Starting phenix.real_space_refine on Thu Jul 2 05:50:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sqh_25385/07_2026/7sqh_25385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqh_25385/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2026/7sqh_25385.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2026/7sqh_25385.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2026/7sqh_25385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2026/7sqh_25385.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2026/7sqh_25385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_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-6108/lib/python3.11/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 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 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 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: 1.54, per 1000 atoms: 0.22 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: 0.51 Conformation dependent library (CDL) restraints added in 290.1 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: 0.19 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: 0.98 Time building geometry restraints manager: 0.64 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 - 17.63: 3639 17.63 - 35.26: 365 35.26 - 52.89: 119 52.89 - 70.52: 19 70.52 - 88.15: 13 Dihedral angle restraints: 4155 sinusoidal: 1641 harmonic: 2514 Sorted by residual: dihedral pdb=" CA PHE A 204 " pdb=" C PHE A 204 " pdb=" N SER A 205 " pdb=" CA SER A 205 " ideal model delta harmonic sigma weight residual 180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE B 204 " pdb=" C PHE B 204 " pdb=" N SER B 205 " pdb=" CA SER B 205 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE C 204 " pdb=" C PHE C 204 " pdb=" N SER C 205 " pdb=" CA SER C 205 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4152 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: 3.730 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.320 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 16.660 88.145 2517 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/Z covalent geometry : bond 0.00556 / 0.38 ( 7104) covalent geometry : angle 0.73997 / 0.46 ( 9621) hydrogen bonds : bond 0.08196 / 5.31 ( 286) hydrogen bonds : angle 3.59231 / 2.62 ( 831) link_NAG-ASN : bond 0.00813 / 0.58 ( 12) link_NAG-ASN : angle 3.05765 / 2.43 ( 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 : 0.253 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: 0.8225 time to fit residues: 217.7653 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... A 124 GLN A 143 GLN A 152 GLN A 266 ASN 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 = 0.3609 r_free = 0.3609 target = 0.106295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089503 restraints weight = 12368.295| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.87 r_work: 0.3161 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7116 Z= 0.154 Angle : 0.586 9.140 9657 Z= 0.290 Chirality : 0.046 0.335 1098 Planarity : 0.004 0.047 1200 Dihedral : 4.383 18.233 912 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.94 % Allowed : 26.28 % Favored : 71.78 % 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: 2.10 (0.29), residues: 843 helix: 3.41 (0.27), residues: 312 sheet: 0.61 (0.27), residues: 312 loop : -0.46 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 110 TYR 0.008 0.001 TYR B 227 PHE 0.023 0.001 PHE C 92 TRP 0.008 0.001 TRP A 230 HIS 0.006 0.002 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 7104) covalent geometry : angle 0.55576 / 0.28 ( 9621) hydrogen bonds : bond 0.03017 / 2.08 ( 286) hydrogen bonds : angle 3.10065 / 2.28 ( 831) link_NAG-ASN : bond 0.00876 / 0.61 ( 12) link_NAG-ASN : angle 3.09028 / 2.50 ( 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 206 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7763 (t80) cc_final: 0.7544 (t80) REVERT: A 153 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7799 (mtp85) REVERT: A 156 TYR cc_start: 0.8404 (p90) cc_final: 0.8083 (p90) REVERT: A 180 ARG cc_start: 0.8435 (mtp180) cc_final: 0.8209 (mtp180) REVERT: A 224 GLU cc_start: 0.7708 (tp30) cc_final: 0.7382 (tp30) REVERT: A 275 LYS cc_start: 0.8262 (ttmm) cc_final: 0.8044 (mtpp) REVERT: A 294 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7965 (tmmt) REVERT: B 208 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: B 275 LYS cc_start: 0.8288 (mttm) cc_final: 0.8078 (mttm) REVERT: C 72 PHE cc_start: 0.7905 (m-10) cc_final: 0.7696 (m-80) REVERT: C 95 LYS cc_start: 0.8718 (mttt) cc_final: 0.8480 (mtmm) REVERT: C 133 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7402 (tm-30) REVERT: C 266 ASN cc_start: 0.9027 (t0) cc_final: 0.8719 (t0) REVERT: C 326 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8223 (mm) REVERT: C 333 LYS cc_start: 0.8526 (tttt) cc_final: 0.8102 (ttpt) outliers start: 14 outliers final: 4 residues processed: 198 average time/residue: 0.7768 time to fit residues: 159.4766 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU 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 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.0070 chunk 40 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3601 r_free = 0.3601 target = 0.104688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.087379 restraints weight = 12165.034| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.90 r_work: 0.3150 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7116 Z= 0.137 Angle : 0.548 8.773 9657 Z= 0.273 Chirality : 0.045 0.334 1098 Planarity : 0.003 0.032 1200 Dihedral : 4.266 19.093 912 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 2.07 (0.29), residues: 843 helix: 3.42 (0.27), residues: 312 sheet: 0.64 (0.28), residues: 312 loop : -0.60 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 110 TYR 0.007 0.001 TYR C 201 PHE 0.026 0.001 PHE B 72 TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7104) covalent geometry : angle 0.51844 / 0.27 ( 9621) hydrogen bonds : bond 0.03041 / 2.10 ( 286) hydrogen bonds : angle 3.05987 / 2.26 ( 831) link_NAG-ASN : bond 0.00887 / 0.63 ( 12) link_NAG-ASN : angle 2.94599 / 2.39 ( 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 : 0.270 Fit side-chains REVERT: A 63 LYS cc_start: 0.8015 (tptp) cc_final: 0.7749 (tmmt) REVERT: A 92 PHE cc_start: 0.7722 (t80) cc_final: 0.7497 (t80) REVERT: A 153 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7848 (mtp85) REVERT: A 156 TYR cc_start: 0.8513 (p90) cc_final: 0.8074 (p90) REVERT: A 180 ARG cc_start: 0.8424 (mtp180) cc_final: 0.8214 (mtp180) REVERT: A 224 GLU cc_start: 0.7713 (tp30) cc_final: 0.7295 (tp30) REVERT: A 275 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8050 (mtpp) REVERT: A 294 LYS cc_start: 0.8339 (tmmt) cc_final: 0.8061 (tmmt) REVERT: B 91 ASP cc_start: 0.8500 (m-30) cc_final: 0.8286 (m-30) REVERT: B 212 GLN cc_start: 0.8319 (pt0) cc_final: 0.8068 (mt0) REVERT: C 72 PHE cc_start: 0.7916 (m-10) cc_final: 0.7704 (m-80) REVERT: C 87 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7794 (tpm-80) REVERT: C 95 LYS cc_start: 0.8726 (mttt) cc_final: 0.8485 (mtmm) REVERT: C 133 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7256 (tm-30) REVERT: C 176 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 180 ARG cc_start: 0.8284 (mtp180) cc_final: 0.7824 (mtp180) REVERT: C 241 LYS cc_start: 0.8990 (mttm) cc_final: 0.8779 (mttp) REVERT: C 266 ASN cc_start: 0.9001 (t0) cc_final: 0.8676 (t0) REVERT: C 326 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (mm) REVERT: C 333 LYS cc_start: 0.8586 (tttt) cc_final: 0.8158 (ttpt) outliers start: 19 outliers final: 5 residues processed: 209 average time/residue: 0.7908 time to fit residues: 171.4089 Evaluate side-chains 202 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B 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: 0.6980 chunk 63 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3585 r_free = 0.3585 target = 0.106427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.090877 restraints weight = 12518.484| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.77 