Starting phenix.real_space_refine on Tue Mar 3 16:22:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqh_25385/03_2026/7sqh_25385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqh_25385/03_2026/7sqh_25385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sqh_25385/03_2026/7sqh_25385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqh_25385/03_2026/7sqh_25385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sqh_25385/03_2026/7sqh_25385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqh_25385/03_2026/7sqh_25385.map" } resolution = 2.5 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4500 2.51 5 N 1134 2.21 5 O 1287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6954 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2255 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2255 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2255 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 1.78, per 1000 atoms: 0.26 Number of scatterers: 6954 At special positions: 0 Unit cell: (81.4625, 81.4625, 126.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1287 8.00 N 1134 7.00 C 4500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 280.5 milliseconds 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1638 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 38.6% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 57 through 95 removed outlier: 3.793A pdb=" N LYS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 removed outlier: 3.515A pdb=" N LYS A 179 " --> pdb=" O GLU A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.649A pdb=" N PHE A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.305A pdb=" N SER A 277 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 278 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.638A pdb=" N ASN A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 302' Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.906A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 95 removed outlier: 3.793A pdb=" N LYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 removed outlier: 3.515A pdb=" N LYS B 179 " --> pdb=" O GLU B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 206 through 212 removed outlier: 3.649A pdb=" N PHE B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.305A pdb=" N SER B 277 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 278 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.639A pdb=" N ASN B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 302' Processing helix chain 'B' and resid 302 through 339 removed outlier: 3.906A pdb=" N THR B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 95 removed outlier: 3.793A pdb=" N LYS C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 removed outlier: 3.515A pdb=" N LYS C 179 " --> pdb=" O GLU C 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.649A pdb=" N PHE C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.305A pdb=" N SER C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA C 278 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.639A pdb=" N ASN C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 302 through 339 removed outlier: 3.906A pdb=" N THR C 306 " --> pdb=" O ASN C 302 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 107 current: chain 'A' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 181 through 189 current: chain 'A' and resid 254 through 266 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 266 current: chain 'B' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 181 through 189 current: chain 'B' and resid 254 through 266 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 266 current: chain 'C' and resid 181 through 189 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 181 through 189 current: chain 'C' and resid 254 through 266 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.120A pdb=" N ASP A 200 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.121A pdb=" N ASP B 200 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.120A pdb=" N ASP C 200 " --> pdb=" O TYR C 119 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 831 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: 1.13 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1086 1.27 - 1.41: 1809 1.41 - 1.54: 4098 1.54 - 1.67: 60 1.67 - 1.81: 51 Bond restraints: 7104 Sorted by residual: