Starting phenix.real_space_refine on Fri Jul 25 03:49:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqh_25385/07_2025/7sqh_25385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqh_25385/07_2025/7sqh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2025/7sqh_25385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2025/7sqh_25385.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2025/7sqh_25385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqh_25385/07_2025/7sqh_25385.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} 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: 5.11, per 1000 atoms: 0.73 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: 1.63 Conformation dependent library (CDL) restraints added in 936.3 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: 0.61 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: 1.71 Time building geometry restraints manager: 1.97 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.940 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.320 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (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 TRP 0.007 0.001 TRP B 330 HIS 0.003 0.001 HIS B 130 PHE 0.014 0.001 PHE C 204 TYR 0.022 0.001 TYR A 132 ARG 0.003 0.000 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 12) link_NAG-ASN : angle 3.05765 ( 36) hydrogen bonds : bond 0.08196 ( 286) hydrogen bonds : angle 3.59231 ( 831) covalent geometry : bond 0.00556 ( 7104) covalent geometry : angle 0.73997 ( 9621) *********************** 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 : 0.818 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7058 (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: 0.8229 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 1.7357 time to fit residues: 459.4504 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 : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.105518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089976 restraints weight = 12405.776| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.71 r_work: 0.3146 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7116 Z= 0.199 Angle : 0.642 9.419 9657 Z= 0.311 Chirality : 0.048 0.347 1098 Planarity : 0.004 0.045 1200 Dihedral : 12.562 69.184 1164 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.63 % Allowed : 25.86 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.29), residues: 843 helix: 3.27 (0.27), residues: 312 sheet: 0.65 (0.27), residues: 306 loop : -0.60 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.003 0.001 HIS B 98 PHE 0.024 0.002 PHE C 92 TYR 0.008 0.001 TYR C 227 ARG 0.012 0.001 ARG B 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00981 ( 12) link_NAG-ASN : angle 3.16032 ( 36) hydrogen bonds : bond 0.03326 ( 286) hydrogen bonds : angle 3.13918 ( 831) covalent geometry : bond 0.00475 ( 7104) covalent geometry : angle 0.61389 ( 9621) *********************** 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 213 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7754 (t80) cc_final: 0.7547 (t80) REVERT: A 95 LYS cc_start: 0.8690 (mttt) cc_final: 0.8417 (mttp) REVERT: A 153 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7796 (mtp85) REVERT: A 156 TYR cc_start: 0.8483 (p90) cc_final: 0.8086 (p90) REVERT: A 180 ARG cc_start: 0.8420 (mtp180) cc_final: 0.8196 (mtp180) REVERT: A 224 GLU cc_start: 0.7772 (tp30) cc_final: 0.7388 (tp30) REVERT: A 275 LYS cc_start: 0.8265 (ttmm) cc_final: 0.8053 (mtpp) REVERT: A 294 LYS cc_start: 0.8346 (tmmt) cc_final: 0.8009 (tmmt) REVERT: B 77 LEU cc_start: 0.8532 (mm) cc_final: 0.8317 (mm) REVERT: B 224 GLU cc_start: 0.7770 (tp30) cc_final: 0.7525 (tp30) REVERT: B 275 LYS cc_start: 0.8316 (mttm) cc_final: 0.8101 (mttm) REVERT: C 72 PHE cc_start: 0.7874 (m-10) cc_final: 0.7672 (m-80) REVERT: C 95 LYS cc_start: 0.8715 (mttt) cc_final: 0.8505 (mtmm) REVERT: C 147 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8046 (tpp) REVERT: C 266 ASN cc_start: 0.9031 (t0) cc_final: 0.8684 (t0) REVERT: C 326 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8252 (mm) REVERT: C 333 LYS cc_start: 0.8595 (tttt) cc_final: 0.8185 (ttpt) outliers start: 19 outliers final: 6 residues processed: 201 average time/residue: 1.6526 