Starting phenix.real_space_refine on Thu Jul 2 22:55:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2026/8dps_27641.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 36 5.16 5 C 6752 2.51 5 N 1826 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10610 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2382 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 280} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1262 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Chain: "C" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1566 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 25, 'TRANS': 174} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: D, E, F, I, J Time building chain proxies: 2.59, per 1000 atoms: 0.24 Number of scatterers: 10610 At special positions: 0 Unit cell: (148.03, 129.69, 90.39, 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 36 16.00 O 1996 8.00 N 1826 7.00 C 6752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 81 " distance=2.04 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 160 " distance=2.05 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 32 " distance=2.04 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 81 " distance=2.04 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 160 " distance=2.05 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 108 " distance=2.04 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 158 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM10499 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM10432 O5 NAG G 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM10580 O5 NAG A 402 .*. O " rejected from bonding due to valence issues. Atom "HETATM10608 O5 NAG D 402 .*. O " rejected from bonding due to valence issues. Atom "HETATM10566 O5 NAG A 401 .*. O " rejected from bonding due to valence issues. Atom "HETATM10594 O5 NAG D 401 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 401 " - " ASN A 21 " " NAG A 402 " - " ASN A 135 " " NAG D 401 " - " ASN D 21 " " NAG D 402 " - " ASN D 135 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN C 172 " " NAG I 1 " - " ASN D 61 " " NAG J 1 " - " ASN F 172 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 234.9 milliseconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 24 sheets defined 24.5% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.866A pdb=" N ALA A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 43 removed outlier: 3.856A pdb=" N SER B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.572A pdb=" N LEU B 64 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 65 " --> pdb=" O GLY B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.746A pdb=" N VAL B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 4.394A pdb=" N THR B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 126 Processing helix chain 'B' and resid 145 through 157 Processing helix chain 'B' and resid 159 through 178 removed outlier: 3.738A pdb=" N ASP B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.865A pdb=" N ALA D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 43 removed outlier: 3.855A pdb=" N SER E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.571A pdb=" N LEU E 64 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY E 65 " --> pdb=" O GLY E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 65' Processing helix chain 'E' and resid 68 through 94 removed outlier: 3.746A pdb=" N VAL E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 4.393A pdb=" N THR E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 126 Processing helix chain 'E' and resid 145 through 157 Processing helix chain 'E' and resid 159 through 178 removed outlier: 3.738A pdb=" N ASP E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.718A pdb=" N ALA A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.622A pdb=" N ASN A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 83 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 161 removed outlier: 4.190A pdb=" N ASP A 125 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASN A 109 