bond pdb=" C GLN C 152 " pdb=" O GLN C 152 " ideal model delta sigma weight residual 1.234 1.138 0.096 1.26e-02 6.30e+03 5.86e+01 bond pdb=" C ARG C 180 " pdb=" O ARG C 180 " ideal model delta sigma weight residual 1.235 1.146 0.090 1.26e-02 6.30e+03 5.07e+01 bond pdb=" C GLN B 152 " pdb=" O GLN B 152 " ideal model delta sigma weight residual 1.234 1.153 0.081 1.22e-02 6.72e+03 4.37e+01 bond pdb=" C TYR B 132 " pdb=" O TYR B 132 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.14e-02 7.69e+03 3.95e+01 bond pdb=" C GLN A 152 " pdb=" O GLN A 152 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.26e-02 6.30e+03 3.83e+01 ... (remaining 7099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 9094 1.46 - 2.93: 438 2.93 - 4.39: 58 4.39 - 5.85: 17 5.85 - 7.32: 14 Bond angle restraints: 9621 Sorted by residual: angle pdb=" CA ARG B 180 " pdb=" C ARG B 180 " pdb=" O ARG B 180 " ideal model delta sigma weight residual 122.14 114.88 7.26 1.24e+00 6.50e-01 3.43e+01 angle pdb=" CA ARG A 180 " pdb=" C ARG A 180 " pdb=" O ARG A 180 " ideal model delta sigma weight residual 122.45 115.48 6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" O HIS B 131 " pdb=" C HIS B 131 " pdb=" N TYR B 132 " ideal model delta sigma weight residual 123.15 116.72 6.43 1.30e+00 5.92e-01 2.44e+01 angle pdb=" O HIS A 131 " pdb=" C HIS A 131 " pdb=" N TYR A 132 " ideal model delta sigma weight residual 123.15 116.90 6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" O HIS C 131 " pdb=" C HIS C 131 " pdb=" N TYR C 132 " ideal model delta sigma weight residual 123.15 117.42 5.73 1.30e+00 5.92e-01 1.95e+01 ... (remaining 9616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 3950 21.16 - 42.32: 313 42.32 - 63.48: 104 63.48 - 84.65: 12 84.65 - 105.81: 28 Dihedral angle restraints: 4407 sinusoidal: 1893 harmonic: 2514 Sorted by residual: dihedral pdb=" C2 NAG C 404 " pdb=" C3 NAG C 404 " pdb=" C4 NAG C 404 " pdb=" O4 NAG C 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.30 105.81 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 404 " pdb=" C3 NAG A 404 " pdb=" C4 NAG A 404 " pdb=" O4 NAG A 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.33 105.78 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG B 404 " pdb=" C3 NAG B 404 " pdb=" C4 NAG B 404 " pdb=" O4 NAG B 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.34 105.77 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 893 0.057 - 0.114: 166 0.114 - 0.170: 33 0.170 - 0.227: 2 0.227 - 0.284: 4 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA ARG B 180 " pdb=" N ARG B 180 " pdb=" C ARG B 180 " pdb=" CB ARG B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1095 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 132 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR B 132 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR B 132 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 133 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 132 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR A 132 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 132 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A 133 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 132 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C TYR C 132 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR C 132 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 133 " 0.018 2.00e-02 2.50e+03 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1410 2.79 - 3.31: 6126 3.31 - 3.84: 11152 3.84 - 4.37: 13265 4.37 - 4.90: 23067 Nonbonded interactions: 55020 Sorted by model distance: nonbonded pdb=" O ASP C 269 " pdb=" OD1 ASP C 269 " model vdw 2.257 3.040 nonbonded pdb=" O ASP B 269 " pdb=" OD1 ASP B 269 " model vdw 2.258 3.040 nonbonded pdb=" O ASP A 269 " pdb=" OD1 ASP A 269 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 119 " pdb=" OH TYR C 156 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR B 119 " pdb=" OH TYR B 156 " model vdw 2.266 3.040 ... (remaining 55015 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 4.520 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.006 0.096 7116 Z= 0.376 Angle : 0.762 8.210 9657 Z= 0.468 Chirality : 0.050 0.284 1098 Planarity : 0.004 0.037 1200 Dihedral : 19.411 105.807 2769 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % 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: 