0) outliers start: 18 outliers final: 16 residues processed: 93 average time/residue: 0.5325 time to fit residues: 52.8519 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 216 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 GLN 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 244 ARG Chi-restraints excluded: chain C residue 260 GLU 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: 9.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 30 optimal weight: 7.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.070163 restraints weight = 11512.950| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.58 r_work: 0.2713 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8208 Z= 0.221 Angle : 1.043 59.095 11166 Z= 0.556 Chirality : 0.049 0.304 1242 Planarity : 0.004 0.060 1398 Dihedral : 10.555 73.540 1347 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 19.03 % Favored : 78.84 % 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 aren not related in a simple way. whole: 0.85 (0.28), residues: 984 helix: 1.56 (0.35), residues: 267 sheet: 1.09 (0.29), residues: 312 loop : -0.51 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 244 TYR 0.017 0.002 TYR C 90 PHE 0.037 0.002 PHE C 92 TRP 0.011 0.001 TRP C 259 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8190) covalent geometry : angle 1.01761 (11121) SS BOND : bond 0.01753 ( 9) SS BOND : angle 3.02101 ( 18) hydrogen bonds : bond 0.03461 ( 244) hydrogen bonds : angle 4.47061 ( 669) link_NAG-ASN : bond 0.02770 ( 9) link_NAG-ASN : angle 4.13954 ( 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: 18 poor density : 80 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8971 (ttm-80) cc_final: 0.8706 (ttt-90) REVERT: A 322 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8430 (ptmm) REVERT: B 216 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8426 (pptt) REVERT: B 265 TRP cc_start: 0.8732 (m100) cc_final: 0.7825 (m-10) REVERT: C 260 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: C 275 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8010 (mt0) outliers start: 18 outliers final: 16 residues processed: 93 average time/residue: 0.5236 time to fit residues: 51.9762 Evaluate side-chains 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 216 LYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 GLN 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 244 ARG Chi-restraints excluded: chain C residue 260 GLU 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: 4.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070109 restraints weight = 11451.465| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.58 r_work: 0.2713 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8208 Z= 0.221 Angle : 1.043 59.092 11166 Z= 0.556 Chirality : 0.049 0.304 1242 Planarity : 0.004 0.060 1398 Dihedral : 10.555 73.540 1347 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 19.15 % 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 aren not related in a simple way. whole: 0.85 (0.28), residues: 984 helix: 1.56 (0.35), residues: 267 sheet: 1.09 (0.29), residues: 312 loop : -0.51 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 244 TYR 0.017 0.002 TYR C 90 PHE 0.037 0.002 PHE C 92 TRP 0.011 0.001 TRP C 259 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8190) covalent geometry : angle 1.01755 (11121) SS BOND : bond 0.01792 ( 9) SS BOND : angle 3.02849 ( 18) hydrogen bonds : bond 0.03461 ( 244) hydrogen bonds : angle 4.47061 ( 669) link_NAG-ASN : bond 0.02772 ( 9) link_NAG-ASN : angle 4.13960 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3561.90 seconds wall clock time: 61 minutes 20.00 seconds (3680.00 seconds total)