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS A 199 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 114 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'A' and resid 204 through 210 removed outlier: 5.680A pdb=" N ASN A 205 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR A 223 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA8, first strand: chain 'C' and resid 95 through 99 Processing sheet with id=AA9, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 206 removed outlier: 4.137A pdb=" N LEU C 202 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER C 217 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL C 204 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG C 215 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 247 through 249 Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 10 removed outlier: 6.717A pdb=" N ALA D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 15 through 17 removed outlier: 5.621A pdb=" N ASN D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE D 83 " --> pdb=" O ASN D 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 removed outlier: 4.191A pdb=" N ASP D 125 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASN D 109 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS D 199 " --> pdb=" O CYS D 112 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL D 114 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AB8, first strand: chain 'D' and resid 150 through 151 Processing sheet with id=AB9, first strand: chain 'D' and resid 204 through 210 removed outlier: 5.681A pdb=" N ASN D 205 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 223 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AC2, first strand: chain 'F' and resid 95 through 99 Processing sheet with id=AC3, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC4, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AC5, first strand: chain 'F' and resid 200 through 206 removed outlier: 4.138A pdb=" N LEU F 202 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER F 217 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL F 204 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG F 215 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 247 through 249 492 hydrogen bonds defined for protein. 1266 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: 1.48 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3405 1.35 - 1.48: 2940 1.48 - 1.61: 4513 1.61 - 1.75: 2 1.75 - 1.88: 44 Bond restraints: 10904 Sorted by residual: bond pdb=" CB TRP A 142 " pdb=" CG TRP A 142 " ideal model delta sigma weight residual 1.498 1.404 0.094 3.10e-02 1.04e+03 9.10e+00 bond pdb=" CB TRP D 142 " pdb=" CG TRP D 142 " ideal model delta sigma weight residual 1.498 1.405 0.093 3.10e-02 1.04e+03 9.08e+00 bond pdb=" CB CYS A 160 " pdb=" SG CYS A 160 " ideal model delta sigma weight residual 1.808 1.879 -0.071 3.30e-02 9.18e+02 4.69e+00 bond pdb=" CB CYS D 160 " pdb=" SG CYS D 160 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CG LEU C 186 " pdb=" CD2 LEU C 186 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.41e+00 ... (remaining 10899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 14696 4.52 - 9.03: 178 9.03 - 13.55: 18 13.55 - 18.07: 8 18.07 - 22.59: 2 Bond angle restraints: 14902 Sorted by residual: angle pdb=" C ALA D 148 " pdb=" N ASP D 149 " pdb=" CA ASP D 149 " ideal model delta sigma weight residual 120.94 132.46 -11.52 1.57e+00 4.06e-01 5.38e+01 angle pdb=" C ALA A 148 " pdb=" N ASP A 149 " pdb=" CA ASP A 149 " ideal model delta sigma weight residual 120.94 132.42 -11.48 1.57e+00 4.06e-01 5.34e+01 angle pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " pdb=" SG CYS A 150 " ideal model delta sigma weight residual 114.40 129.32 -14.92 2.30e+00 1.89e-01 4.21e+01 angle pdb=" CA CYS D 150 " pdb=" CB CYS D 150 " pdb=" SG CYS D 150 " ideal model delta sigma weight residual 114.40 129.31 -14.91 2.30e+00 1.89e-01 4.20e+01 angle pdb=" CA LEU E 173 " pdb=" CB LEU E 173 " pdb=" CG LEU E 173 " ideal model delta sigma weight residual 116.30 138.89 -22.59 