1.93 (0.29), residues: 843 helix: 3.21 (0.27), residues: 312 sheet: 0.58 (0.27), residues: 312 loop : -0.53 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.022 0.001 TYR A 132 PHE 0.014 0.001 PHE C 204 TRP 0.007 0.001 TRP B 330 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 7104) covalent geometry : angle 0.73997 ( 9621) hydrogen bonds : bond 0.08196 ( 286) hydrogen bonds : angle 3.59231 ( 831) link_NAG-ASN : bond 0.00813 ( 12) link_NAG-ASN : angle 3.05765 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7059 (t80) cc_final: 0.6852 (t80) REVERT: A 122 GLN cc_start: 0.8847 (mm110) cc_final: 0.8488 (mm110) REVERT: A 153 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7166 (mtp85) REVERT: A 180 ARG cc_start: 0.7846 (mtp180) cc_final: 0.7618 (mtp180) REVERT: A 253 ARG cc_start: 0.7686 (ptm-80) cc_final: 0.7002 (ptm-80) REVERT: A 297 ASP cc_start: 0.8455 (t0) cc_final: 0.8182 (t0) REVERT: A 325 LYS cc_start: 0.7909 (ttmt) cc_final: 0.7692 (ttmt) REVERT: B 72 PHE cc_start: 0.6920 (m-10) cc_final: 0.6677 (m-80) REVERT: B 87 ARG cc_start: 0.7355 (tpm-80) cc_final: 0.7111 (tpp80) REVERT: B 91 ASP cc_start: 0.8205 (m-30) cc_final: 0.7920 (m-30) REVERT: B 247 THR cc_start: 0.9088 (m) cc_final: 0.8847 (t) REVERT: B 275 LYS cc_start: 0.8027 (mttm) cc_final: 0.7747 (ttmm) REVERT: B 296 GLN cc_start: 0.8308 (tt0) cc_final: 0.8092 (tp40) REVERT: C 72 PHE cc_start: 0.7282 (m-10) cc_final: 0.6994 (m-80) REVERT: C 266 ASN cc_start: 0.8740 (t0) cc_final: 0.8452 (t0) REVERT: C 275 LYS cc_start: 0.8050 (mttm) cc_final: 0.7809 (ttmm) REVERT: C 297 ASP cc_start: 0.8530 (t0) cc_final: 0.8230 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.8874 time to fit residues: 234.5856 Evaluate side-chains 184 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 143 GLN A 152 GLN A 266 ASN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 212 GLN B 266 ASN C 143 GLN C 152 GLN C 279 GLN C 293 GLN C 296 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.105845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089375 restraints weight = 12413.060| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.83 r_work: 0.3160 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7116 Z= 0.154 Angle : 0.613 9.071 9657 Z= 0.296 Chirality : 0.047 0.329 1098 Planarity : 0.004 0.046 1200 Dihedral : 12.870 70.771 1164 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.07 % Allowed : 26.28 % Favored : 71.65 % 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: 2.09 (0.29), residues: 843 helix: 3.41 (0.27), residues: 312 sheet: 0.60 (0.27), residues: 312 loop : -0.45 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 110 TYR 0.008 0.001 TYR B 227 PHE 0.024 0.001 PHE C 92 TRP 0.008 0.001 TRP A 230 HIS 0.005 0.002 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7104) covalent geometry : angle 0.58516 ( 9621) hydrogen bonds : bond 0.03033 ( 286) hydrogen bonds : angle 3.09464 ( 831) link_NAG-ASN : bond 0.00884 ( 12) link_NAG-ASN : angle 3.07027 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7728 (t80) cc_final: 0.7501 (t80) REVERT: A 153 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7829 (mtp85) REVERT: A 156 TYR cc_start: 0.8406 (p90) cc_final: 0.8065 (p90) REVERT: A 180 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8196 (mtp180) REVERT: A 224 GLU cc_start: 0.7694 (tp30) cc_final: 0.7354 (tp30) REVERT: A 275 LYS cc_start: 0.8264 (ttmm) cc_final: 0.8049 (mtpp) REVERT: A 294 LYS cc_start: 0.8299 (tmmt) cc_final: 0.7950 (tmmt) REVERT: B 208 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: B 275 LYS cc_start: 0.8280 (mttm) cc_final: 0.8069 (mttm) REVERT: C 72 PHE cc_start: 0.7906 (m-10) cc_final: 0.7696 (m-80) REVERT: C 95 LYS cc_start: 0.8698 (mttt) cc_final: 0.8471 (mtmm) REVERT: C 133 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 147 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8006 (tpp) REVERT: C 266 ASN cc_start: 0.9027 (t0) cc_final: 0.8717 (t0) REVERT: C 326 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8231 (mm) REVERT: C 333 LYS cc_start: 0.8513 (tttt) cc_final: 0.8090 (ttpt) outliers start: 15 outliers final: 3 residues processed: 200 average time/residue: 0.7632 time to fit residues: 158.0188 Evaluate side-chains 202 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 GLN C 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.086575 