Starting phenix.real_space_refine on Fri Dec 27 23:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqh_25385/12_2024/7sqh_25385.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqh_25385/12_2024/7sqh_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_25385/12_2024/7sqh_25385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqh_25385/12_2024/7sqh_25385.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqh_25385/12_2024/7sqh_25385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqh_25385/12_2024/7sqh_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-5532/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: 5.18, per 1000 atoms: 0.74 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: 1.78 Conformation dependent library (CDL) restraints added in 942.0 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: 0.63 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: 1.78 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1086 1.27 - 1.41: 1809 1.41 - 1.54: 4098 1.54 - 1.67: 60 1.67 - 1.81: 51 Bond restraints: 7104 Sorted by residual: bond pdb=" C GLN C 152 " pdb=" O GLN C 152 " ideal model delta sigma weight residual 1.234 1.138 0.096 1.26e-02 6.30e+03 5.86e+01 bond pdb=" C ARG C 180 " pdb=" O ARG C 180 " ideal model delta sigma weight residual 1.235 1.146 0.090 1.26e-02 6.30e+03 5.07e+01 bond pdb=" C GLN B 152 " pdb=" O GLN B 152 " ideal model delta sigma weight residual 1.234 1.153 0.081 1.22e-02 6.72e+03 4.37e+01 bond pdb=" C TYR B 132 " pdb=" O TYR B 132 " ideal model delta sigma weight residual 1.235 1.163 0.072 1.14e-02 7.69e+03 3.95e+01 bond pdb=" C GLN A 152 " pdb=" O GLN A 152 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.26e-02 6.30e+03 3.83e+01 ... (remaining 7099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 9094 1.46 - 2.93: 438 2.93 - 4.39: 58 4.39 - 5.85: 17 5.85 - 7.32: 14 Bond angle restraints: 9621 Sorted by residual: angle pdb=" CA ARG B 180 " pdb=" C ARG B 180 " pdb=" O ARG B 180 " ideal model delta sigma weight residual 122.14 114.88 7.26 1.24e+00 6.50e-01 3.43e+01 angle pdb=" CA ARG A 180 " pdb=" C ARG A 180 " pdb=" O ARG A 180 " ideal model delta sigma weight residual 122.45 115.48 6.97 1.30e+00 5.92e-01 2.87e+01 angle pdb=" O HIS B 131 " pdb=" C HIS B 131 " pdb=" N TYR B 132 " ideal model delta sigma weight residual 123.15 116.72 6.43 1.30e+00 5.92e-01 2.44e+01 angle pdb=" O HIS A 131 " pdb=" C HIS A 131 " pdb=" N TYR A 132 " ideal model delta sigma weight residual 123.15 116.90 6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" O HIS C 131 " pdb=" C HIS C 131 " pdb=" N TYR C 132 " ideal model delta sigma weight residual 123.15 117.42 5.73 1.30e+00 5.92e-01 1.95e+01 ... (remaining 9616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 3950 21.16 - 42.32: 313 42.32 - 63.48: 104 63.48 - 84.65: 12 84.65 - 105.81: 28 Dihedral angle restraints: 4407 sinusoidal: 1893 harmonic: 2514 Sorted by residual: dihedral pdb=" C2 NAG C 404 " pdb=" C3 NAG C 404 " pdb=" C4 NAG C 404 " pdb=" O4 NAG C 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.30 105.81 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG A 404 " pdb=" C3 NAG A 404 " pdb=" C4 NAG A 404 " pdb=" O4 NAG A 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.33 105.78 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG B 404 " pdb=" C3 NAG B 404 " pdb=" C4 NAG B 404 " pdb=" O4 NAG B 404 " ideal model delta sinusoidal sigma weight residual 175.11 69.34 105.77 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 893 0.057 - 0.114: 166 0.114 - 0.170: 33 0.170 - 0.227: 2 0.227 - 0.284: 4 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA ARG B 180 " pdb=" N ARG B 180 " pdb=" C ARG B 180 " pdb=" CB ARG B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 148 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 148 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1095 not shown) Planarity restraints: 1212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 132 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR B 132 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR B 132 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 