3.50e+00 8.16e-02 4.16e+01 ... (remaining 14897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 6082 16.97 - 33.94: 493 33.94 - 50.91: 95 50.91 - 67.88: 34 67.88 - 84.85: 14 Dihedral angle restraints: 6718 sinusoidal: 2854 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 32 " pdb=" CB CYS A 32 " ideal model delta sinusoidal sigma weight residual 93.00 44.57 48.43 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 32 " pdb=" CB CYS D 32 " ideal model delta sinusoidal sigma weight residual 93.00 44.60 48.40 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" C PHE A 147 " pdb=" N PHE A 147 " pdb=" CA PHE A 147 " pdb=" CB PHE A 147 " ideal model delta harmonic sigma weight residual -122.60 -135.89 13.29 0 2.50e+00 1.60e-01 2.83e+01 ... (remaining 6715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 1674 0.179 - 0.359: 20 0.359 - 0.538: 10 0.538 - 0.717: 0 0.717 - 0.897: 4 Chirality restraints: 1708 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 61 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 172 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 1705 not shown) Planarity restraints: 1894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.240 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" CG ASN A 61 " -0.097 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.494 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.403 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 61 " 0.240 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" CG ASN D 61 " -0.098 2.00e-02 2.50e+03 pdb=" OD1 ASN D 61 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN D 61 " -0.494 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.402 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 172 " -0.109 2.00e-02 2.50e+03 1.31e-01 2.15e+02 pdb=" CG ASN C 172 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C 172 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 172 " 0.218 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.158 2.00e-02 2.50e+03 ... (remaining 1891 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 211 2.63 - 3.20: 9855 3.20 - 3.77: 16271 3.77 - 4.33: 21793 4.33 - 4.90: 36372 Nonbonded interactions: 84502 Sorted by model distance: nonbonded pdb=" O THR A 144 " pdb=" ND1 HIS A 145 " model vdw 2.063 3.120 nonbonded pdb=" O THR D 144 " pdb=" ND1 HIS D 145 " model vdw 2.064 3.120 nonbonded pdb=" OG1 THR A 58 " pdb=" OG SER A 66 " model vdw 2.087 3.040 nonbonded pdb=" OG1 THR D 58 " pdb=" OG SER D 66 " model vdw 2.088 3.040 nonbonded pdb=" OG SER A 261 " pdb=" OG SER C 247 " model vdw 2.114 3.040 ... (remaining 84497 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.008 0.094 10930 Z= 0.338 Angle : 1.820 49.774 14968 Z= 0.838 Chirality : 0.081 0.897 1708 Planarity : 0.006 0.050 1886 Dihedral : 13.554 84.854 4178 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.52 % Allowed : 2.35 % Favored : 97.13 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1308 helix: 1.10 (0.29), residues: 238 sheet: 0.22 (0.23), residues: 420 loop : -1.37 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 121 TYR 0.021 0.004 TYR C 89 PHE 0.047 0.004 PHE F 230 TRP 0.042 0.004 TRP A 45 HIS 0.008 0.002 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.34 (10904) covalent geometry : angle 1.40053 / 0.74 (14902) SS BOND : bond 0.00839 / 0.50 ( 12) SS BOND : angle 3.73599 / 2.01 ( 24) hydrogen bonds : bond 0.23379 / 15.22 ( 452) hydrogen bonds : angle 8.03459 / 5.56 ( 1266) link_BETA1-4 : bond 0.00954 / 0.44 ( 6) link_BETA1-4 : angle 2.55199 / 1.57 ( 18) link_NAG-ASN : bond 0.02228 / 1.04 ( 8) link_NAG-ASN : angle 28.79182 / 16.36 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7598 (t0) REVERT: C 99 GLN cc_start: 0.5717 (pm20) cc_final: 0.5500 (pm20) REVERT: C 105 ASN cc_start: 0.7783 (p0) cc_final: 0.7476 (p0) REVERT: C 125 SER cc_start: 0.8145 (t) cc_final: 0.7579 (m) REVERT: D 62 ARG cc_start: 0.7243 (mtp-110) cc_final: 0.7022 (ptp-110) REVERT: D 109 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (t0) REVERT: F 99 GLN cc_start: 0.5867 (pm20) cc_final: 