restraints weight = 12306.190| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.82 r_work: 0.3147 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7116 Z= 0.147 Angle : 0.584 8.706 9657 Z= 0.283 Chirality : 0.046 0.324 1098 Planarity : 0.003 0.032 1200 Dihedral : 8.085 58.185 1164 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.63 % Allowed : 26.97 % Favored : 70.40 % 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: 2.04 (0.29), residues: 843 helix: 3.39 (0.27), residues: 312 sheet: 0.63 (0.28), residues: 312 loop : -0.61 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 259 TYR 0.006 0.001 TYR C 201 PHE 0.028 0.001 PHE B 72 TRP 0.009 0.001 TRP A 230 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7104) covalent geometry : angle 0.55720 ( 9621) hydrogen bonds : bond 0.03156 ( 286) hydrogen bonds : angle 3.08430 ( 831) link_NAG-ASN : bond 0.00946 ( 12) link_NAG-ASN : angle 2.93443 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.285 Fit side-chains REVERT: A 63 LYS cc_start: 0.8017 (tptp) cc_final: 0.7746 (tmmt) REVERT: A 92 PHE cc_start: 0.7807 (t80) cc_final: 0.7582 (t80) REVERT: A 153 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7829 (mtp85) REVERT: A 180 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8205 (mtp180) REVERT: A 224 GLU cc_start: 0.7680 (tp30) cc_final: 0.7254 (tp30) REVERT: A 275 LYS cc_start: 0.8257 (ttmm) cc_final: 0.8054 (mtpp) REVERT: A 294 LYS cc_start: 0.8330 (tmmt) cc_final: 0.7930 (tmmt) REVERT: B 91 ASP cc_start: 0.8522 (m-30) cc_final: 0.8289 (m-30) REVERT: B 212 GLN cc_start: 0.8311 (pt0) cc_final: 0.8093 (mt0) REVERT: B 294 LYS cc_start: 0.8339 (tmmt) cc_final: 0.8132 (tmmt) REVERT: C 87 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7792 (tpm-80) REVERT: C 95 LYS cc_start: 0.8719 (mttt) cc_final: 0.8506 (mtmm) REVERT: C 133 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7231 (tm-30) REVERT: C 176 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8164 (mt-10) REVERT: C 180 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7837 (mtp180) REVERT: C 241 LYS cc_start: 0.9003 (mttm) cc_final: 0.8794 (mttp) REVERT: C 266 ASN cc_start: 0.8998 (t0) cc_final: 0.8657 (t0) REVERT: C 326 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8256 (mm) REVERT: C 333 LYS cc_start: 0.8630 (tttt) cc_final: 0.8140 (ttpp) outliers start: 19 outliers final: 4 residues processed: 209 average time/residue: 0.8321 time to fit residues: 179.9464 Evaluate side-chains 201 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.090332 restraints weight = 12489.307| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.79 r_work: 0.3134 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7116 Z= 0.163 Angle : 0.582 8.842 9657 Z= 0.286 Chirality : 0.045 0.330 1098 Planarity : 0.004 0.046 1200 Dihedral : 6.913 57.769 1164 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 28.22 % Favored : 69.29 % 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: 2.05 (0.29), residues: 843 helix: 3.39 (0.27), residues: 309 sheet: 0.74 (0.28), residues: 306 loop : -0.68 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 110 TYR 0.008 0.001 TYR C 201 PHE 0.028 0.002 PHE C 72 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7104) covalent geometry : angle 0.55059 ( 9621) hydrogen bonds : bond 0.03204 ( 286) hydrogen bonds : angle 3.15848 ( 831) link_NAG-ASN : bond 0.00941 ( 12) link_NAG-ASN : angle 3.15105 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8047 (tptp) cc_final: 0.7809 (tmmt) REVERT: A 92 PHE cc_start: 0.7879 (t80) cc_final: 0.7670 (t80) REVERT: A 124 GLN cc_start: 0.8027 (mm110) cc_final: 0.7798 (mm110) REVERT: A 153 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7855 (mtp85) REVERT: A 180 ARG cc_start: 0.8403 (mtp180) cc_final: 0.8177 (mtp180) REVERT: A 224 GLU cc_start: 0.7728 (tp30) cc_final: 0.7278 (tp30) REVERT: A 294 LYS cc_start: 0.8332 (tmmt) cc_final: 0.8057 (tmmt) REVERT: A 333 LYS cc_start: 0.8726 (tttt) cc_final: 0.8227 (ttpp) REVERT: B 212 GLN cc_start: 0.8272 (pt0) cc_final: 0.8063 (mt0) REVERT: B 333 LYS cc_start: 0.8732 (tttt) cc_final: 0.8200 (ttpp) REVERT: C 87 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7799 (tpm-80) REVERT: C 95 LYS cc_start: 0.8712 (mttt) cc_final: 0.8493 (mttm) REVERT: C 176 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8177 (mt-10) REVERT: C 180 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7819 (mtp180) REVERT: C 266 ASN cc_start: 0.9028 (t0) cc_final: 0.8728 (t0) REVERT: C 326 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8309 (mm) REVERT: C 333 LYS cc_start: 0.8688 (tttt) cc_final: 0.8238 (ttpp) outliers start: 18 outliers final: 9 residues processed: 210 average time/residue: 0.8487 time to fit residues: 184.2139 Evaluate side-chains 213 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089233 restraints weight = 12496.326| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.71 r_work: 0.3126 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7116 Z= 0.167 Angle : 0.589 8.924 9657 Z= 0.290 Chirality : 0.045 0.334 1098 Planarity : 0.004 0.055 1200 Dihedral : 6.133 55.955 1164 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.32 % Allowed : 27.52 % Favored : 69.16 % 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: 1.94 (0.29), residues: 843 helix: 3.24 (0.27), residues: 309 sheet: 0.72 (0.29), residues: 306 loop : -0.71 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 110 TYR 0.008 0.001 TYR C 201 PHE 0.036 0.002 PHE C 72 TRP 0.009 0.001 TRP A 230 HIS 0.001 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7104) covalent geometry : angle 0.55612 ( 9621) hydrogen bonds : bond 0.03348 ( 286) hydrogen bonds : angle 3.21614 ( 831) link_NAG-ASN : bond 0.00952 ( 12) link_NAG-ASN : angle 3.21810 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.277 Fit side-chains REVERT: A 63 LYS cc_start: 0.8085 (tptp) cc_final: 0.7826 (tmmt) REVERT: A 92 PHE cc_start: 0.7900 (t80) cc_final: 0.7698 (t80) REVERT: A 122 GLN cc_start: 0.9070 (mm110) cc_final: 0.8830 (mm110) REVERT: A 124 GLN cc_start: 0.8023 (mm110) cc_final: 0.7770 (mm110) REVERT: A 147 MET cc_start: 0.8380 (ttm) cc_final: 0.8043 (ttm) REVERT: A 153 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7840 (mtp85) REVERT: A 224 GLU cc_start: 0.7772 (tp30) cc_final: 0.7329 (tp30) REVERT: A 294 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8003 (tmmt) REVERT: A 333 LYS cc_start: 0.8775 (tttt) cc_final: 0.8307 (ttpp) REVERT: B 77 LEU cc_start: 0.8594 (mt) cc_final: 0.8383 (mm) REVERT: B 162 ASN cc_start: 0.5707 (OUTLIER) cc_final: 0.5348 (m110) REVERT: B 333 LYS cc_start: 0.8785 (tttt) cc_final: 0.8303 (ttpp) REVERT: C 87 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7857 (tpm-80) REVERT: C 95 LYS cc_start: 0.8734 (mttt) cc_final: 0.8523 (mttm) REVERT: C 176 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 180 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7835 (mtp180) REVERT: C 266 ASN cc_start: 0.9015 (t0) cc_final: 0.8769 (t0) REVERT: C 326 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8314 (mm) REVERT: C 333 LYS cc_start: 0.8762 (tttt) cc_final: 0.8305 (ttpp) outliers start: 24 outliers final: 7 residues processed: 216 average time/residue: 0.8502 time to fit residues: 189.9864 Evaluate side-chains 219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 293 GLN B 293 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089436 restraints weight = 12563.899| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.71 r_work: 0.3129 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7116 Z= 0.153 Angle : 0.588 8.793 9657 Z= 0.289 Chirality : 0.045 0.330 1098 Planarity : 0.004 0.040 1200 Dihedral : 5.832 53.882 1164 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 29.60 % Favored : 67.91 % 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: 1.94 (0.29), residues: 843 helix: 3.26 (0.27), residues: 309 sheet: 0.70 (0.29), residues: 306 loop : -0.70 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 110 TYR 0.008 0.001 TYR C 201 PHE 0.027 0.002 PHE C 72 TRP 0.007 0.001 TRP A 230 HIS 0.002 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7104) covalent geometry : angle 0.55897 ( 9621) hydrogen bonds : bond 0.03262 ( 286) hydrogen bonds : angle 3.22997 ( 831) link_NAG-ASN : bond 0.00916 ( 12) link_NAG-ASN : angle 3.06488 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.283 Fit side-chains REVERT: A 63 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7863 (tmmt) REVERT: A 92 PHE cc_start: 0.7879 (t80) cc_final: 0.7674 (t80) REVERT: A 124 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7679 (mm-40) REVERT: A 133 GLU cc_start: 0.7531 (tm-30) cc_final: 