r_work: 0.3128 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- 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 = 0.12 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7116 Z= 0.194 Angle : 0.600 9.230 9657 Z= 0.296 Chirality : 0.046 0.353 1098 Planarity : 0.004 0.045 1200 Dihedral : 4.427 20.005 912 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.07 % Allowed : 28.63 % 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: 1.99 (0.29), residues: 843 helix: 3.34 (0.27), residues: 309 sheet: 0.63 (0.28), residues: 312 loop : -0.60 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.009 0.001 TYR B 111 PHE 0.028 0.002 PHE B 72 TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 ( 7104) covalent geometry : angle 0.57124 / 0.29 ( 9621) hydrogen bonds : bond 0.03380 / 2.36 ( 286) hydrogen bonds : angle 3.17683 / 2.35 ( 831) link_NAG-ASN : bond 0.01001 / 0.72 ( 12) link_NAG-ASN : angle 3.06714 / 2.46 ( 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 217 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.195 Fit side-chains REVERT: A 63 LYS cc_start: 0.8043 (tptp) cc_final: 0.7806 (tmmt) REVERT: A 92 PHE cc_start: 0.7914 (t80) cc_final: 0.7706 (t80) REVERT: A 153 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7869 (mtp85) REVERT: A 180 ARG cc_start: 0.8411 (mtp180) cc_final: 0.8176 (mtp180) REVERT: A 224 GLU cc_start: 0.7767 (tp30) cc_final: 0.7302 (tp30) REVERT: A 294 LYS cc_start: 0.8336 (tmmt) cc_final: 0.8066 (tmmt) REVERT: A 333 LYS cc_start: 0.8729 (tttt) cc_final: 0.8226 (ttpp) REVERT: B 162 ASN cc_start: 0.5536 (OUTLIER) cc_final: 0.5245 (t0) REVERT: B 212 GLN cc_start: 0.8271 (pt0) cc_final: 0.8056 (mt0) REVERT: B 333 LYS cc_start: 0.8727 (tttt) cc_final: 0.8200 (ttpp) REVERT: C 87 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7804 (tpm-80) REVERT: C 95 LYS cc_start: 0.8724 (mttt) cc_final: 0.8497 (mttm) REVERT: C 180 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7823 (mtp180) REVERT: C 266 ASN cc_start: 0.9031 (t0) cc_final: 0.8718 (t0) REVERT: C 326 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8313 (mm) REVERT: C 333 LYS cc_start: 0.8700 (tttt) cc_final: 0.8258 (ttpp) outliers start: 15 outliers final: 7 residues processed: 207 average time/residue: 0.8003 time to fit residues: 171.6570 Evaluate side-chains 221 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 118 LEU 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 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: 0.9990 chunk 38 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 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 = 0.3596 r_free = 0.3596 target = 0.106855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090017 restraints weight = 12310.295| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.93 r_work: 0.3150 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7116 Z= 0.124 Angle : 0.559 8.676 9657 Z= 0.277 Chirality : 0.045 0.329 1098 Planarity : 0.003 0.042 1200 Dihedral : 4.281 19.947 912 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.90 % Allowed : 27.80 % 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: 2.09 (0.29), residues: 843 helix: 3.44 (0.27), residues: 309 sheet: 0.71 (0.28), residues: 306 loop : -0.61 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 110 TYR 0.007 0.001 TYR C 201 PHE 0.028 0.001 PHE C 72 TRP 0.007 0.001 TRP A 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 7104) covalent geometry : angle 0.52953 / 0.27 ( 9621) hydrogen bonds : bond 0.02999 / 2.07 ( 286) hydrogen bonds : angle 3.11195 / 2.29 ( 831) link_NAG-ASN : bond 0.00884 / 0.63 ( 12) link_NAG-ASN : angle 2.96408 / 2.38 ( 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: 21 poor density : 212 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7813 (tmmt) REVERT: A 92 PHE cc_start: 0.7757 (t80) cc_final: 0.7529 (t80) REVERT: A 153 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7850 (mtp85) REVERT: A 224 GLU cc_start: 0.7719 (tp30) cc_final: 0.7248 (tp30) REVERT: A 294 LYS cc_start: 0.8356 (tmmt) cc_final: 0.8088 (tmmt) REVERT: A 333 LYS cc_start: 0.8717 (tttt) cc_final: 0.8198 (ttpp) REVERT: B 333 LYS cc_start: 0.8726 (tttt) cc_final: 0.8175 (ttpp) REVERT: C 87 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7854 (tpm-80) REVERT: C 95 LYS cc_start: 0.8695 (mttt) cc_final: 0.8469 (mttm) REVERT: C 176 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8133 (mt-10) REVERT: C 180 ARG cc_start: 0.8301 (mtp180) cc_final: 0.7833 (mtp180) REVERT: C 266 ASN cc_start: 0.9002 (t0) cc_final: 0.8702 (t0) REVERT: C 326 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8267 (mm) REVERT: C 333 LYS cc_start: 0.8653 (tttt) cc_final: 0.8293 (ttpt) outliers start: 21 outliers final: 7 residues processed: 218 average time/residue: 0.7814 time to fit residues: 176.3941 Evaluate side-chains 217 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 124 GLN Chi-restraints excluded: chain B residue 118 LEU 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 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: 0.0670 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 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 = 0.3565 r_free = 0.3565 target = 0.102575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086595 restraints weight = 12583.757| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.77 r_work: 0.3130 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7116 Z= 0.167 Angle : 0.580 8.998 9657 Z= 0.288 Chirality : 0.046 0.344 1098 Planarity : 0.004 0.040 1200 Dihedral : 4.369 19.460 912 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.21 % Allowed : 29.32 % Favored : 68.46 % 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: 1.98 (0.29), residues: 843 helix: 3.30 (0.27), residues: 309 sheet: 0.69 (0.29), residues: 306 loop : -0.67 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 180 TYR 0.008 0.001 TYR B 74 PHE 0.037 0.002 PHE C 72 TRP 0.007 0.001 TRP A 230 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 7104) covalent geometry : angle 0.55151 / 0.28 ( 9621) hydrogen bonds : bond 0.03327 / 2.32 ( 286) hydrogen bonds : angle 3.17245 / 2.34 ( 831) link_NAG-ASN : bond 0.00935 / 0.66 ( 12) link_NAG-ASN : angle 3.01045 / 2.42 ( 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 242 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.284 Fit side-chains REVERT: A 63 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7821 (tmmt) REVERT: A 92 PHE cc_start: 0.7874 (t80) cc_final: 0.7666 (t80) REVERT: A 124 GLN cc_start: 0.8075 (mm110) cc_final: 0.7818 (mm110) REVERT: A 133 GLU cc_start: 0.7557 (tm-30) cc_final: 0.5150 (tm-30) REVERT: A 153 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7820 (mtp85) REVERT: A 180 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7683 (ttp-110) REVERT: A 224 GLU cc_start: 0.7753 (tp30) cc_final: 0.7315 (tp30) REVERT: A 294 LYS cc_start: 0.8305 (tmmt) cc_final: 0.8014 (tmmt) REVERT: A 333 LYS cc_start: 0.8757 (tttt) cc_final: 0.8289 (ttpp) REVERT: B 162 ASN cc_start: 0.5693 (OUTLIER) cc_final: 0.5219 (m-40) REVERT: B 333 LYS cc_start: 0.8765 (tttt) cc_final: 0.8279 (ttpp) REVERT: C 87 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7866 (tpm-80) REVERT: C 176 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 180 ARG cc_start: 0.8308 (mtp180) cc_final: 0.7852 (mtp180) REVERT: C 266 ASN cc_start: 0.9028 (t0) cc_final: 0.8768 (t0) REVERT: C 326 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8317 (mm) REVERT: C 333 LYS cc_start: 0.8737 (tttt) cc_final: 0.8365 (ttpp) outliers start: 16 outliers final: 7 residues processed: 230 average time/residue: 0.7986 time to fit residues: 189.9964 Evaluate side-chains 209 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 302 ASN 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 302 ASN 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: 0.