0.5591 (pm20) REVERT: F 256 GLU cc_start: 0.6659 (tp30) cc_final: 0.6332 (tp30) outliers start: 6 outliers final: 0 residues processed: 177 average time/residue: 0.0877 time to fit residues: 22.8518 Evaluate side-chains 123 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain D residue 109 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN C 114 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.174882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150321 restraints weight = 14358.924| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.52 r_work: 0.3869 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10930 Z= 0.185 Angle : 0.913 18.356 14968 Z= 0.429 Chirality : 0.049 0.249 1708 Planarity : 0.005 0.041 1886 Dihedral : 6.703 57.775 1698 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.96 % Allowed : 9.22 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1308 helix: 0.93 (0.30), residues: 264 sheet: 0.56 (0.23), residues: 408 loop : -0.41 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 111 TYR 0.024 0.002 TYR D 239 PHE 0.026 0.002 PHE F 106 TRP 0.018 0.002 TRP D 222 HIS 0.005 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (10904) covalent geometry : angle 0.84931 / 0.41 (14902) SS BOND : bond 0.00497 / 0.29 ( 12) SS BOND : angle 2.41980 / 1.44 ( 24) hydrogen bonds : bond 0.05548 / 3.69 ( 452) hydrogen bonds : angle 6.08947 / 4.21 ( 1266) link_BETA1-4 : bond 0.01053 / 0.48 ( 6) link_BETA1-4 : angle 2.06058 / 1.26 ( 18) link_NAG-ASN : bond 0.01154 / 0.56 ( 8) link_NAG-ASN : angle 7.91849 / 4.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7943 (t0) cc_final: 0.7175 (t0) REVERT: C 125 SER cc_start: 0.8279 (t) cc_final: 0.7969 (m) REVERT: C 151 ASP cc_start: 0.5084 (OUTLIER) cc_final: 0.4453 (m-30) REVERT: C 272 SER cc_start: 0.6520 (m) cc_final: 0.6262 (m) REVERT: D 33 MET cc_start: 0.6471 (tmm) cc_final: 0.6259 (tmm) REVERT: D 109 ASN cc_start: 0.7797 (t0) cc_final: 0.6959 (t0) REVERT: F 256 GLU cc_start: 0.6848 (tp30) cc_final: 0.6350 (tp30) outliers start: 11 outliers final: 6 residues processed: 179 average time/residue: 0.0984 time to fit residues: 25.2686 Evaluate side-chains 139 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 126 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN C 114 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.174361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149846 restraints weight = 14630.338| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.51 r_work: 0.3860 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10930 Z= 0.145 Angle : 0.772 17.280 14968 Z= 0.365 Chirality : 0.048 0.336 1708 Planarity : 0.004 0.042 1886 Dihedral : 6.240 57.850 1694 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.43 % Allowed : 11.39 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1308 helix: 1.18 (0.32), residues: 252 sheet: 0.53 (0.23), residues: 418 loop : -0.08 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 62 TYR 0.020 0.002 TYR D 239 PHE 0.024 0.002 PHE C 106 TRP 0.026 0.001 TRP D 222 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10904) covalent geometry : angle 0.72425 / 0.35 (14902) SS BOND : bond 0.00293 / 0.17 ( 12) SS BOND : angle 1.61901 / 0.98 ( 24) hydrogen bonds : bond 0.04593 / 3.07 ( 452) hydrogen bonds : angle 5.73174 / 4.03 ( 1266) link_BETA1-4 : bond 0.00797 / 0.36 ( 6) link_BETA1-4 : angle 2.09901 / 1.26 ( 18) link_NAG-ASN : bond 0.00600 / 0.31 ( 8) link_NAG-ASN : angle 6.34420 / 3.44 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8008 (t0) cc_final: 0.7266 (t0) REVERT: A 177 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 42 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7870 (mtpp) REVERT: C 114 GLN cc_start: 0.8416 (mt0) cc_final: 0.6567 (pp30) REVERT: C 188 VAL cc_start: 0.8384 (t) cc_final: 0.8119 (t) REVERT: C 193 ILE cc_start: 0.8025 (tp) cc_final: 0.7735 (tt) REVERT: C 256 GLU cc_start: 0.6740 (tp30) cc_final: 0.6215 (tp30) REVERT: C 272 SER cc_start: 0.6495 (m) cc_final: 0.6281 (m) REVERT: D 109 ASN cc_start: 0.7786 (t0) cc_final: 0.6966 (t0) REVERT: D 177 