0.6473 (tm-30) REVERT: A 147 MET cc_start: 0.8412 (ttm) cc_final: 0.8102 (ttm) REVERT: A 153 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7884 (mtp85) REVERT: A 180 ARG cc_start: 0.8072 (mtp180) cc_final: 0.7535 (ttp-170) REVERT: A 224 GLU cc_start: 0.7749 (tp30) cc_final: 0.7318 (tp30) REVERT: A 294 LYS cc_start: 0.8347 (tmmt) cc_final: 0.8050 (tmmt) REVERT: A 333 LYS cc_start: 0.8816 (tttt) cc_final: 0.8364 (ttpp) REVERT: B 77 LEU cc_start: 0.8600 (mt) cc_final: 0.8393 (mm) REVERT: B 162 ASN cc_start: 0.5753 (OUTLIER) cc_final: 0.5405 (m-40) REVERT: B 333 LYS cc_start: 0.8766 (tttt) cc_final: 0.8291 (ttpp) REVERT: C 87 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7886 (tpm-80) REVERT: C 95 LYS cc_start: 0.8732 (mttt) cc_final: 0.8526 (mttm) REVERT: C 176 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 180 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7845 (mtp180) REVERT: C 266 ASN cc_start: 0.9019 (t0) cc_final: 0.8753 (t0) REVERT: C 326 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8308 (mm) REVERT: C 333 LYS cc_start: 0.8780 (tttt) cc_final: 0.8328 (ttpp) outliers start: 18 outliers final: 9 residues processed: 215 average time/residue: 0.8536 time to fit residues: 189.7990 Evaluate side-chains 219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 212 GLN B 293 GLN B 296 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.104279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088942 restraints weight = 12383.818| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.69 r_work: 0.3128 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7116 Z= 0.159 Angle : 0.604 9.631 9657 Z= 0.295 Chirality : 0.046 0.331 1098 Planarity : 0.004 0.045 1200 Dihedral : 5.436 49.685 1164 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.77 % Allowed : 28.35 % Favored : 68.88 % 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: 1.90 (0.29), residues: 843 helix: 3.21 (0.27), residues: 309 sheet: 0.67 (0.29), residues: 306 loop : -0.69 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 110 TYR 0.008 0.001 TYR C 201 PHE 0.026 0.002 PHE C 72 TRP 0.007 0.001 TRP A 230 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7104) covalent geometry : angle 0.57487 ( 9621) hydrogen bonds : bond 0.03327 ( 286) hydrogen bonds : angle 3.24104 ( 831) link_NAG-ASN : bond 0.00928 ( 12) link_NAG-ASN : angle 3.07891 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.278 Fit side-chains REVERT: A 63 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7878 (tmmt) REVERT: A 122 GLN cc_start: 0.9108 (mm110) cc_final: 0.8865 (mm110) REVERT: A 124 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 133 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6261 (tm-30) REVERT: A 147 MET cc_start: 0.8433 (ttm) cc_final: 0.8132 (ttm) REVERT: A 180 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7447 (ttp-170) REVERT: A 224 GLU cc_start: 0.7782 (tp30) cc_final: 0.7344 (tp30) REVERT: A 294 LYS cc_start: 0.8330 (tmmt) cc_final: 0.8066 (tmmt) REVERT: A 329 LYS cc_start: 0.8571 (tttt) cc_final: 0.8363 (tttt) REVERT: A 333 LYS cc_start: 0.8846 (tttt) cc_final: 0.8407 (ttpp) REVERT: B 77 LEU cc_start: 0.8618 (mt) cc_final: 0.8412 (mm) REVERT: B 162 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5679 (m-40) REVERT: B 188 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8313 (ppp80) REVERT: B 333 LYS cc_start: 0.8795 (tttt) cc_final: 0.8350 (ttpp) REVERT: C 87 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7843 (tpm-80) REVERT: C 95 LYS cc_start: 0.8729 (mttt) cc_final: 0.8513 (mttm) REVERT: C 176 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8151 (mt-10) REVERT: C 180 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7831 (mtp180) REVERT: C 266 ASN cc_start: 0.9019 (t0) cc_final: 0.8774 (t0) REVERT: C 326 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8331 (mm) REVERT: C 333 LYS cc_start: 0.8806 (tttt) cc_final: 0.8392 (ttpp) outliers start: 20 outliers final: 10 residues processed: 219 average time/residue: 0.8335 time to fit residues: 188.5912 Evaluate side-chains 220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 130 HIS B 143 GLN B 212 GLN B 293 GLN B 296 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088750 restraints weight = 12602.262| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.66 r_work: 0.3129 