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3570 r_free = 0.3570 target = 0.103694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088563 restraints weight = 12450.097| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.65 r_work: 0.3129 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3037 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= 0.172 Angle : 0.604 9.542 9657 Z= 0.297 Chirality : 0.046 0.339 1098 Planarity : 0.004 0.044 1200 Dihedral : 4.415 19.411 912 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.90 % Allowed : 28.77 % Favored : 68.33 % 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: 3.23 (0.27), residues: 309 sheet: 0.67 (0.29), residues: 306 loop : -0.69 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 110 TYR 0.008 0.001 TYR C 201 PHE 0.031 0.002 PHE C 72 TRP 0.011 0.001 TRP A 230 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 7104) covalent geometry : angle 0.57693 / 0.29 ( 9621) hydrogen bonds : bond 0.03400 / 2.38 ( 286) hydrogen bonds : angle 3.24313 / 2.38 ( 831) link_NAG-ASN : bond 0.00930 / 0.66 ( 12) link_NAG-ASN : angle 2.99216 / 2.39 ( 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 231 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7873 (tmmt) REVERT: A 124 GLN cc_start: 0.8062 (mm110) cc_final: 0.7777 (mm110) REVERT: A 153 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7859 (mtp85) REVERT: A 224 GLU cc_start: 0.7769 (tp30) cc_final: 0.7337 (tp30) REVERT: A 294 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8008 (tmmt) REVERT: A 329 LYS cc_start: 0.8583 (tttt) cc_final: 0.8376 (tttt) REVERT: A 333 LYS cc_start: 0.8836 (tttt) cc_final: 0.8399 (ttpp) REVERT: B 77 LEU cc_start: 0.8616 (mt) cc_final: 0.8412 (mm) REVERT: B 162 ASN cc_start: 0.5924 (OUTLIER) cc_final: 0.5623 (m110) REVERT: B 333 LYS cc_start: 0.8788 (tttt) cc_final: 0.8364 (ttpp) REVERT: C 87 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7818 (tpm-80) REVERT: C 95 LYS cc_start: 0.8654 (mttt) cc_final: 0.8441 (mttm) REVERT: C 176 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8117 (mt-10) REVERT: C 180 ARG cc_start: 0.8296 (mtp180) cc_final: 0.7821 (mtp180) REVERT: C 266 ASN cc_start: 0.9019 (t0) cc_final: 0.8775 (t0) REVERT: C 326 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8320 (mm) REVERT: C 333 LYS cc_start: 0.8800 (tttt) cc_final: 0.8408 (ttpp) outliers start: 21 outliers final: 9 residues processed: 219 average time/residue: 0.6767 time to fit residues: 153.6266 Evaluate side-chains 213 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 297 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 162 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: 0.5980 chunk 10 optimal weight: 0.0670 chunk 63 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.104862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089471 restraints weight = 12601.484| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.70 r_work: 0.3134 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7116 Z= 0.136 Angle : 0.590 9.953 9657 Z= 0.290 Chirality : 0.045 0.331 1098 Planarity : 0.004 0.054 1200 Dihedral : 4.354 19.781 912 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.94 % Allowed : 29.88 % 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: 1.95 (0.29), residues: 843 helix: 3.28 (0.27), residues: 309 sheet: 0.66 (0.29), residues: 306 loop : -0.65 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 110 TYR 0.007 0.001 TYR C 201 PHE 0.030 0.002 PHE C 72 TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7104) covalent geometry : angle 0.56331 / 0.28 ( 9621) hydrogen bonds : bond 0.03203 / 2.23 ( 286) hydrogen bonds : angle 3.21584 / 2.35 ( 831) link_NAG-ASN : bond 0.00890 / 0.63 ( 12) link_NAG-ASN : angle 2.93149 / 2.35 ( 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: 14 poor density : 213 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (tmmt) REVERT: A 124 GLN cc_start: 0.8072 (mm110) cc_final: 0.7778 (mm110) REVERT: A 153 ARG cc_start: 0.8220 (mtp85) cc_final: 0.7856 (mtp85) REVERT: A 224 GLU cc_start: 0.7760 (tp30) cc_final: 0.7320 (tp30) REVERT: A 294 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7945 (tmmt) REVERT: A 329 LYS cc_start: 0.8565 (tttt) cc_final: 0.8360 (tttt) REVERT: A 333 