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 296 SER cc_start: 0.7060 (m) cc_final: 0.6783 (p) REVERT: F 256 GLU cc_start: 0.6843 (tp30) cc_final: 0.6369 (tp30) REVERT: F 272 SER cc_start: 0.6541 (m) cc_final: 0.6319 (m) outliers start: 28 outliers final: 12 residues processed: 172 average time/residue: 0.0933 time to fit residues: 23.0811 Evaluate side-chains 139 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 HIS ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139010 restraints weight = 14866.613| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.64 r_work: 0.3702 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10930 Z= 0.245 Angle : 0.841 15.648 14968 Z= 0.402 Chirality : 0.050 0.280 1708 Planarity : 0.005 0.044 1886 Dihedral : 6.513 57.054 1694 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.96 % Allowed : 12.87 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1308 helix: 0.60 (0.33), residues: 262 sheet: -0.05 (0.23), residues: 418 loop : -0.21 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 118 TYR 0.025 0.003 TYR D 57 PHE 0.027 0.003 PHE C 106 TRP 0.029 0.002 TRP A 222 HIS 0.006 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (10904) covalent geometry : angle 0.79600 / 0.39 (14902) SS BOND : bond 0.00284 / 0.15 ( 12) SS BOND : angle 1.80243 / 1.07 ( 24) hydrogen bonds : bond 0.04745 / 3.17 ( 452) hydrogen bonds : angle 5.69032 / 3.93 ( 1266) link_BETA1-4 : bond 0.00799 / 0.37 ( 6) link_BETA1-4 : angle 2.40950 / 1.45 ( 18) link_NAG-ASN : bond 0.00742 / 0.37 ( 8) link_NAG-ASN : angle 6.31082 / 3.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7297 (pt) REVERT: A 109 ASN cc_start: 0.7960 (t0) cc_final: 0.6737 (t0) REVERT: B 42 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7624 (mtpp) REVERT: C 256 GLU cc_start: 0.6845 (tp30) cc_final: 0.6201 (tp30) REVERT: C 272 SER cc_start: 0.6704 (m) cc_final: 0.6498 (m) REVERT: D 96 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7363 (pt) REVERT: D 109 ASN cc_start: 0.7924 (t0) cc_final: 0.6658 (t0) REVERT: E 42 LYS cc_start: 0.7899 (mtpp) cc_final: 0.7659 (mtpp) REVERT: F 256 GLU cc_start: 0.6772 (tp30) cc_final: 0.6405 (tp30) outliers start: 34 outliers final: 24 residues processed: 162 average time/residue: 0.0900 time to fit residues: 21.4676 Evaluate side-chains 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.170123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145650 restraints weight = 14527.902| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.53 r_work: 0.3820 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 10930 Z= 0.135 Angle : 0.734 14.221 14968 Z= 0.346 Chirality : 0.046 0.263 1708 Planarity : 0.004 0.040 1886 Dihedral : 6.101 57.525 1694 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.09 % Allowed : 15.48 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1308 helix: 1.04 (0.34), residues: 252 sheet: 0.03 (0.24), residues: 424 loop : 0.08 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 118 TYR 0.017 0.001 TYR D 239 PHE 0.024 0.002 PHE C 230 TRP 0.025 0.001 TRP A 222 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10904) covalent geometry : angle 0.69382 / 0.34 (14902) SS BOND : bond 0.00376 / 0.22 ( 12) SS BOND : angle 1.68723 / 0.99 ( 24) hydrogen bonds : bond 0.04020 / 2.69 ( 452) hydrogen bonds : angle 5.44759 / 3.81 ( 1266) link_BETA1-4 : bond 0.00825 / 0.38 ( 6) link_BETA1-4 : angle 2.01608 / 1.22 ( 18) link_NAG-ASN : bond 0.00837 / 0.42 ( 8) link_NAG-ASN : angle 5.58993 / 3.