Starting phenix.real_space_refine on Sun Dec 29 14:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dps_27641/12_2024/8dps_27641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dps_27641/12_2024/8dps_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dps_27641/12_2024/8dps_27641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dps_27641/12_2024/8dps_27641.map" model { file = "/net/cci-nas-00/data/ceres_data/8dps_27641/12_2024/8dps_27641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dps_27641/12_2024/8dps_27641.cif" } resolution = 3.47 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= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9 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, I, E, F, J Time building chain proxies: 7.22, per 1000 atoms: 0.68 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=6, 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 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: 3.12 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.33 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: 3.50 Time building geometry restraints manager: 3.54 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 - 19.09: 6173 19.09 - 38.18: 444 38.18 - 57.28: 71 57.28 - 76.37: 40 76.37 - 95.46: 10 Dihedral angle restraints: 6738 sinusoidal: 2874 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=" 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 dihedral pdb=" C PHE D 147 " pdb=" N PHE D 147 " pdb=" CA PHE D 147 " pdb=" CB PHE D 147 " ideal model delta harmonic sigma weight residual -122.60 -135.84 13.24 0 2.50e+00 1.60e-01 2.81e+01 ... (remaining 6735 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: 2.03 - 2.61: 171 2.61 - 3.18: 9545 3.18 - 3.75: 16222 3.75 - 4.33: 21957 4.33 - 4.90: 36625 Nonbonded interactions: 84520 Sorted by model distance: nonbonded pdb=" SG CYS F 148 " pdb=" SG CYS F 158 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS D 112 " pdb=" SG CYS D 122 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS D 6 " pdb=" SG CYS D 32 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS D 26 " pdb=" SG CYS D 81 " model vdw 2.040 3.760 nonbonded pdb=" SG CYS F 98 " pdb=" SG CYS F 108 " model vdw 2.040 3.760 ... (remaining 84515 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 '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: 0.010 Normalize map: mean=0, sd=1: 0.630 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.920 Find NCS groups from input model: 0.300 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 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 10904 Z= 0.494 Angle : 1.401 22.586 14902 Z= 0.742 Chirality : 0.081 0.897 1708 Planarity : 0.006 0.050 1886 Dihedral : 14.649 95.461 4216 Min Nonbonded Distance : 2.033 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 (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: -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 TRP 0.042 0.004 TRP A 45 HIS 0.008 0.002 HIS A 49 PHE 0.047 0.004 PHE F 230 TYR 0.021 0.004 TYR C 89 ARG 0.023 0.002 ARG C 121 *********************** 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 : 1.142 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: 0.7477 (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: 0.5590 (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: 0.2236 time to fit residues: 56.4601 Evaluate side-chains 124 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10904 Z= 0.271 Angle : 0.839 13.123 14902 Z= 0.408 Chirality : 0.049 0.266 1708 Planarity : 0.005 0.040 1886 Dihedral : 7.994 57.787 1736 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.96 % Allowed : 9.74 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.23 (0.22), residues: 1308 helix: 0.90 (0.30), residues: 264 sheet: 0.59 (0.24), residues: 408 loop : -0.39 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 222 HIS 0.005 0.001 HIS F 229 PHE 0.027 0.003 PHE F 106 TYR 0.025 0.002 TYR D 239 ARG 0.006 0.001 ARG D 259 *********************** 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 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7847 (t0) cc_final: 0.6996 (t0) REVERT: C 125 SER cc_start: 0.8080 (t) cc_final: 0.7717 (m) REVERT: C 151 ASP cc_start: 0.5219 (OUTLIER) cc_final: 0.4569 (m-30) REVERT: C 272 SER cc_start: 0.6334 (m) cc_final: 0.6069 (m) REVERT: D 33 MET cc_start: 0.6641 (tmm) cc_final: 0.6427 (tmm) REVERT: D 109 ASN cc_start: 0.7635 (t0) cc_final: 0.6392 (t0) REVERT: E 56 THR cc_start: 0.8042 (t) cc_final: 0.7790 (t) REVERT: F 151 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.4878 (m-30) REVERT: F 256 GLU cc_start: 0.6538 (tp30) cc_final: 0.6122 (tp30) outliers start: 11 outliers final: 4 residues processed: 181 average time/residue: 0.2407 time to fit residues: 60.6477 Evaluate side-chains 131 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 151 ASP 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 65 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10904 Z= 0.275 Angle : 0.747 10.510 14902 Z= 0.367 Chirality : 0.048 0.279 1708 Planarity : 0.005 0.044 1886 Dihedral : 6.520 57.627 1732 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.43 % Allowed : 12.70 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.40 (0.23), residues: 1308 helix: 1.07 (0.32), residues: 252 sheet: 0.48 (0.24), residues: 414 loop : -0.10 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 222 HIS 0.004 0.001 HIS C 229 PHE 0.025 0.002 PHE C 106 TYR 0.020 0.002 TYR D 239 ARG 0.006 0.001 ARG D 62 *********************** 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 165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 33 MET cc_start: 0.7047 (tmm) cc_final: 0.6822 (tmm) REVERT: A 109 ASN cc_start: 0.7869 (t0) cc_final: 0.7040 (t0) REVERT: B 42 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7669 (mtpp) REVERT: C 256 GLU cc_start: 0.6566 (tp30) cc_final: 0.6123 (tp30) REVERT: C 272 SER cc_start: 0.6486 (m) cc_final: 0.6270 (m) REVERT: D 109 ASN cc_start: 0.7714 (t0) cc_final: 0.6497 (t0) REVERT: D 296 SER cc_start: 0.7006 (m) cc_final: 0.6702 (p) REVERT: E 42 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7704 (mtpp) REVERT: E 56 THR cc_start: 0.8067 (t) cc_final: 0.7786 (t) REVERT: F 151 ASP cc_start: 0.5502 (OUTLIER) cc_final: 0.4935 (m-30) REVERT: F 256 GLU cc_start: 0.6450 (tp30) cc_final: 0.6081 (tp30) outliers start: 28 outliers final: 14 residues processed: 158 average time/residue: 0.2212 time to fit residues: 50.7002 Evaluate side-chains 135 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE 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 B residue 72 VAL 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 E residue 72 VAL Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS C 114 GLN ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 86 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10904 Z= 0.366 Angle : 0.785 11.007 14902 Z= 0.385 Chirality : 0.050 0.320 1708 Planarity : 0.005 0.043 1886 Dihedral : 6.661 57.243 1732 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.39 % Allowed : 13.04 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.00 (0.23), residues: 1308 helix: 0.76 (0.33), residues: 250 sheet: 0.05 (0.24), residues: 422 loop : -0.22 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 222 HIS 0.005 0.001 HIS B 49 PHE 0.026 0.002 PHE C 106 TYR 0.019 0.003 TYR A 57 ARG 0.006 0.001 ARG E 118 *********************** 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: 39 poor density : 131 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7052 (tmm) cc_final: 0.6752 (tmm) REVERT: A 96 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7244 (pt) REVERT: A 109 ASN cc_start: 0.7886 (t0) cc_final: 0.6657 (t0) REVERT: B 56 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7395 (t) REVERT: C 215 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7067 (ttt90) REVERT: C 256 GLU cc_start: 0.6444 (tp30) cc_final: 0.5963 (tp30) REVERT: D 96 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7267 (pt) REVERT: D 109 ASN cc_start: 0.7846 (t0) cc_final: 0.6876 (t0) REVERT: E 42 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7689 (mtpp) REVERT: E 56 THR cc_start: 0.7703 (OUTLIER) cc_final: 0.7436 (t) REVERT: F 151 ASP cc_start: 0.5900 (OUTLIER) cc_final: 0.4758 (m-30) REVERT: F 256 GLU cc_start: 0.6201 (tp30) cc_final: 0.5971 (tp30) outliers start: 39 outliers final: 27 residues processed: 159 average time/residue: 0.2287 time to fit residues: 52.0721 Evaluate side-chains 154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 A residue 299 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR 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 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 27 VAL 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 166 THR 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 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 151 ASP 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 104 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10904 Z= 0.216 Angle : 0.691 12.453 14902 Z= 0.336 Chirality : 0.047 0.324 1708 Planarity : 0.005 0.041 1886 Dihedral : 6.261 57.358 1732 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.04 % Allowed : 15.39 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.19 (0.24), residues: 1308 helix: 0.95 (0.34), residues: 250 sheet: 0.03 (0.24), residues: 422 loop : 0.00 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 222 HIS 0.003 0.001 HIS C 229 PHE 0.025 0.002 PHE C 230 TYR 0.017 0.002 TYR D 239 ARG 0.004 0.000 ARG B 118 *********************** 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 186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7927 (t0) cc_final: 0.6724 (t0) REVERT: B 29 LEU cc_start: 0.8603 (tt) cc_final: 0.8065 (tt) REVERT: B 56 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7400 (t) REVERT: B 157 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7556 (pp) REVERT: B 162 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7181 (mp) REVERT: C 215 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7220 (ttt90) REVERT: C 256 GLU cc_start: 0.6361 (tp30) cc_final: 0.5931 (tp30) REVERT: D 109 ASN cc_start: 0.7772 (t0) cc_final: 0.6461 (t0) REVERT: D 191 ASN cc_start: 0.7775 (t0) cc_final: 0.7571 (t0) REVERT: E 56 THR cc_start: 0.7688 (OUTLIER) cc_final: 0.7439 (t) REVERT: F 256 GLU cc_start: 0.6032 (tp30) cc_final: 0.5820 (tp30) outliers start: 35 outliers final: 25 residues processed: 173 average time/residue: 0.2299 time to fit residues: 56.7624 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 27 VAL 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 166 THR 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 56 THR 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 131 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10904 Z= 0.295 Angle : 0.726 10.915 14902 Z= 0.357 Chirality : 0.048 0.317 1708 Planarity : 0.005 0.041 1886 Dihedral : 6.423 56.671 1732 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.39 % Allowed : 16.96 % 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 (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: 0.02 (0.24), residues: 1308 helix: 0.92 (0.34), residues: 250 sheet: -0.21 (0.24), residues: 424 loop : -0.04 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 291 HIS 0.006 0.001 HIS C 229 PHE 0.021 0.002 PHE C 230 TYR 0.017 0.002 TYR A 8 ARG 0.007 0.001 ARG A 62 *********************** 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 178 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7009 (tmm) cc_final: 0.6670 (tmm) REVERT: A 62 ARG cc_start: 0.7405 (mtp-110) cc_final: 0.6853 (ttm-80) REVERT: A 109 ASN cc_start: 0.7978 (t0) cc_final: 0.6754 (t0) REVERT: B 29 LEU cc_start: 0.8566 (tt) cc_final: 0.8208 (tt) REVERT: B 56 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7431 (t) REVERT: B 157 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7586 (pp) REVERT: C 215 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7292 (ttt90) REVERT: C 256 GLU cc_start: 0.6461 (tp30) cc_final: 0.5990 (tp30) REVERT: D 62 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.6902 (ttm-80) REVERT: D 109 ASN cc_start: 0.7840 (t0) cc_final: 0.6861 (t0) REVERT: E 56 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7478 (t) REVERT: E 157 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7540 (pp) REVERT: E 162 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7266 (mp) REVERT: F 256 GLU cc_start: 0.6121 (tp30) cc_final: 0.5883 (tp30) outliers start: 39 outliers final: 29 residues processed: 169 average time/residue: 0.2266 time to fit residues: 54.7447 Evaluate side-chains 161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 67 LEU 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 27 VAL 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 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 109 