time to fit residues: 344.1466 Evaluate side-chains 205 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU 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 C residue 96 LEU Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 157 THR 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 48 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.103665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088051 restraints weight = 12447.135| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.68 r_work: 0.3124 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7116 Z= 0.220 Angle : 0.628 9.079 9657 Z= 0.305 Chirality : 0.048 0.343 1098 Planarity : 0.004 0.037 1200 Dihedral : 8.231 57.012 1164 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.90 % Allowed : 26.97 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 843 helix: 3.07 (0.28), residues: 315 sheet: 0.57 (0.28), residues: 312 loop : -0.63 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 230 HIS 0.003 0.001 HIS C 98 PHE 0.028 0.002 PHE B 72 TYR 0.008 0.001 TYR C 201 ARG 0.013 0.001 ARG C 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00977 ( 12) link_NAG-ASN : angle 3.02996 ( 36) hydrogen bonds : bond 0.03690 ( 286) hydrogen bonds : angle 3.24929 ( 831) covalent geometry : bond 0.00530 ( 7104) covalent geometry : angle 0.60092 ( 9621) *********************** 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 225 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8072 (tptp) cc_final: 0.7788 (tmmt) REVERT: A 92 PHE cc_start: 0.7908 (t80) cc_final: 0.7690 (t80) REVERT: A 153 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7804 (mtp85) REVERT: A 180 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8158 (mtp180) REVERT: A 224 GLU cc_start: 0.7826 (tp30) cc_final: 0.7318 (tp30) REVERT: A 294 LYS cc_start: 0.8387 (tmmt) cc_final: 0.8016 (tmmt) REVERT: A 333 LYS cc_start: 0.8717 (tttt) cc_final: 0.8266 (ttpp) REVERT: B 77 LEU cc_start: 0.8607 (mm) cc_final: 0.8370 (mm) REVERT: B 91 ASP cc_start: 0.8568 (m-30) cc_final: 0.8364 (m-30) REVERT: B 147 MET cc_start: 0.8608 (tpt) cc_final: 0.8393 (tpp) REVERT: B 212 GLN cc_start: 0.8282 (pt0) cc_final: 0.8054 (mt0) REVERT: B 224 GLU cc_start: 0.7903 (tp30) cc_final: 0.7652 (tp30) REVERT: B 275 LYS cc_start: 0.8311 (mttm) cc_final: 0.8097 (mttm) REVERT: B 333 LYS cc_start: 0.8769 (tttt) cc_final: 0.8287 (ttpp) REVERT: C 87 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (tpm-80) REVERT: C 95 LYS cc_start: 0.8740 (mttt) cc_final: 0.8511 (mttm) REVERT: C 133 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7192 (tm-30) REVERT: C 180 ARG cc_start: 0.8277 (mtp180) cc_final: 0.7844 (mtp180) REVERT: C 275 LYS cc_start: 0.8363 (mtpp) cc_final: 0.8162 (mtpp) REVERT: C 326 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8316 (mm) REVERT: C 333 LYS cc_start: 0.8720 (tttt) cc_final: 0.8395 (ttpt) outliers start: 21 outliers final: 6 residues processed: 215 average time/residue: 1.7309 time to fit residues: 385.3014 Evaluate side-chains 205 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 129 LYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 293 GLN C 143 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 = 0.3562 r_free = 0.3562 target = 0.104521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089038 restraints weight = 12523.514| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.77 r_work: 0.3111 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7116 Z= 0.221 Angle : 0.625 9.018 9657 Z= 0.305 Chirality : 0.047 0.340 1098 Planarity : 0.004 0.045 1200 Dihedral : 6.761 56.320 1164 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.32 % Allowed : 26.69 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 843 helix: 3.08 (0.27), residues: 312 sheet: 0.60 (0.29), residues: 312 loop : -0.67 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 HIS 0.003 0.001 HIS A 98 PHE 0.026 0.002 PHE C 72 TYR 0.009 0.001 TYR C 201 ARG 0.004 0.000 ARG C 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00973 ( 12) link_NAG-ASN : angle 3.07377 ( 36) hydrogen bonds : bond 0.03613 ( 286) hydrogen bonds : angle 3.29923 ( 831) covalent geometry : bond 0.00530 ( 7104) covalent geometry : angle 0.59690 ( 9621) *********************** 