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8032 (t0) cc_final: 0.7235 (t0) REVERT: B 29 LEU cc_start: 0.8701 (tt) cc_final: 0.8121 (tt) REVERT: B 42 LYS cc_start: 0.7793 (mtpp) cc_final: 0.7565 (mtpp) REVERT: C 215 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7513 (ttt90) REVERT: C 256 GLU cc_start: 0.6647 (tp30) cc_final: 0.6156 (tp30) REVERT: D 109 ASN cc_start: 0.7904 (t0) cc_final: 0.6706 (t0) REVERT: E 29 LEU cc_start: 0.8660 (tt) cc_final: 0.8150 (tt) REVERT: E 42 LYS cc_start: 0.7839 (mtpp) cc_final: 0.7603 (mtpp) REVERT: F 256 GLU cc_start: 0.6619 (tp30) cc_final: 0.6301 (tp30) outliers start: 24 outliers final: 19 residues processed: 169 average time/residue: 0.0909 time to fit residues: 22.0618 Evaluate side-chains 148 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 66 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.164708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.140288 restraints weight = 14716.277| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.53 r_work: 0.3722 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10930 Z= 0.211 Angle : 0.787 11.923 14968 Z= 0.374 Chirality : 0.049 0.269 1708 Planarity : 0.005 0.041 1886 Dihedral : 6.337 56.761 1694 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.61 % Allowed : 16.70 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1308 helix: 0.84 (0.34), residues: 250 sheet: -0.25 (0.23), residues: 422 loop : -0.06 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 118 TYR 0.016 0.002 TYR A 8 PHE 0.027 0.002 PHE F 106 TRP 0.023 0.002 TRP D 291 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (10904) covalent geometry : angle 0.74879 / 0.37 (14902) SS BOND : bond 0.00320 / 0.17 ( 12) SS BOND : angle 1.61214 / 0.95 ( 24) hydrogen bonds : bond 0.04303 / 2.87 ( 452) hydrogen bonds : angle 5.49121 / 3.83 ( 1266) link_BETA1-4 : bond 0.00713 / 0.33 ( 6) link_BETA1-4 : angle 2.20929 / 1.33 ( 18) link_NAG-ASN : bond 0.00773 / 0.39 ( 8) link_NAG-ASN : angle 5.62854 / 3.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8095 (t0) cc_final: 0.6897 (t0) REVERT: A 222 TRP cc_start: 0.7897 (p90) cc_final: 0.7645 (p90) REVERT: B 29 LEU cc_start: 0.8712 (tt) cc_final: 0.8350 (tt) REVERT: B 42 LYS cc_start: 0.7754 (mtpp) cc_final: 0.7480 (mtpp) REVERT: C 215 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7444 (ttt90) REVERT: C 256 GLU cc_start: 0.6812 (tp30) cc_final: 0.6267 (tp30) REVERT: D 62 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.7380 (ptm160) REVERT: D 109 ASN cc_start: 0.7963 (t0) cc_final: 0.7042 (t0) REVERT: E 29 LEU cc_start: 0.8770 (tt) cc_final: 0.8504 (tt) REVERT: E 42 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7511 (mtpp) REVERT: F 256 GLU cc_start: 0.6512 (tp30) cc_final: 0.6190 (tp30) outliers start: 30 outliers final: 25 residues processed: 165 average time/residue: 0.0960 time to fit residues: 23.0412 Evaluate side-chains 162 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 192 SER Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.166251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141921 restraints weight = 14649.198| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.53 r_work: 0.3778 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10930 Z= 0.170 Angle : 0.751 11.651 14968 Z= 0.358 Chirality : 0.047 0.262 1708 Planarity : 0.005 0.040 1886 Dihedral : 6.248 56.905 1694 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.52 % Allowed : 17.83 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1308 helix: 0.98 (0.34), residues: 246 sheet: -0.35 (0.23), residues: 428 loop : -0.02 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 93 TYR 0.017 0.002 TYR A 8 PHE 0.027 0.002 PHE F 230 TRP 0.020 0.002 TRP D 222 HIS 0.004 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10904) covalent geometry : angle 0.71713 / 0.35 (14902) SS BOND : bond 0.00355 / 0.20 ( 12) SS BOND : angle 1.66541 / 0.96 ( 24) hydrogen bonds : bond 0.04090 / 2.74 ( 452) hydrogen bonds : angle 5.43375 / 3.80 ( 1266) link_BETA1-4 : bond 0.00752 / 0.35 ( 6) link_BETA1-4 : angle 2.10225 / 1.26 ( 18) link_NAG-ASN : bond 0.00663 / 0.33 ( 8) link_NAG-ASN : angle 5.16770 / 2.85 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8106 (t0) cc_final: 0.6906 (t0) REVERT: A 222 TRP cc_start: 0.7799 (p90) cc_final: 0.7590 (p90) REVERT: B 29 LEU cc_start: 0.8697 (tt) cc_final: 0.8164 (tt) REVERT: B 157 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7584 (pp) REVERT: C 215 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7425 (ttt90) REVERT: C 256 GLU cc_start: 0.6731 (tp30) cc_final: 0.6217 (tp30) REVERT: D 33 MET cc_start: 0.6971 (tmm) cc_final: 