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 0.0970 chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10904 Z= 0.241 Angle : 0.695 10.289 14902 Z= 0.341 Chirality : 0.047 0.271 1708 Planarity : 0.005 0.040 1886 Dihedral : 6.257 56.911 1732 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.39 % Allowed : 18.00 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.08 (0.24), residues: 1308 helix: 1.06 (0.34), residues: 246 sheet: -0.27 (0.24), residues: 424 loop : 0.04 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 222 HIS 0.005 0.001 HIS C 229 PHE 0.024 0.002 PHE F 230 TYR 0.016 0.002 TYR D 8 ARG 0.006 0.000 ARG A 128 *********************** 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 182 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7016 (tmm) cc_final: 0.6671 (tmm) REVERT: A 109 ASN cc_start: 0.7854 (t0) cc_final: 0.6646 (t0) REVERT: A 222 TRP cc_start: 0.7753 (p90) cc_final: 0.7549 (p90) REVERT: B 29 LEU cc_start: 0.8450 (tt) cc_final: 0.7977 (tt) REVERT: B 56 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7402 (t) REVERT: B 157 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7473 (pp) REVERT: C 215 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7265 (ttt90) REVERT: C 256 GLU cc_start: 0.6383 (tp30) cc_final: 0.5763 (tp30) REVERT: D 62 ARG cc_start: 0.7483 (mtp-110) cc_final: 0.7272 (ptm160) REVERT: D 109 ASN cc_start: 0.7821 (t0) cc_final: 0.6847 (t0) REVERT: E 56 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7478 (t) REVERT: E 157 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7249 (pp) REVERT: F 256 GLU cc_start: 0.6060 (tp30) cc_final: 0.5814 (tp30) outliers start: 39 outliers final: 28 residues processed: 171 average time/residue: 0.2299 time to fit residues: 55.3452 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 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 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 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 160 VAL 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 50 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10904 Z= 0.247 Angle : 0.716 10.751 14902 Z= 0.349 Chirality : 0.048 0.303 1708 Planarity : 0.005 0.041 1886 Dihedral : 6.366 56.614 1732 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.22 % Allowed : 18.35 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.00 (0.24), residues: 1308 helix: 1.04 (0.34), residues: 246 sheet: -0.32 (0.24), residues: 426 loop : -0.02 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 291 HIS 0.003 0.001 HIS E 49 PHE 0.029 0.002 PHE F 230 TYR 0.017 0.002 TYR A 8 ARG 0.006 0.000 ARG A 128 *********************** 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: 37 poor density : 133 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7842 (t0) cc_final: 0.6644 (t0) REVERT: A 222 TRP cc_start: 0.7783 (p90) cc_final: 0.7561 (p90) REVERT: B 29 LEU cc_start: 0.8484 (tt) cc_final: 0.8026 (tt) REVERT: B 56 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7316 (t) REVERT: B 157 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (pp) REVERT: C 215 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7284 (ttt90) REVERT: C 256 GLU cc_start: 0.6409 (tp30) cc_final: 0.5777 (tp30) REVERT: D 62 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7129 (ttm-80) REVERT: D 109 ASN cc_start: 0.7803 (t0) cc_final: 0.6828 (t0) REVERT: E 56 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7493 (t) REVERT: E 157 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7234 (pp) REVERT: F 256 GLU cc_start: 0.6120 (tp30) cc_final: 0.5913 (tp30) outliers start: 37 outliers final: 27 residues processed: 161 average time/residue: 0.2221 time to fit residues: 51.2605 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 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 27 VAL 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 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 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 109 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 50 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10904 Z= 0.205 Angle : 0.696 10.646 14902 Z= 0.338 Chirality : 0.047 0.321 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.348 56.679 1732 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.78 % Allowed : 