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 235 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.849 Fit side-chains REVERT: A 63 LYS cc_start: 0.8157 (tptp) cc_final: 0.7874 (tmmt) REVERT: A 122 GLN cc_start: 0.9081 (mm110) cc_final: 0.8837 (mm110) REVERT: A 124 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7833 (mm110) REVERT: A 153 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7866 (mtp85) REVERT: A 180 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8188 (mtp180) REVERT: A 224 GLU cc_start: 0.7831 (tp30) cc_final: 0.7313 (tp30) REVERT: A 294 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8020 (tmmt) REVERT: A 329 LYS cc_start: 0.8605 (tttt) cc_final: 0.8350 (tttt) REVERT: A 333 LYS cc_start: 0.8806 (tttt) cc_final: 0.8348 (ttpp) REVERT: B 147 MET cc_start: 0.8677 (tpt) cc_final: 0.8443 (tpp) REVERT: B 212 GLN cc_start: 0.8280 (pt0) cc_final: 0.8069 (mt0) REVERT: B 224 GLU cc_start: 0.7975 (tp30) cc_final: 0.7689 (tp30) REVERT: B 227 TYR cc_start: 0.8685 (m-80) cc_final: 0.8452 (m-80) REVERT: B 333 LYS cc_start: 0.8791 (tttt) cc_final: 0.8275 (ttpp) REVERT: C 87 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7875 (tpm-80) REVERT: C 95 LYS cc_start: 0.8735 (mttt) cc_final: 0.8519 (mttm) REVERT: C 133 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7363 (tm-30) REVERT: C 180 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7831 (mtp180) REVERT: C 326 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (mm) REVERT: C 333 LYS cc_start: 0.8780 (tttt) cc_final: 0.8297 (ttpp) outliers start: 24 outliers final: 11 residues processed: 219 average time/residue: 1.6963 time to fit residues: 384.7647 Evaluate side-chains 220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 GLN 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 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 293 GLN B 293 GLN C 130 HIS C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084447 restraints weight = 12414.030| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.69 r_work: 0.3142 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7116 Z= 0.143 Angle : 0.619 12.493 9657 Z= 0.295 Chirality : 0.046 0.324 1098 Planarity : 0.004 0.038 1200 Dihedral : 6.721 55.126 1164 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.46 % Allowed : 27.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.30), residues: 843 helix: 3.24 (0.27), residues: 312 sheet: 0.57 (0.29), residues: 312 loop : -0.56 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 230 HIS 0.003 0.001 HIS C 130 PHE 0.034 0.001 PHE C 72 TYR 0.007 0.001 TYR C 201 ARG 0.009 0.000 ARG C 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00934 ( 12) link_NAG-ASN : angle 3.17469 ( 36) hydrogen bonds : bond 0.03243 ( 286) hydrogen bonds : angle 3.24334 ( 831) covalent geometry : bond 0.00324 ( 7104) covalent geometry : angle 0.58869 ( 9621) *********************** 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 235 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.850 Fit side-chains REVERT: A 63 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7869 (tmmt) REVERT: A 122 GLN cc_start: 0.9058 (mm110) cc_final: 0.8819 (mm110) REVERT: A 124 GLN cc_start: 0.8122 (mm110) cc_final: 0.7849 (mm110) REVERT: A 170 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8557 (mm) REVERT: A 224 GLU cc_start: 0.7801 (tp30) cc_final: 0.7326 (tp30) REVERT: A 294 LYS cc_start: 0.8411 (tmmt) cc_final: 0.8031 (tmmt) REVERT: A 333 LYS cc_start: 0.8786 (tttt) cc_final: 0.8331 (ttpp) REVERT: B 224 GLU cc_start: 0.7933 (tp30) cc_final: 0.7694 (tp30) REVERT: B 227 TYR cc_start: 0.8645 (m-80) cc_final: 0.8405 (m-80) REVERT: B 294 LYS cc_start: 0.8357 (tmmt) cc_final: 0.8143 (tmmt) REVERT: B 326 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 333 LYS cc_start: 0.8785 (tttt) cc_final: 0.8287 (ttpp) REVERT: C 87 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7838 (tpm-80) REVERT: C 95 LYS cc_start: 0.8632 (mttt) cc_final: 0.8423 (mttm) REVERT: C 133 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7355 (tm-30) REVERT: C 180 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7821 (mtp180) REVERT: C 326 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (mm) REVERT: C 333 LYS cc_start: 0.8788 (tttt) cc_final: 0.8317 (ttpp) outliers start: 25 outliers final: 12 residues processed: 220 average time/residue: 1.7302 time to fit residues: 394.5949 Evaluate side-chains 221 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 170 ILE 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 118 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 326 LEU 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 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 59 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 296 GLN C 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.099761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083972 restraints weight = 12467.637| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.69 r_work: 0.3127 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7116 Z= 0.179 Angle : 0.616 8.860 9657 Z= 0.297 Chirality : 0.048 0.448 1098 Planarity : 0.004 0.043 1200 Dihedral : 6.113 52.298 1164 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.46 % Allowed : 27.80 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 843 helix: 3.10 (0.27), residues: 312 sheet: 0.55 (0.29), residues: 312 loop : -0.61 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 HIS 0.002 0.001 HIS A 130 PHE 0.031 0.002 PHE C 72 TYR 0.008 0.001 TYR C 201 ARG 0.009 0.001 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.01033 ( 12) link_NAG-ASN : angle 3.41971 ( 36) hydrogen bonds : bond 0.03494 ( 286) hydrogen bonds : angle 3.27854 ( 831) covalent geometry : bond 0.00425 ( 7104) covalent geometry : angle 0.58094 ( 9621) *********************** 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 235 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.806 Fit side-chains REVERT: A 63 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7899 (tmmt) REVERT: A 122 GLN cc_start: 0.9070 (mm110) cc_final: 0.8811 (mm110) REVERT: A 124 GLN cc_start: 0.8133 (mm110) cc_final: 0.7837 (mm110) REVERT: A 133 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6596 (tm-30) REVERT: A 170 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8555 (mm) REVERT: A 180 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7541 (ttp-170) REVERT: A 224 GLU cc_start: 0.7845 (tp30) cc_final: 0.7367 (tp30) REVERT: A 294 LYS cc_start: 0.8451 (tmmt) cc_final: 0.7996 (tmmt) REVERT: A 329 LYS cc_start: 0.8554 (tttt) cc_final: 0.8342 (tttt) REVERT: A 333 LYS cc_start: 0.8830 (tttt) cc_final: 0.8389 (ttpp) REVERT: B 224 GLU cc_start: 0.7965 (tp30) cc_final: 0.7697 (tp30) REVERT: B 227 TYR cc_start: 0.8661 (m-80) cc_final: 0.8376 (m-80) REVERT: B 333 LYS cc_start: 0.8800 (tttt) cc_final: 0.8356 (ttpp) REVERT: C 87 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7832 (tpm-80) REVERT: C 95 LYS cc_start: 0.8643 (mttt) cc_final: 0.8438 (mttm) REVERT: C 180 ARG cc_start: 0.8281 (mtp180) cc_final: 0.7825 (mtp180) REVERT: C 188 ARG cc_start: 0.8520 (ttt90) cc_final: 0.8246 (ttt90) REVERT: C 326 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8358 (mm) REVERT: C 333 LYS cc_start: 0.8789 (tttt) cc_final: 0.8374 (ttpp) outliers start: 25 outliers final: 11 residues processed: 219 average time/residue: 1.7696 time to fit residues: 400.9773 Evaluate side-chains 221 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 170 ILE 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 118 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR 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 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 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3562 r_free = 0.3562 target = 0.100757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.085035 restraints weight = 12286.295| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.69 r_work: 0.3124 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7116 Z= 0.154 Angle : 0.607 9.590 9657 Z= 0.294 Chirality : 0.046 0.315 1098 Planarity : 0.004 0.044 1200 Dihedral : 5.664 47.547 1164 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.90 % Allowed : 29.32 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.29), residues: 843 helix: 3.14 (0.27), residues: 312 sheet: 0.63 (0.29), residues: 306 loop : -0.68 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 230 HIS 0.002 0.001 HIS A 98 PHE 0.026 