133 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 132 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR A 132 " -0.056 2.00e-02 2.50e+03 pdb=" O TYR A 132 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A 133 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 132 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C TYR C 132 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR C 132 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 133 " 0.018 2.00e-02 2.50e+03 ... (remaining 1209 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1410 2.79 - 3.31: 6126 3.31 - 3.84: 11152 3.84 - 4.37: 13265 4.37 - 4.90: 23067 Nonbonded interactions: 55020 Sorted by model distance: nonbonded pdb=" O ASP C 269 " pdb=" OD1 ASP C 269 " model vdw 2.257 3.040 nonbonded pdb=" O ASP B 269 " pdb=" OD1 ASP B 269 " model vdw 2.258 3.040 nonbonded pdb=" O ASP A 269 " pdb=" OD1 ASP A 269 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR C 119 " pdb=" OH TYR C 156 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR B 119 " pdb=" OH TYR B 156 " model vdw 2.266 3.040 ... (remaining 55015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.880 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.670 ------------------------------------------------------------------------------- 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 7104 Z= 0.361 Angle : 0.740 7.318 9621 Z= 0.465 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 *********************** 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 : 0.829 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: 1.9579 time to fit residues: 517.6158 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 : 0.741 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.7580 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7104 Z= 0.310 Angle : 0.609 7.102 9621 Z= 0.303 Chirality : 0.048 0.344 1098 Planarity : 0.004 0.046 1200 Dihedral : 12.892 71.126 1164 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.21 % Allowed : 26.00 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.29), residues: 843 helix: 3.30 (0.27), residues: 312 sheet: 0.68 (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 0.005 0.002 HIS A 98 PHE 0.023 0.002 PHE C 92 TYR 0.008 0.001 TYR C 227 ARG 0.013 0.001 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1686 Ramachandran restraints generated. 843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8567 (mttt) cc_final: 0.8199 (mtmm) REVERT: A 153 ARG cc_start: 0.7427 (mtp85) cc_final: 0.7172 (mtp85) REVERT: A 156 TYR cc_start: 0.8312 (p90) cc_final: 0.7976 (p90) REVERT: A 180 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7496 (mtp180) REVERT: A 224 GLU cc_start: 0.7332 (tp30) cc_final: 0.7041 (tp30) REVERT: A 275 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7776 (mtpp) REVERT: A 325 LYS cc_start: 0.7945 (ttmt) cc_final: 0.7738 (ttmt) REVERT: B 72 PHE cc_start: 0.6970 (m-10) cc_final: 0.6739 (m-80) REVERT: B 77 LEU cc_start: 0.7936 (mm) cc_final: 0.7692 (mm) REVERT: B 91 ASP cc_start: 0.8264 (m-30) cc_final: 0.8054 (m-30) REVERT: B 208 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: B 275 LYS cc_start: 0.8131 (mttm) cc_final: 0.7901 (mttm) REVERT: C 72 PHE cc_start: 0.7300 (m-10) cc_final: 0.7005 (m-80) REVERT: C 95 LYS cc_start: 0.8548 (mttt) cc_final: 0.8276 (mtmm) REVERT: C 133 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6782 (tm-30) REVERT: C 266 ASN cc_start: 0.8783 (t0) cc_final: 0.8451 (t0) REVERT: C 297 ASP cc_start: 0.8762 (t0) cc_final: 0.8520 (t0) REVERT: C 326 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7879 (mm) REVERT: C 333 LYS cc_start: 0.8288 (tttt) cc_final: 0.7853 (ttpt) outliers start: 16 outliers final: 5 residues processed: 199 average time/residue: 1.8448 time to fit residues: 380.0738 Evaluate side-chains 202 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 195 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 208 GLN Chi-restraints excluded: chain C residue 96 LEU 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 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 0.0040 