LYS cc_start: 0.8839 (tttt) cc_final: 0.8397 (ttpp) REVERT: B 77 LEU cc_start: 0.8621 (mt) cc_final: 0.8417 (mm) REVERT: B 162 ASN cc_start: 0.6025 (OUTLIER) cc_final: 0.5756 (m110) REVERT: B 188 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8292 (ppp80) REVERT: B 294 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8264 (tmmt) REVERT: B 333 LYS cc_start: 0.8786 (tttt) cc_final: 0.8356 (ttpp) REVERT: C 87 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7830 (tpm-80) REVERT: C 95 LYS cc_start: 0.8659 (mttt) cc_final: 0.8445 (mttm) REVERT: C 176 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8124 (mt-10) REVERT: C 180 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7846 (mtp180) REVERT: C 266 ASN cc_start: 0.9012 (t0) cc_final: 0.8753 (t0) REVERT: C 326 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8300 (mm) REVERT: C 333 LYS cc_start: 0.8800 (tttt) cc_final: 0.8392 (ttpp) outliers start: 14 outliers final: 7 residues processed: 216 average time/residue: 0.6623 time to fit residues: 148.2463 Evaluate side-chains 218 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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 162 ASN Chi-restraints excluded: chain B residue 188 ARG 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 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN B 143 GLN B 212 GLN B 293 GLN B 296 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 = 0.3566 r_free = 0.3566 target = 0.100644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084542 restraints weight = 12407.535| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.71 r_work: 0.3136 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7116 Z= 0.144 Angle : 0.612 9.503 9657 Z= 0.299 Chirality : 0.045 0.328 1098 Planarity : 0.004 0.048 1200 Dihedral : 4.353 20.509 912 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.80 % Allowed : 30.29 % 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: 1.90 (0.29), residues: 843 helix: 3.22 (0.27), residues: 309 sheet: 0.72 (0.29), residues: 312 loop : -0.84 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 110 TYR 0.007 0.001 TYR C 201 PHE 0.029 0.002 PHE C 72 TRP 0.008 0.001 TRP A 230 HIS 0.003 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7104) covalent geometry : angle 0.58660 / 0.29 ( 9621) hydrogen bonds : bond 0.03252 / 2.28 ( 286) hydrogen bonds : angle 3.22518 / 2.35 ( 831) link_NAG-ASN : bond 0.00896 / 0.64 ( 12) link_NAG-ASN : angle 2.91768 / 2.33 ( 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 225 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.216 Fit side-chains REVERT: A 63 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7904 (tmmt) REVERT: A 124 GLN cc_start: 0.8088 (mm110) cc_final: 0.7796 (mm110) REVERT: A 180 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7444 (ttp-170) REVERT: A 208 GLN cc_start: 0.8606 (tp40) cc_final: 0.8390 (mm-40) REVERT: A 224 GLU cc_start: 0.7776 (tp30) cc_final: 0.7333 (tp30) REVERT: A 294 LYS cc_start: 0.8403 (tmmt) cc_final: 0.8116 (tmmt) REVERT: A 331 MET cc_start: 0.7389 (tmm) cc_final: 0.7029 (tmm) REVERT: A 333 LYS cc_start: 0.8846 (tttt) cc_final: 0.8404 (ttpp) REVERT: B 162 ASN cc_start: 0.6079 (OUTLIER) cc_final: 0.5774 (m-40) REVERT: B 188 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8290 (ppp80) REVERT: B 294 LYS cc_start: 0.8549 (tmmt) cc_final: 0.8270 (tmmt) REVERT: B 333 LYS cc_start: 0.8793 (tttt) cc_final: 0.8343 (ttpp) REVERT: C 87 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7859 (tpm-80) REVERT: C 95 LYS cc_start: 0.8651 (mttt) cc_final: 0.8437 (mttm) REVERT: C 176 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8169 (mt-10) REVERT: C 266 ASN cc_start: 0.9022 (t0) cc_final: 0.8752 (t0) REVERT: C 326 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8304 (mm) REVERT: C 333 LYS cc_start: 0.8777 (tttt) cc_final: 0.8365 (ttpp) outliers start: 13 outliers final: 6 residues processed: 214 average time/residue: 0.7080 time to fit residues: 156.7233 Evaluate side-chains 211 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.0000 