0.002 PHE C 72 TYR 0.008 0.001 TYR C 201 ARG 0.010 0.001 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00906 ( 12) link_NAG-ASN : angle 3.15844 ( 36) hydrogen bonds : bond 0.03321 ( 286) hydrogen bonds : angle 3.26043 ( 831) covalent geometry : bond 0.00366 ( 7104) covalent geometry : angle 0.57629 ( 9621) *********************** 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 : 0.804 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7945 (tmmt) REVERT: A 122 GLN cc_start: 0.9070 (mm110) cc_final: 0.8799 (mm110) REVERT: A 124 GLN cc_start: 0.8110 (mm110) cc_final: 0.7819 (mm110) REVERT: A 170 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8553 (mm) REVERT: A 224 GLU cc_start: 0.7847 (tp30) cc_final: 0.7383 (tp30) REVERT: A 294 LYS cc_start: 0.8378 (tmmt) cc_final: 0.7960 (tmmt) REVERT: A 329 LYS cc_start: 0.8565 (tttt) cc_final: 0.8355 (tttt) REVERT: A 333 LYS cc_start: 0.8861 (tttt) cc_final: 0.8407 (ttpp) REVERT: B 188 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8319 (ppp80) REVERT: B 224 GLU cc_start: 0.8007 (tp30) cc_final: 0.7762 (tp30) REVERT: B 227 TYR cc_start: 0.8616 (m-80) cc_final: 0.8388 (m-80) REVERT: B 294 LYS cc_start: 0.8348 (tmmt) cc_final: 0.8132 (tmmt) REVERT: B 333 LYS cc_start: 0.8818 (tttt) cc_final: 0.8366 (ttpp) REVERT: C 87 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7838 (tpm-80) REVERT: C 95 LYS cc_start: 0.8676 (mttt) cc_final: 0.8465 (mttm) REVERT: C 180 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7836 (mtp180) REVERT: C 188 ARG cc_start: 0.8523 (ttt90) cc_final: 0.8219 (ttt90) REVERT: C 275 LYS cc_start: 0.8367 (mtpp) cc_final: 0.8163 (mtpp) REVERT: C 326 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (mm) REVERT: C 333 LYS cc_start: 0.8807 (tttt) cc_final: 0.8381 (ttpp) outliers start: 21 outliers final: 12 residues processed: 216 average time/residue: 1.7370 time to fit residues: 388.2257 Evaluate side-chains 215 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 96 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 118 LEU 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 306 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 293 GLN A 296 GLN C 143 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 = 0.3551 r_free = 0.3551 target = 0.099289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083725 restraints weight = 12379.860| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.65 r_work: 0.3124 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3288 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= 0.165 Angle : 0.619 10.242 9657 Z= 0.298 Chirality : 0.047 0.322 1098 Planarity : 0.004 0.054 1200 Dihedral : 5.413 42.919 1164 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.49 % Allowed : 29.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.29), residues: 843 helix: 3.05 (0.27), residues: 312 sheet: 0.68 (0.29), residues: 312 loop : -0.88 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.002 0.001 HIS B 98 PHE 0.027 0.002 PHE B 72 TYR 0.009 0.001 TYR B 74 ARG 0.011 0.001 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 12) link_NAG-ASN : angle 3.07357 ( 36) hydrogen bonds : bond 0.03382 ( 286) hydrogen bonds : angle 3.31746 ( 831) covalent geometry : bond 0.00393 ( 7104) covalent geometry : angle 0.59093 ( 9621) *********************** 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 224 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7963 (tmmt) REVERT: A 122 GLN cc_start: 0.9079 (mm110) cc_final: 0.8796 (mm110) REVERT: A 124 GLN cc_start: 0.8127 (mm110) cc_final: 0.7841 (mm110) REVERT: A 170 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 224 GLU cc_start: 0.7882 (tp30) cc_final: 0.7403 (tp30) REVERT: A 294 LYS cc_start: 0.8435 (tmmt) cc_final: 0.7957 (tmmt) REVERT: A 329 LYS cc_start: 0.8554 (tttt) cc_final: 0.8351 (tttt) REVERT: A 331 MET cc_start: 0.7416 (tmm) cc_final: 0.7056 (tmm) REVERT: A 333 LYS cc_start: 0.8875 (tttt) cc_final: 0.8466 (ttpp) REVERT: B 156 TYR cc_start: 0.8662 (p90) cc_final: 0.8444 (p90) REVERT: B 188 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8318 (ppp80) REVERT: B 224 GLU cc_start: 0.8029 (tp30) cc_final: 0.7804 (tp30) REVERT: B 227 TYR cc_start: 0.8634 (m-80) cc_final: 0.8384 (m-80) REVERT: B 294 LYS cc_start: 0.8377 (tmmt) cc_final: 0.8160 (tmmt) REVERT: B 333 LYS cc_start: 0.8816 (tttt) cc_final: 0.8373 (ttpp) REVERT: C 87 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7840 (tpm-80) REVERT: C 95 LYS cc_start: 0.8679 (mttt) cc_final: 0.8472 (mttm) REVERT: C 176 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 180 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7834 (mtp180) REVERT: C 188 ARG cc_start: 0.8517 (ttt90) cc_final: 0.8208 (ttt90) REVERT: C 275 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8156 (mtpp) REVERT: C 326 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8357 (mm) REVERT: C 333 LYS cc_start: 0.8808 (tttt) cc_final: 0.8416 (ttpp) outliers start: 18 outliers final: 8 residues processed: 213 average time/residue: 1.6888 time to fit residues: 372.4259 Evaluate side-chains 212 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 118 LEU 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 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 34 optimal weight: 0.0980 chunk 56 optimal weight: 6.9990 chunk 57 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 212 GLN C 143 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 = 0.3553 r_free = 0.3553 target = 0.099508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.083820 restraints weight = 12549.977| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.68 r_work: 0.3122 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7116 Z= 0.154 Angle : 0.615 8.864 9657 Z= 0.298 Chirality : 0.046 0.320 1098 Planarity : 0.004 0.049 1200 Dihedral : 4.909 31.204 1164 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.63 % Allowed : 29.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.29), residues: 843 helix: 3.08 (0.27), residues: 312 sheet: 0.68 (0.29), residues: 312 loop : -0.90 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 304 HIS 0.002 0.001 HIS B 98 PHE 0.026 0.002 PHE B 92 TYR 0.008 0.001 TYR B 74 ARG 0.010 0.001 ARG A 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 12) link_NAG-ASN : angle 2.98768 ( 36) hydrogen bonds : bond 0.03319 ( 286) hydrogen bonds : angle 3.28740 ( 831) covalent geometry : bond 0.00366 ( 7104) covalent geometry : angle 0.58872 ( 9621) *********************** 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 227 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7984 (tmmt) REVERT: A 122 GLN cc_start: 0.9086 (mm110) cc_final: 0.8835 (mm110) REVERT: A 124 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 153 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7907 (mtp85) REVERT: A 170 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 224 GLU cc_start: 0.7895 (tp30) cc_final: 0.7409 (tp30) REVERT: A 294 LYS cc_start: 0.8438 (tmmt) cc_final: 0.8028 (tmmt) REVERT: A 329 LYS cc_start: 0.8572 (tttt) cc_final: 0.8364 (tttt) REVERT: A 331 MET cc_start: 0.7444 (tmm) cc_final: 0.7109 (tmm) REVERT: A 333 LYS cc_start: 0.8866 (tttt) cc_final: 0.8459 (ttpp) REVERT: B 156 TYR cc_start: 0.8662 (p90) cc_final: 0.8415 (p90) REVERT: B 188 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8305 (ppp80) REVERT: B 224 GLU cc_start: 0.8040 (tp30) cc_final: 0.7826 (tp30) REVERT: B 294 LYS cc_start: 0.8413 (tmmt) cc_final: 0.8201 (tmmt) REVERT: B 333 LYS cc_start: 0.8849 (tttt) cc_final: 0.8406 (ttpp) REVERT: C 87 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7797 (tpm-80) REVERT: C 95 LYS cc_start: 0.8693 (mttt) cc_final: 0.8480 (mttm) REVERT: C 176 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 180 ARG cc_start: 0.8283 (mtp180) cc_final: 0.7841 (mtp180) REVERT: C 188 ARG cc_start: 0.8517 (ttt90) cc_final: 0.8250 (ttt90) REVERT: C 326 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8368 (mm) REVERT: C 329 LYS cc_start: 0.8466 (tttt) cc_final: 0.7976 (ttpp) REVERT: C 333 LYS cc_start: 0.8827 (tttt) cc_final: 0.8432 (ttpp) outliers start: 19 outliers final: 11 residues processed: 213 average time/residue: 1.6347 time to fit residues: 360.9453 Evaluate side-chains 221 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain A residue 170 ILE 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 118 LEU 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 306 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 