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7104 Z= 0.254 Angle : 0.571 6.712 9621 Z= 0.283 Chirality : 0.046 0.324 1098 Planarity : 0.003 0.034 1200 Dihedral : 8.435 57.934 1164 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.63 % Allowed : 27.11 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.29), residues: 843 helix: 3.21 (0.27), residues: 315 sheet: 0.60 (0.28), residues: 312 loop : -0.57 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 230 HIS 0.002 0.001 HIS B 130 PHE 0.024 0.001 PHE B 92 TYR 0.007 0.001 TYR C 201 ARG 0.020 0.001 ARG C 259 *********************** 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 224 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.867 Fit side-chains REVERT: A 63 LYS cc_start: 0.8006 (tptp) cc_final: 0.7690 (tmmt) REVERT: A 153 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7130 (mtp85) REVERT: A 180 ARG cc_start: 0.7701 (mtp180) cc_final: 0.7470 (mtp180) REVERT: A 224 GLU cc_start: 0.7359 (tp30) cc_final: 0.6992 (tp30) REVERT: A 275 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7802 (mtpp) REVERT: A 325 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7750 (ttmt) REVERT: A 333 LYS cc_start: 0.8449 (tttt) cc_final: 0.7910 (ttpp) REVERT: B 72 PHE cc_start: 0.6922 (m-10) cc_final: 0.6702 (m-80) REVERT: B 77 LEU cc_start: 0.7981 (mm) cc_final: 0.7712 (mm) REVERT: B 91 ASP cc_start: 0.8318 (m-30) cc_final: 0.8110 (m-30) REVERT: B 325 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7716 (ttmt) REVERT: B 333 LYS cc_start: 0.8452 (tttt) cc_final: 0.7851 (ttpp) REVERT: C 72 PHE cc_start: 0.7290 (m-10) cc_final: 0.7014 (m-80) REVERT: C 87 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7136 (tpm-80) REVERT: C 95 LYS cc_start: 0.8552 (mttt) cc_final: 0.8319 (mtmm) REVERT: C 132 TYR cc_start: 0.8971 (m-80) cc_final: 0.8081 (m-10) REVERT: C 133 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6671 (tm-30) REVERT: C 176 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 180 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7322 (mtp180) REVERT: C 266 ASN cc_start: 0.8754 (t0) cc_final: 0.8463 (t0) REVERT: C 275 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7952 (mtpp) REVERT: C 326 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7923 (mm) REVERT: C 333 LYS cc_start: 0.8347 (tttt) cc_final: 0.7824 (ttpp) outliers start: 19 outliers final: 4 residues processed: 214 average time/residue: 1.7954 time to fit residues: 397.9883 Evaluate side-chains 204 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 198 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 0.0670 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 212 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7104 Z= 0.227 Angle : 0.561 7.431 9621 Z= 0.280 Chirality : 0.045 0.325 1098 Planarity : 0.003 0.043 1200 Dihedral : 7.131 57.259 1164 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 28.63 % Favored : 69.57 % 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: 2.00 (0.29), residues: 843 helix: 3.32 (0.27), residues: 312 sheet: 0.59 (0.28), residues: 312 loop : -0.53 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.003 0.001 HIS A 98 PHE 0.024 0.001 PHE B 92 TYR 0.008 0.001 TYR B 111 ARG 0.008 0.001 ARG B 110 *********************** 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 230 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 1.084 Fit side-chains REVERT: A 63 LYS cc_start: 0.8019 (tptp) cc_final: 0.7722 (tmmt) REVERT: A 153 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7175 (mtp85) REVERT: A 180 ARG cc_start: 0.7682 (mtp180) cc_final: 0.7461 (mtp180) REVERT: A 224 GLU cc_start: 0.7300 (tp30) cc_final: 0.6934 (tp30) REVERT: A 275 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7852 (mtpp) REVERT: A 333 LYS cc_start: 0.8485 (tttt) cc_final: 0.7922 (ttpp) REVERT: B 72 PHE cc_start: 0.6913 (m-10) cc_final: 0.6709 (m-80) REVERT: B 77 LEU cc_start: 0.8005 (mm) cc_final: 0.7758 (mm) REVERT: B 91 ASP cc_start: 0.8328 (m-30) cc_final: 0.8116 (m-30) REVERT: B 162 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.5219 (m-40) REVERT: B 333 LYS cc_start: 0.8507 (tttt) cc_final: 0.7899 (ttpp) REVERT: C 72 PHE cc_start: 0.7291 (m-10) cc_final: 0.7022 (m-80) REVERT: C 87 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7140 (tpm-80) REVERT: C 95 LYS cc_start: 0.8554 (mttt) cc_final: 0.8293 (mttm) REVERT: C 132 TYR cc_start: 0.9028 (m-80) cc_final: 0.8200 (m-10) REVERT: C 176 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 180 ARG cc_start: 0.7562 (mtp180) cc_final: 0.7273 (mtp180) REVERT: C 266 ASN cc_start: 0.8801 (t0) cc_final: 0.8515 (t0) REVERT: C 326 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7908 (mm) REVERT: C 333 LYS cc_start: 0.8320 (tttt) cc_final: 0.7835 (ttpp) outliers start: 13 outliers final: 7 residues processed: 221 average time/residue: 1.7825 time to fit residues: 407.9146 Evaluate side-chains 207 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN B 212 GLN B 293 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7104 Z= 0.286 Angle : 0.569 8.335 9621 Z= 0.287 Chirality : 0.046 0.337 1098 Planarity : 0.004 0.035 1200 Dihedral : 6.350 55.335 1164 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 28.35 % Favored : 69.43 % 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: 1.96 (0.29), residues: 843 helix: 3.24 (0.27), residues: 312 sheet: 0.69 (0.29), residues: 306 loop : -0.68 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 230 HIS 0.002 0.001 HIS A 98 PHE 0.026 0.001 PHE B 92 TYR 0.009 0.001 TYR C 201 ARG 0.007 0.001 ARG C 259 *********************** 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 226 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 63 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7764 (tmmt) REVERT: A 153 ARG cc_start: 0.7438 (mtp85) cc_final: 0.7224 (mtp85) REVERT: A 224 GLU cc_start: 0.7363 (tp30) cc_final: 0.6997 (tp30) REVERT: A 275 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7892 (mtpp) REVERT: A 333 LYS cc_start: 0.8508 (tttt) cc_final: 0.8004 (ttpp) REVERT: B 72 PHE cc_start: 0.6937 (m-10) cc_final: 0.6721 (m-80) REVERT: B 91 ASP cc_start: 0.8331 (m-30) cc_final: 0.8124 (m-30) REVERT: B 333 LYS cc_start: 0.8526 (tttt) cc_final: 0.7958 (ttpp) REVERT: C 72 PHE cc_start: 0.7291 (m-10) cc_final: 0.6996 (m-80) REVERT: C 87 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7217 (tpm-80) REVERT: C 95 LYS cc_start: 0.8567 (mttt) cc_final: 0.8323 (mttm) REVERT: C 180 ARG cc_start: 0.7573 (mtp180) cc_final: 0.7285 (mtp180) REVERT: C 266 ASN cc_start: 0.8812 (t0) cc_final: 0.8574 (t0) REVERT: C 326 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7936 (mm) REVERT: C 333 LYS cc_start: 0.8395 (tttt) cc_final: 0.7856 (ttpp) outliers start: 16 outliers final: 10 residues processed: 213 average time/residue: 1.8097 time to fit residues: 399.2225 Evaluate side-chains 225 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain A residue 302 ASN 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 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 143 GLN B 212 GLN C 279 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7104 Z= 0.220 Angle : 0.563 8.713 9621 Z= 0.283 Chirality : 0.045 0.326 1098 Planarity : 0.004 0.049 1200 Dihedral : 5.913 52.411 1164 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.04 % Allowed : 28.35 % Favored : 68.60 % 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: 1.97 (0.29), residues: 843 helix: 3.27 (0.27), residues: 312 sheet: 0.67 (0.29), residues: 306 loop : -0.66 (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 0.001 PHE C 92 TYR 0.007 0.001 TYR C 201 ARG 0.010 0.001 ARG A 110 *********************** 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 237 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.905 Fit side-chains REVERT: A 63 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7781 (tmmt) REVERT: A 153 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7215 (mtp85) REVERT: A 180 ARG cc_start: 0.7354 (mtp180) cc_final: 0.7073 (ttp-170) REVERT: A 224 GLU cc_start: 0.7330 (tp30) cc_final: 0.7017 (tp30) REVERT: A 275 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7907 (mtpp) REVERT: A 333 LYS cc_start: 0.8533 (tttt) cc_final: 0.8022 (ttpp) REVERT: B 72 PHE