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086282 restraints weight = 12488.538| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.77 r_work: 0.3129 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3282 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= 0.156 Angle : 0.636 11.970 9657 Z= 0.308 Chirality : 0.046 0.331 1098 Planarity : 0.004 0.048 1200 Dihedral : 4.383 20.670 912 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 30.98 % Favored : 67.22 % 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: 1.81 (0.29), residues: 843 helix: 3.10 (0.26), residues: 309 sheet: 0.71 (0.29), residues: 312 loop : -0.87 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 259 TYR 0.008 0.001 TYR C 201 PHE 0.032 0.002 PHE C 72 TRP 0.008 0.001 TRP A 304 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 7104) covalent geometry : angle 0.61089 / 0.30 ( 9621) hydrogen bonds : bond 0.03336 / 2.32 ( 286) hydrogen bonds : angle 3.32516 / 2.41 ( 831) link_NAG-ASN : bond 0.00903 / 0.64 ( 12) link_NAG-ASN : angle 2.93392 / 2.34 ( 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 223 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7920 (tmmt) REVERT: A 124 GLN cc_start: 0.8101 (mm110) cc_final: 0.7825 (mm110) REVERT: A 224 GLU cc_start: 0.7811 (tp30) cc_final: 0.7343 (tp30) REVERT: A 294 LYS cc_start: 0.8392 (tmmt) cc_final: 0.8052 (tmmt) REVERT: A 331 MET cc_start: 0.7424 (tmm) cc_final: 0.7095 (tmm) REVERT: A 333 LYS cc_start: 0.8880 (tttt) cc_final: 0.8467 (ttpp) REVERT: B 162 ASN cc_start: 0.6148 (OUTLIER) cc_final: 0.5820 (m-40) REVERT: B 188 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8292 (ppp80) REVERT: B 294 LYS cc_start: 0.8561 (tmmt) cc_final: 0.8275 (tmmt) REVERT: B 333 LYS cc_start: 0.8815 (tttt) cc_final: 0.8349 (ttpp) REVERT: C 87 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7905 (tpm-80) REVERT: C 95 LYS cc_start: 0.8668 (mttt) cc_final: 0.8428 (mttm) REVERT: C 133 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7165 (tm-30) REVERT: C 176 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 188 ARG cc_start: 0.8446 (ttt90) cc_final: 0.8153 (ttm170) REVERT: C 266 ASN cc_start: 0.9031 (t0) cc_final: 0.8779 (t0) REVERT: C 275 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8125 (mtpp) REVERT: C 326 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8363 (mm) REVERT: C 333 LYS cc_start: 0.8797 (tttt) cc_final: 0.8393 (ttpp) outliers start: 13 outliers final: 7 residues processed: 213 average time/residue: 0.7406 time to fit residues: 163.3894 Evaluate side-chains 218 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 188 ARG 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 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN B 212 GLN B 293 GLN B 296 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 = 0.3560 r_free = 0.3560 target = 0.101531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.085417 restraints weight = 12266.582| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.74 r_work: 0.3122 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7116 Z= 0.171 Angle : 0.638 10.909 9657 Z= 0.313 Chirality : 0.046 0.339 1098 Planarity : 0.004 0.048 1200 Dihedral : 4.439 20.816 912 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.94 % Allowed : 30.84 % Favored : 67.22 % 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: 1.81 (0.29), residues: 843 helix: 3.12 (0.27), residues: 309 sheet: 0.71 (0.29), residues: 312 loop : -0.91 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 259 TYR 0.008 0.001 TYR B 74 PHE 0.031 0.002 PHE C 72 TRP 0.009 0.001 TRP A 304 HIS 0.002 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 7104) covalent geometry : angle 0.61245 / 0.31 ( 9621) hydrogen bonds : bond 0.03440 / 2.39 ( 286) hydrogen bonds : angle 3.28760 / 2.41 ( 831) link_NAG-ASN : bond 0.00919 / 0.65 ( 12) link_NAG-ASN : angle 2.97653 / 2.37 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3543.25 seconds wall clock time: 61 minutes 4.50 seconds (3664.50 seconds total)