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 79 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 296 GLN B 143 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 = 0.3558 r_free = 0.3558 target = 0.100812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.085101 restraints weight = 12547.813| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.72 r_work: 0.3121 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3409 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= 0.151 Angle : 0.623 11.645 9657 Z= 0.301 Chirality : 0.046 0.322 1098 Planarity : 0.004 0.046 1200 Dihedral : 4.656 23.030 1164 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.35 % Allowed : 30.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 843 helix: 3.05 (0.27), residues: 312 sheet: 0.68 (0.29), residues: 312 loop : -0.90 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.002 0.001 HIS B 98 PHE 0.030 0.002 PHE C 92 TYR 0.008 0.001 TYR C 201 ARG 0.012 0.001 ARG C 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00916 ( 12) link_NAG-ASN : angle 2.96400 ( 36) hydrogen bonds : bond 0.03320 ( 286) hydrogen bonds : angle 3.29969 ( 831) covalent geometry : bond 0.00358 ( 7104) covalent geometry : angle 0.59770 ( 9621) ********************** 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 228 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8001 (tmmt) REVERT: A 122 GLN cc_start: 0.9098 (mm110) cc_final: 0.8860 (mm110) REVERT: A 124 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7805 (mm-40) REVERT: A 153 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7899 (mtp85) REVERT: A 170 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 224 GLU cc_start: 0.7907 (tp30) cc_final: 0.7404 (tp30) REVERT: A 294 LYS cc_start: 0.8456 (tmmt) cc_final: 0.8015 (tmmt) REVERT: A 331 MET cc_start: 0.7459 (tmm) cc_final: 0.7118 (tmm) REVERT: A 333 LYS cc_start: 0.8888 (tttt) cc_final: 0.8489 (ttpp) REVERT: B 156 TYR cc_start: 0.8663 (p90) cc_final: 0.8419 (p90) REVERT: B 188 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8284 (ppp80) REVERT: B 224 GLU cc_start: 0.8056 (tp30) cc_final: 0.7843 (tp30) REVERT: B 333 LYS cc_start: 0.8861 (tttt) cc_final: 0.8408 (ttpp) REVERT: C 87 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7805 (tpm-80) REVERT: C 95 LYS cc_start: 0.8696 (mttt) cc_final: 0.8483 (mttm) REVERT: C 180 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7850 (mtp180) REVERT: C 188 ARG cc_start: 0.8521 (ttt90) cc_final: 0.8231 (ttt90) REVERT: C 275 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8177 (mtpp) REVERT: C 326 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8418 (mm) REVERT: C 333 LYS cc_start: 0.8853 (tttt) cc_final: 0.8458 (ttpp) outliers start: 17 outliers final: 9 residues processed: 217 average time/residue: 2.0921 time to fit residues: 470.3779 Evaluate side-chains 210 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 118 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 212 GLN B 293 GLN ** B 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 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 = 0.3558 r_free = 0.3558 target = 0.100003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084342 restraints weight = 12384.108| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.67 r_work: 0.3132 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7116 Z= 0.139 Angle : 0.624 11.034 9657 Z= 0.303 Chirality : 0.046 0.320 1098 Planarity : 0.004 0.044 1200 Dihedral : 4.472 21.463 1164 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 30.71 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.29), residues: 843 helix: 3.08 (0.27), residues: 312 sheet: 0.63 (0.29), residues: 312 loop : -0.88 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.002 0.001 HIS B 98 PHE 0.031 0.001 PHE B 72 TYR 0.007 0.001 TYR C 201 ARG 0.010 0.001 ARG C 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00905 ( 12) link_NAG-ASN : angle 2.90712 ( 36) hydrogen bonds : bond 0.03257 ( 286) hydrogen bonds : angle 3.28038 ( 831) covalent geometry : bond 0.00326 ( 7104) covalent geometry : angle 0.59928 ( 9621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9307.05 seconds wall clock time: 161 minutes 45.59 seconds (9705.59 seconds total)