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7116 Z= 0.164 Angle : 0.599 9.791 9657 Z= 0.294 Chirality : 0.046 0.330 1098 Planarity : 0.004 0.041 1200 Dihedral : 5.032 41.797 1164 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.63 % Allowed : 29.18 % Favored : 68.19 % 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: 1.84 (0.29), residues: 843 helix: 3.16 (0.27), residues: 309 sheet: 0.71 (0.29), residues: 312 loop : -0.89 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 259 TYR 0.008 0.001 TYR C 201 PHE 0.029 0.002 PHE C 92 TRP 0.011 0.001 TRP A 230 HIS 0.003 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7104) covalent geometry : angle 0.57060 ( 9621) hydrogen bonds : bond 0.03369 ( 286) hydrogen bonds : angle 3.28324 ( 831) link_NAG-ASN : bond 0.00935 ( 12) link_NAG-ASN : angle 3.05855 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.285 Fit side-chains REVERT: A 63 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7957 (tmmt) REVERT: A 124 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7784 (mm-40) REVERT: A 133 GLU cc_start: 0.7573 (tm-30) cc_final: 0.6112 (tm-30) REVERT: A 180 ARG cc_start: 0.8062 (mtp180) cc_final: 0.7445 (ttp-170) REVERT: A 224 GLU cc_start: 0.7839 (tp30) cc_final: 0.7390 (tp30) REVERT: A 294 LYS cc_start: 0.8359 (tmmt) cc_final: 0.8035 (tmmt) REVERT: A 329 LYS cc_start: 0.8544 (tttt) cc_final: 0.8341 (tttt) REVERT: A 333 LYS cc_start: 0.8871 (tttt) cc_final: 0.8428 (ttpp) REVERT: B 77 LEU cc_start: 0.8624 (mt) cc_final: 0.8420 (mm) REVERT: B 162 ASN cc_start: 0.6122 (OUTLIER) cc_final: 0.5891 (m110) REVERT: B 188 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8324 (ppp80) REVERT: B 333 LYS cc_start: 0.8804 (tttt) cc_final: 0.8384 (ttpp) REVERT: C 87 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7881 (tpm-80) REVERT: C 95 LYS cc_start: 0.8713 (mttt) cc_final: 0.8494 (mttm) REVERT: C 176 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8133 (mt-10) REVERT: C 266 ASN cc_start: 0.9028 (t0) cc_final: 0.8806 (t0) REVERT: C 326 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8381 (mm) REVERT: C 333 LYS cc_start: 0.8797 (tttt) cc_final: 0.8409 (ttpp) outliers start: 19 outliers final: 10 residues processed: 212 average time/residue: 0.8556 time to fit residues: 187.5020 Evaluate side-chains 213 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 143 GLN B 212 GLN B 293 GLN C 130 HIS C 143 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090926 restraints weight = 12380.726| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.74 r_work: 0.3138 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7116 Z= 0.139 Angle : 0.625 10.511 9657 Z= 0.304 Chirality : 0.045 0.323 1098 Planarity : 0.004 0.051 1200 Dihedral : 4.724 33.435 1164 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.94 % Allowed : 30.43 % Favored : 67.63 % 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: 1.89 (0.29), residues: 843 helix: 3.20 (0.27), residues: 309 sheet: 0.73 (0.29), residues: 312 loop : -0.86 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 110 TYR 0.008 0.001 TYR B 227 PHE 0.028 0.001 PHE C 72 TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7104) covalent geometry : angle 0.59901 ( 9621) hydrogen bonds : bond 0.03207 ( 286) hydrogen bonds : angle 3.25230 ( 831) link_NAG-ASN : bond 0.00897 ( 12) link_NAG-ASN : angle 2.99266 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.316 Fit side-chains REVERT: A 63 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7971 (tmmt) REVERT: A 122 GLN cc_start: 0.9102 (mm110) cc_final: 0.8840 (mm110) REVERT: A 124 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7809 (mm-40) REVERT: A 180 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7396 (ttp-170) REVERT: A 224 GLU cc_start: 0.7814 (tp30) cc_final: 0.7344 (tp30) REVERT: A 294 LYS cc_start: 0.8361 (tmmt) cc_final: 0.7966 (tmmt) REVERT: A 329 LYS cc_start: 0.8544 (tttt) cc_final: 0.8338 (tttt) REVERT: A 331 MET cc_start: 0.7419 (tmm) cc_final: 0.7053 (tmm) REVERT: A 333 LYS cc_start: 0.8902 (tttt) cc_final: 0.8494 (ttpp) REVERT: B 162 ASN cc_start: 0.6184 (OUTLIER) cc_final: 0.5868 (m110) REVERT: B 188 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8277 (ppp80) REVERT: B 294 LYS cc_start: 0.8334 (tmmt) cc_final: 0.8102 (tmmt) REVERT: B 333 LYS cc_start: 0.8807 (tttt) cc_final: 0.8360 (ttpp) REVERT: C 87 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (tpm-80) REVERT: C 95 LYS cc_start: 0.8717 (mttt) cc_final: 0.8488 (mttm) REVERT: C 133 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7138 (tm-30) REVERT: C 176 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8133 (mt-10) REVERT: C 266 ASN cc_start: 0.9016 (t0) cc_final: 0.8761 (t0) REVERT: C 326 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8327 (mm) REVERT: C 333 LYS cc_start: 0.8820 (tttt) cc_final: 0.8424 (ttpp) outliers start: 14 outliers final: 6 residues processed: 213 average time/residue: 0.8462 time to fit residues: 186.3085 Evaluate side-chains 214 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.0040 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 130 HIS B 143 GLN B 212 GLN B 293 GLN B 296 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090487 restraints weight = 12586.825| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.70 r_work: 0.3163 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7116 Z= 0.115 Angle : 0.615 9.981 9657 Z= 0.298 Chirality : 0.045 0.312 1098 Planarity : 0.004 0.055 1200 Dihedral : 4.412 24.751 1164 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.52 % Allowed : 31.12 % Favored : 67.36 % 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: 1.93 (0.29), residues: 843 helix: 3.26 (0.27), residues: 309 sheet: 0.52 (0.28), residues: 330 loop : -0.56 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 110 TYR 0.007 0.001 TYR B 227 PHE 0.028 0.001 PHE C 92 TRP 0.007 0.001 TRP A 304 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7104) covalent geometry : angle 0.58942 ( 9621) hydrogen bonds : bond 0.03023 ( 286) hydrogen bonds : angle 3.23976 ( 831) link_NAG-ASN : bond 0.00869 ( 12) link_NAG-ASN : angle 2.93121 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7923 (tmmt) REVERT: A 122 GLN cc_start: 0.9077 (mm110) cc_final: 0.8846 (mm110) REVERT: A 124 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7770 (mm-40) REVERT: A 224 GLU cc_start: 0.7819 (tp30) cc_final: 0.7347 (tp30) REVERT: A 294 LYS cc_start: 0.8335 (tmmt) cc_final: 0.8032 (tmmt) REVERT: A 331 MET cc_start: 0.7406 (tmm) cc_final: 0.7055 (tmm) REVERT: A 333 LYS cc_start: 0.8887 (tttt) cc_final: 0.8455 (ttpp) REVERT: B 162 ASN cc_start: 0.6088 (OUTLIER) cc_final: 0.5878 (m110) REVERT: B 188 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8200 (ppp80) REVERT: B 294 LYS cc_start: 0.8360 (tmmt) cc_final: 0.8115 (tmmt) REVERT: B 333 LYS cc_start: 0.8793 (tttt) cc_final: 0.8407 (ttpp) REVERT: C 87 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7839 (tpm-80) REVERT: C 95 LYS cc_start: 0.8762 (mttt) cc_final: 0.8549 (mttm) REVERT: C 133 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7156 (tm-30) REVERT: C 176 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 266 ASN cc_start: 0.9013 (t0) cc_final: 0.8736 (t0) REVERT: C 326 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8402 (mm) REVERT: C 333 LYS cc_start: 0.8873 (tttt) cc_final: 0.8542 (ttpp) outliers start: 11 outliers final: 4 residues processed: 211 average time/residue: 0.8654 time to fit residues: 188.6151 Evaluate side-chains 204 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN B 130 HIS B 212 GLN B 293 GLN C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087625 restraints weight = 12260.422| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.75 r_work: 0.3142 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7116 Z= 0.147 Angle : 0.623 11.022 9657 Z= 0.305 Chirality : 0.046 0.324 1098 Planarity : 0.004 0.052 1200 Dihedral : 4.335 20.996 1164 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.80 % Allowed : 30.71 % Favored : 67.50 % 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: 1.91 (0.29), residues: 843 helix: 3.21 (0.27), residues: 309 sheet: 0.56 (0.28), residues: 330 loop : -0.61 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 110 TYR 0.008 0.001 TYR B 74 PHE 0.028 0.002 PHE C 72 TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7104) covalent geometry : angle 0.59643 ( 9621) hydrogen bonds : bond 0.03221 ( 286) hydrogen bonds : angle 3.24263 ( 831) link_NAG-ASN : bond 0.00899 ( 12) link_NAG-ASN : angle 3.00415 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3825.40 seconds wall clock time: 65 minutes 49.35 seconds (3949.35 seconds total)