18.78 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.24), residues: 1308 helix: 1.12 (0.34), residues: 246 sheet: -0.26 (0.24), residues: 416 loop : 0.07 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 222 HIS 0.004 0.001 HIS F 229 PHE 0.039 0.002 PHE F 230 TYR 0.017 0.001 TYR D 8 ARG 0.007 0.000 ARG A 128 *********************** 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 169 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6771 (tmm) cc_final: 0.6481 (tmm) REVERT: A 109 ASN cc_start: 0.7803 (t0) cc_final: 0.6622 (t0) REVERT: B 29 LEU cc_start: 0.8452 (tt) cc_final: 0.8002 (tt) REVERT: B 56 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7307 (t) REVERT: B 118 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7807 (tpp80) REVERT: C 256 GLU cc_start: 0.6341 (tp30) cc_final: 0.5704 (tp30) REVERT: D 62 ARG cc_start: 0.7464 (mtp-110) cc_final: 0.7218 (ttp-110) REVERT: D 109 ASN cc_start: 0.7933 (t0) cc_final: 0.6612 (t0) REVERT: E 56 THR cc_start: 0.7695 (OUTLIER) cc_final: 0.7471 (t) REVERT: F 256 GLU cc_start: 0.6070 (tp30) cc_final: 0.5855 (tp30) outliers start: 32 outliers final: 26 residues processed: 160 average time/residue: 0.2292 time to fit residues: 52.1704 Evaluate side-chains 156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 THR Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 56 THR 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 D residue 21 ASN Chi-restraints excluded: chain D residue 27 VAL 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 56 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP 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 75 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 109 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10904 Z= 0.209 Angle : 0.703 10.442 14902 Z= 0.338 Chirality : 0.046 0.256 1708 Planarity : 0.005 0.038 1886 Dihedral : 6.355 56.565 1732 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.52 % Allowed : 19.48 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.17 (0.24), residues: 1308 helix: 1.13 (0.34), residues: 246 sheet: -0.18 (0.24), residues: 410 loop : 0.06 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 222 HIS 0.005 0.001 HIS F 229 PHE 0.034 0.002 PHE C 230 TYR 0.017 0.002 TYR F 122 ARG 0.007 0.000 ARG A 128 ********************** 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 156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 33 MET cc_start: 0.6779 (tmm) cc_final: 0.6496 (tmm) REVERT: A 109 ASN cc_start: 0.7782 (t0) cc_final: 0.6610 (t0) REVERT: B 29 LEU cc_start: 0.8474 (tt) cc_final: 0.8022 (tt) REVERT: B 56 THR cc_start: 0.7526 (OUTLIER) cc_final: 0.7316 (t) REVERT: C 256 GLU cc_start: 0.5998 (tp30) cc_final: 0.5494 (tp30) REVERT: D 62 ARG cc_start: 0.7476 (mtp-110) cc_final: 0.7243 (ttp-110) REVERT: D 109 ASN cc_start: 0.7930 (t0) cc_final: 0.6626 (t0) REVERT: E 56 THR cc_start: 0.7686 (OUTLIER) cc_final: 0.7453 (t) REVERT: F 256 GLU cc_start: 0.6221 (tp30) cc_final: 0.5962 (tp30) outliers start: 29 outliers final: 25 residues processed: 149 average time/residue: 0.2244 time to fit residues: 48.4474 Evaluate side-chains 150 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 41 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 LEU 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 E residue 56 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 151 ASP 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 31 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.143451 restraints weight = 14389.209| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.61 r_work: 0.3794 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10904 Z= 0.220 Angle : 0.706 10.324 14902 Z= 0.338 Chirality : 0.046 0.301 1708 Planarity : 0.005 0.038 1886 Dihedral : 6.374 56.452 1732 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.61 % Allowed : 19.65 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.18 (0.24), residues: 1308 helix: 1.13 (0.34), residues: 246 sheet: -0.21 (0.24), residues: 412 loop : 0.10 (0.27), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 222 HIS 0.004 0.001 HIS F 229 PHE 0.029 0.002 PHE F 230 TYR 0.017 0.002 TYR D 8 ARG 0.007 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.10 seconds wall clock time: 42 minutes 59.89 seconds (2579.89 seconds total)