0.6658 (tmm) REVERT: D 62 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.7416 (ttm-80) REVERT: D 109 ASN cc_start: 0.7989 (t0) cc_final: 0.7064 (t0) REVERT: D 280 MET cc_start: 0.7783 (tmm) cc_final: 0.7493 (tmm) REVERT: E 29 LEU cc_start: 0.8705 (tt) cc_final: 0.8173 (tt) REVERT: E 157 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7510 (pp) REVERT: F 256 GLU cc_start: 0.6400 (tp30) cc_final: 0.6097 (tp30) outliers start: 29 outliers final: 22 residues processed: 166 average time/residue: 0.1025 time to fit residues: 24.4175 Evaluate side-chains 157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143197 restraints weight = 14627.113| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.53 r_work: 0.3793 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10930 Z= 0.156 Angle : 0.748 11.564 14968 Z= 0.355 Chirality : 0.047 0.298 1708 Planarity : 0.005 0.040 1886 Dihedral : 6.206 56.749 1694 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.43 % Allowed : 18.61 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1308 helix: 0.96 (0.34), residues: 246 sheet: -0.36 (0.23), residues: 428 loop : -0.01 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 118 TYR 0.016 0.002 TYR A 8 PHE 0.028 0.002 PHE F 230 TRP 0.028 0.002 TRP D 222 HIS 0.003 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10904) covalent geometry : angle 0.71300 / 0.35 (14902) SS BOND : bond 0.00292 / 0.15 ( 12) SS BOND : angle 1.72434 / 0.96 ( 24) hydrogen bonds : bond 0.03947 / 2.62 ( 452) hydrogen bonds : angle 5.36240 / 3.77 ( 1266) link_BETA1-4 : bond 0.00753 / 0.35 ( 6) link_BETA1-4 : angle 2.00439 / 1.21 ( 18) link_NAG-ASN : bond 0.00671 / 0.33 ( 8) link_NAG-ASN : angle 5.19105 / 3.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8066 (t0) cc_final: 0.6886 (t0) REVERT: B 29 LEU cc_start: 0.8608 (tt) cc_final: 0.8102 (tt) REVERT: C 215 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7422 (ttt90) REVERT: C 256 GLU cc_start: 0.6634 (tp30) cc_final: 0.5967 (tp30) REVERT: D 62 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7345 (ttm-80) REVERT: D 109 ASN cc_start: 0.7968 (t0) cc_final: 0.7069 (t0) REVERT: D 280 MET cc_start: 0.7771 (tmm) cc_final: 0.7504 (tmm) REVERT: E 29 LEU cc_start: 0.8673 (tt) cc_final: 0.8130 (tt) REVERT: E 123 MET cc_start: 0.6406 (mmp) cc_final: 0.5590 (mmt) REVERT: F 256 GLU cc_start: 0.6432 (tp30) cc_final: 0.6180 (tp30) outliers start: 28 outliers final: 22 residues processed: 164 average time/residue: 0.0942 time to fit residues: 22.1408 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 89 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144735 restraints weight = 14669.337| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.47 r_work: 0.3809 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10930 Z= 0.149 Angle : 0.762 13.918 14968 Z= 0.357 Chirality : 0.048 0.287 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.213 56.585 1694 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.26 % Allowed : 18.96 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1308 helix: 0.94 (0.34), residues: 246 sheet: -0.33 (0.23), residues: 426 loop : -0.04 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 93 TYR 0.017 0.002 TYR C 122 PHE 0.035 0.002 PHE F 230 TRP 0.033 0.002 TRP A 222 HIS 0.003 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10904) covalent geometry : angle 0.72224 / 0.35 (14902) SS BOND : bond 0.00298 / 0.16 ( 12) SS BOND : angle 1.63529 / 0.92 ( 24) hydrogen bonds : bond 0.03895 / 2.59 ( 452) hydrogen bonds : angle 5.29660 / 3.73 ( 1266) link_BETA1-4 : bond 0.00767 / 0.35 ( 6) link_BETA1-4 : angle 1.91222 / 1.15 ( 18) link_NAG-ASN : bond 0.00669 / 0.33 ( 8) link_NAG-ASN : angle 5.76077 / 3.