cc_start: 0.6895 (m-10) cc_final: 0.6688 (m-80) REVERT: B 77 LEU cc_start: 0.8033 (mm) cc_final: 0.7828 (mm) REVERT: B 91 ASP cc_start: 0.8327 (m-30) cc_final: 0.8117 (m-30) REVERT: B 333 LYS cc_start: 0.8511 (tttt) cc_final: 0.7937 (ttpp) REVERT: C 72 PHE cc_start: 0.7263 (m-10) cc_final: 0.6979 (m-80) REVERT: C 87 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7233 (tpm-80) REVERT: C 95 LYS cc_start: 0.8569 (mttt) cc_final: 0.8327 (mttm) REVERT: C 132 TYR cc_start: 0.9022 (m-80) cc_final: 0.8240 (m-10) REVERT: C 176 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7596 (mt-10) REVERT: C 180 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7263 (mtp180) REVERT: C 266 ASN cc_start: 0.8799 (t0) cc_final: 0.8549 (t0) REVERT: C 326 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7925 (mm) REVERT: C 333 LYS cc_start: 0.8412 (tttt) cc_final: 0.7886 (ttpp) outliers start: 22 outliers final: 7 residues processed: 223 average time/residue: 1.7677 time to fit residues: 408.2821 Evaluate side-chains 206 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 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 78 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 143 GLN B 212 GLN B 293 GLN C 130 HIS C 143 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7104 Z= 0.261 Angle : 0.586 9.600 9621 Z= 0.291 Chirality : 0.046 0.331 1098 Planarity : 0.004 0.045 1200 Dihedral : 5.745 48.788 1164 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.63 % Allowed : 29.05 % 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: 1.94 (0.29), residues: 843 helix: 3.22 (0.27), residues: 312 sheet: 0.67 (0.29), residues: 306 loop : -0.64 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.003 0.001 HIS B 98 PHE 0.026 0.001 PHE B 92 TYR 0.008 0.001 TYR C 201 ARG 0.010 0.001 ARG C 259 *********************** 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 224 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.821 Fit side-chains REVERT: A 63 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7783 (tmmt) REVERT: A 133 GLU cc_start: 0.6801 (tm-30) cc_final: 0.5780 (tm-30) REVERT: A 153 ARG cc_start: 0.7446 (mtp85) cc_final: 0.7217 (mtp85) REVERT: A 180 ARG cc_start: 0.7373 (mtp180) cc_final: 0.6968 (ttp-170) REVERT: A 224 GLU cc_start: 0.7364 (tp30) cc_final: 0.7035 (tp30) REVERT: A 275 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7924 (mtpp) REVERT: A 329 LYS cc_start: 0.8344 (tttt) cc_final: 0.8100 (tttt) REVERT: A 333 LYS cc_start: 0.8547 (tttt) cc_final: 0.8048 (ttpp) REVERT: B 72 PHE cc_start: 0.6883 (m-10) cc_final: 0.6590 (m-80) REVERT: B 91 ASP cc_start: 0.8332 (m-30) cc_final: 0.8126 (m-30) REVERT: B 188 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7814 (ppp80) REVERT: B 333 LYS cc_start: 0.8542 (tttt) cc_final: 0.8006 (ttpp) REVERT: C 72 PHE cc_start: 0.7259 (m-10) cc_final: 0.6979 (m-80) REVERT: C 87 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7186 (tpm-80) REVERT: C 95 LYS cc_start: 0.8586 (mttt) cc_final: 0.8330 (mttm) REVERT: C 176 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 180 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7240 (mtp180) REVERT: C 266 ASN cc_start: 0.8808 (t0) cc_final: 0.8576 (t0) REVERT: C 326 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7934 (mm) REVERT: C 333 LYS cc_start: 0.8416 (tttt) cc_final: 0.7949 (ttpp) outliers start: 19 outliers final: 10 residues processed: 211 average time/residue: 1.7803 time to fit residues: 388.9379 Evaluate side-chains 219 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 302 ASN 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 Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 B 130 HIS B 143 GLN B 212 GLN B 293 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7104 Z= 0.248 Angle : 0.590 9.901 9621 Z= 0.290 Chirality : 0.046 0.328 1098 Planarity : 0.004 0.053 1200 Dihedral : 5.391 44.616 1164 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.63 % Allowed : 29.46 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.88 (0.29), residues: 843 helix: 3.19 (0.27), residues: 312 sheet: 0.70 (0.29), residues: 312 loop : -0.87 