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8036 (t0) cc_final: 0.6864 (t0) REVERT: B 29 LEU cc_start: 0.8628 (tt) cc_final: 0.8167 (tt) REVERT: C 215 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7570 (ttt90) REVERT: C 256 GLU cc_start: 0.6571 (tp30) cc_final: 0.5913 (tp30) REVERT: D 33 MET cc_start: 0.7011 (tmm) cc_final: 0.6697 (tmm) REVERT: D 62 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7360 (ttp-110) REVERT: D 109 ASN cc_start: 0.7939 (t0) cc_final: 0.7008 (t0) REVERT: D 280 MET cc_start: 0.7678 (tmm) cc_final: 0.7428 (tmm) REVERT: E 29 LEU cc_start: 0.8631 (tt) cc_final: 0.8107 (tt) REVERT: E 123 MET cc_start: 0.6404 (mmp) cc_final: 0.5827 (mmt) REVERT: F 256 GLU cc_start: 0.6383 (tp30) cc_final: 0.6141 (tp30) outliers start: 26 outliers final: 22 residues processed: 162 average time/residue: 0.0963 time to fit residues: 22.4539 Evaluate side-chains 151 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 0.0670 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145539 restraints weight = 14467.751| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.46 r_work: 0.3822 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10930 Z= 0.142 Angle : 0.801 21.279 14968 Z= 0.371 Chirality : 0.051 0.645 1708 Planarity : 0.005 0.050 1886 Dihedral : 6.127 56.577 1694 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.09 % Allowed : 19.04 % Favored : 78.87 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1308 helix: 0.96 (0.34), residues: 246 sheet: -0.29 (0.24), residues: 412 loop : 0.00 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.020 0.002 TYR F 122 PHE 0.038 0.002 PHE C 230 TRP 0.035 0.002 TRP F 282 HIS 0.004 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10904) covalent geometry : angle 0.74250 / 0.36 (14902) SS BOND : bond 0.00420 / 0.27 ( 12) SS BOND : angle 1.71341 / 0.94 ( 24) hydrogen bonds : bond 0.03808 / 2.54 ( 452) hydrogen bonds : angle 5.24616 / 3.70 ( 1266) link_BETA1-4 : bond 0.00719 / 0.32 ( 6) link_BETA1-4 : angle 1.85698 / 1.11 ( 18) link_NAG-ASN : bond 0.00570 / 0.28 ( 8) link_NAG-ASN : angle 7.21265 / 3.91 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8000 (t0) cc_final: 0.6838 (t0) REVERT: B 29 LEU cc_start: 0.8622 (tt) cc_final: 0.8138 (tt) REVERT: C 215 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7575 (ttt90) REVERT: C 256 GLU cc_start: 0.6536 (tp30) cc_final: 0.5874 (tp30) REVERT: D 33 MET cc_start: 0.6971 (tmm) cc_final: 0.6668 (tmm) REVERT: D 109 ASN cc_start: 0.8057 (t0) cc_final: 0.7132 (t0) REVERT: D 280 MET cc_start: 0.7660 (tmm) cc_final: 0.7413 (tmm) REVERT: E 29 LEU cc_start: 0.8636 (tt) cc_final: 0.8106 (tt) REVERT: E 123 MET cc_start: 0.6345 (mmp) cc_final: 0.5764 (mmt) REVERT: F 121 ARG cc_start: 0.6348 (ttp80) cc_final: 0.6131 (ttp-110) REVERT: F 256 GLU cc_start: 0.6504 (tp30) cc_final: 0.6222 (tp30) outliers start: 24 outliers final: 21 residues processed: 158 average time/residue: 0.0845 time to fit residues: 19.2717 Evaluate side-chains 153 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 235 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 129 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.170285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.145361 restraints weight = 14584.299| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.52 r_work: 0.3818 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10930 Z= 0.142 Angle : 0.750 13.773 14968 Z= 0.353 Chirality : 0.047 0.304 1708 Planarity : 0.005 0.038 1886 Dihedral : 5.954 56.524 1694 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.17 % Allowed : 19.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1308 helix: 0.95 (0.34), residues: 246 sheet: -0.28 (0.24), residues: 412 loop : 0.03 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 118 TYR 0.017 0.002 TYR F 122 PHE 0.034 0.002 PHE C 230 TRP 0.034 0.002 TRP C 282 HIS 0.003 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (10904) covalent geometry : angle 0.71270 / 0.34 (14902) SS BOND : bond 0.00286 / 0.15 ( 12) SS BOND : angle 1.64900 / 0.92 ( 24) hydrogen bonds : bond 0.03772 / 2.52 ( 452) hydrogen bonds : angle 5.20565 / 3.66 ( 1266) link_BETA1-4 : bond 0.00788 / 0.36 ( 6) link_BETA1-4 : angle 1.80458 / 1.08 ( 18) link_NAG-ASN : bond 0.00687 / 0.34 ( 8) link_NAG-ASN : angle 5.47291 / 3.27 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2424.94 seconds wall clock time: 42 minutes 24.57 seconds (2544.57 seconds total)