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.004 0.001 HIS B 130 PHE 0.027 0.001 PHE C 92 TYR 0.008 0.001 TYR B 227 ARG 0.011 0.001 ARG A 110 *********************** 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 230 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.862 Fit side-chains REVERT: A 63 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7855 (tmmt) REVERT: A 122 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8484 (mm110) REVERT: A 124 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7258 (mm-40) REVERT: A 133 GLU cc_start: 0.6829 (tm-30) cc_final: 0.5451 (tm-30) REVERT: A 170 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8548 (mm) REVERT: A 180 ARG cc_start: 0.7375 (mtp180) cc_final: 0.6932 (ttp-170) REVERT: A 224 GLU cc_start: 0.7382 (tp30) cc_final: 0.7052 (tp30) REVERT: A 275 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7919 (mtpp) REVERT: A 329 LYS cc_start: 0.8355 (tttt) cc_final: 0.8097 (tttt) REVERT: A 333 LYS cc_start: 0.8568 (tttt) cc_final: 0.8058 (ttpp) REVERT: B 188 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7866 (ppp80) REVERT: B 326 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 333 LYS cc_start: 0.8543 (tttt) cc_final: 0.7997 (ttpp) REVERT: C 72 PHE cc_start: 0.7250 (m-10) cc_final: 0.6970 (m-80) REVERT: C 87 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7176 (tpm-80) REVERT: C 95 LYS cc_start: 0.8596 (mttt) cc_final: 0.8342 (mttm) REVERT: C 180 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7254 (mtp180) REVERT: C 266 ASN cc_start: 0.8806 (t0) cc_final: 0.8574 (t0) REVERT: C 326 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7955 (mm) REVERT: C 333 LYS cc_start: 0.8418 (tttt) cc_final: 0.7949 (ttpp) outliers start: 19 outliers final: 10 residues processed: 217 average time/residue: 1.8630 time to fit residues: 418.2222 Evaluate side-chains 215 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 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 293 GLN B 143 GLN B 212 GLN B 293 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7104 Z= 0.239 Angle : 0.605 10.892 9621 Z= 0.297 Chirality : 0.047 0.390 1098 Planarity : 0.004 0.050 1200 Dihedral : 5.081 36.665 1164 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.49 % Allowed : 30.15 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.15 (0.27), residues: 312 sheet: 0.69 (0.29), residues: 312 loop : -0.85 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.002 0.001 HIS B 98 PHE 0.026 0.001 PHE B 92 TYR 0.008 0.001 TYR B 74 ARG 0.010 0.001 ARG C 259 *********************** 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 224 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.061 Fit side-chains REVERT: A 63 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7862 (tmmt) REVERT: A 153 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7202 (mtp85) REVERT: A 170 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8551 (mm) REVERT: A 180 ARG cc_start: 0.7377 (mtp180) cc_final: 0.6992 (ttp-170) REVERT: A 224 GLU cc_start: 0.7403 (tp30) cc_final: 0.7039 (tp30) REVERT: A 275 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7921 (mtpp) REVERT: A 329 LYS cc_start: 0.8345 (tttt) cc_final: 0.8090 (tttt) REVERT: A 331 MET cc_start: 0.6653 (tmm) cc_final: 0.6336 (tmm) REVERT: A 333 LYS cc_start: 0.8593 (tttt) cc_final: 0.8128 (ttpp) REVERT: B 72 PHE cc_start: 0.6843 (m-80) cc_final: 0.6556 (m-80) REVERT: B 91 ASP cc_start: 0.8192 (m-30) cc_final: 0.7945 (m-30) REVERT: B 188 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7851 (ppp80) REVERT: B 248 LYS cc_start: 0.8902 (tppt) cc_final: 0.8701 (tppp) REVERT: B 326 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 333 LYS cc_start: 0.8553 (tttt) cc_final: 0.8014 (ttpp) REVERT: C 72 PHE cc_start: 0.7253 (m-10) cc_final: 0.6988 (m-80) REVERT: C 87 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7222 (tpm-80) REVERT: C 95 LYS cc_start: 0.8607 (mttt) cc_final: 0.8346 (mttm) REVERT: C 176 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 180 ARG cc_start: 0.7572 (mtp180) cc_final: 0.7259 (mtp180) REVERT: C 266 ASN cc_start: 0.8807 (t0) cc_final: 0.8576 (t0) REVERT: C 326 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7938 (mm) REVERT: C 333 LYS cc_start: 0.8429 (tttt) cc_final: 0.7954 (ttpp) outliers start: 18 outliers final: 8 residues processed: 213 average time/residue: 1.8178 time to fit residues: 401.1260 Evaluate side-chains 211 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 302 ASN Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 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 143 GLN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 143 GLN B 212 GLN B 293 GLN C 143 GLN C 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7104 Z= 0.300 Angle : 0.640 10.436 9621 Z= 0.316 Chirality : 0.048 0.396 1098 Planarity : 0.004 0.056 1200 Dihedral : 5.676 59.125 1164 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 30.15 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.04 (0.27), residues: 312 sheet: 0.52 (0.28), residues: 330 loop : -0.65 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 304 HIS 0.002 0.001 HIS B 98 PHE 0.028 0.002 PHE C 92 TYR 0.010 0.001 TYR C 201 ARG 0.012 0.001 ARG A 110 ********************** 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 230 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.910 Fit side-chains REVERT: A 63 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7901 (tmmt) REVERT: A 153 ARG cc_start: 0.7461 (mtp85) cc_final: 0.7210 (mtp85) REVERT: A 170 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8564 (mm) REVERT: A 180 ARG cc_start: 0.7385 (mtp180) cc_final: 0.6965 (ttp-170) REVERT: A 224 GLU cc_start: 0.7459 (tp30) cc_final: 0.7103 (tp30) REVERT: A 275 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7945 (mtpp) REVERT: A 329 LYS cc_start: 0.8349 (tttt) cc_final: 0.8091 (tttt) REVERT: A 331 MET cc_start: 0.6647 (tmm) cc_final: 0.6357 (tmm) REVERT: A 333 LYS cc_start: 0.8549 (tttt) cc_final: 0.8088 (ttpp) REVERT: B 72 PHE cc_start: 0.6852 (m-80) cc_final: 0.6560 (m-80) REVERT: B 91 ASP cc_start: 0.8170 (m-30) cc_final: 0.7950 (m-30) REVERT: B 188 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7864 (ppp80) REVERT: B 294 LYS cc_start: 0.8166 (tmmt) cc_final: 0.7923 (tmmt) REVERT: B 333 LYS cc_start: 0.8554 (tttt) cc_final: 0.8017 (ttpp) REVERT: C 72 PHE cc_start: 0.7270 (m-10) cc_final: 0.7005 (m-80) REVERT: C 87 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7189 (tpm-80) REVERT: C 95 LYS cc_start: 0.8617 (mttt) cc_final: 0.8353 (mttm) REVERT: C 180 ARG cc_start: 0.7569 (mtp180) cc_final: 0.7297 (mtp180) REVERT: C 326 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7969 (mm) REVERT: C 329 LYS cc_start: 0.8218 (tttt) cc_final: 0.7652 (ttpp) REVERT: C 333 LYS cc_start: 0.8427 (tttt) cc_final: 0.7962 (ttpp) outliers start: 18 outliers final: 11 residues processed: 218 average time/residue: 1.8377 time to fit residues: 414.4036 Evaluate side-chains 220 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 170 ILE Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 188 ARG Chi-restraints excluded: chain B residue 302 ASN 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 Chi-restraints excluded: chain C residue 328 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS B 143 GLN B 212 GLN B 293 GLN C 279 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084494 restraints weight = 12309.410| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.67 r_work: 0.3124 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7104 Z= 0.265 Angle : 0.617 9.943 9621 Z= 0.307 Chirality : 0.048 0.414 1098 Planarity : 0.004 0.059 1200 Dihedral : 5.329 58.940 1164 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.35 % Allowed : 31.12 % Favored : 66.53 % 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: 1.80 (0.29), residues: 843 helix: 3.06 (0.27), residues: 312 sheet: 0.52 (0.28), residues: 330 loop : -0.64 (0.45), residues: 201 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 0.028 0.001 PHE B 92 TYR 0.008 0.001 TYR C 201 ARG 0.011 0.001 ARG A 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5519.98 seconds wall clock time: 99 minutes 57.98 seconds (5997.98 seconds total)