Starting phenix.real_space_refine on Mon Jul 28 22:22:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dps_27641/07_2025/8dps_27641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dps_27641/07_2025/8dps_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_27641/07_2025/8dps_27641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2025/8dps_27641.map" model { file = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2025/8dps_27641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dps_27641/07_2025/8dps_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.39, per 1000 atoms: 0.70 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: 3.28 Conformation dependent library (CDL) restraints added in 1.4 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: 1.76 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: 3.07 Time building geometry restraints manager: 3.81 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: 6180 19.09 - 38.18: 450 38.18 - 57.28: 76 57.28 - 76.37: 40 76.37 - 95.46: 10 Dihedral angle restraints: 6756 sinusoidal: 2892 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 6753 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 0.930 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.050 Find NCS groups from input model: 0.190 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.720 ------------------------------------------------------------------------------- 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 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 : 14.649 95.461 4216 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.02228 ( 8) link_NAG-ASN : angle 28.79182 ( 24) link_BETA1-4 : bond 0.00954 ( 6) link_BETA1-4 : angle 2.55199 ( 18) hydrogen bonds : bond 0.23379 ( 452) hydrogen bonds : angle 8.03459 ( 1266) SS BOND : bond 0.00839 ( 12) SS BOND : angle 3.73599 ( 24) covalent geometry : bond 0.00755 (10904) covalent geometry : angle 1.40053 (14902) *********************** 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 : 1.212 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: 0.2143 time to fit residues: 54.7824 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 : 1.078 ------------------------------------------------------------------------------- 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: 3.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150039 restraints weight = 14316.137| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.52 r_work: 0.3862 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10930 Z= 0.195 Angle : 0.924 18.116 14968 Z= 0.434 Chirality : 0.050 0.275 1708 Planarity : 0.005 0.041 1886 Dihedral : 8.306 58.774 1736 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.96 % Allowed : 9.13 % Favored : 89.91 % 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 (0.22), residues: 1308 helix: 0.93 (0.30), residues: 264 sheet: 0.55 (0.23), residues: 408 loop : -0.44 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 222 HIS 0.004 0.001 HIS A 19 PHE 0.026 0.002 PHE F 106 TYR 0.024 0.002 TYR D 239 ARG 0.007 0.001 ARG D 154 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 8) link_NAG-ASN : angle 7.73896 ( 24) link_BETA1-4 : bond 0.01038 ( 6) link_BETA1-4 : angle 2.35656 ( 18) hydrogen bonds : bond 0.05908 ( 452) hydrogen bonds : angle 6.09851 ( 1266) SS BOND : bond 0.00491 ( 12) SS BOND : angle 2.33600 ( 24) covalent geometry : bond 0.00432 (10904) covalent geometry : angle 0.86303 (14902) *********************** 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 185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 109 ASN cc_start: 0.7894 (t0) cc_final: 0.7165 (t0) REVERT: C 125 SER cc_start: 0.8296 (t) cc_final: 0.7954 (m) REVERT: C 151 ASP cc_start: 0.5087 (OUTLIER) cc_final: 0.4446 (m-30) REVERT: C 272 SER cc_start: 0.6505 (m) cc_final: 0.6253 (m) REVERT: D 33 MET cc_start: 0.6407 (tmm) cc_final: 0.6200 (tmm) REVERT: F 99 GLN cc_start: 0.5951 (pm20) cc_final: 0.5528 (pm20) REVERT: F 256 GLU cc_start: 0.6877 (tp30) cc_final: 0.6373 (tp30) outliers start: 11 outliers final: 6 residues processed: 180 average time/residue: 0.2636 time to fit residues: 66.7204 Evaluate side-chains 137 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 66 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145175 restraints weight = 14712.676| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.53 r_work: 0.3810 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2342 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= 0.184 Angle : 0.801 15.664 14968 Z= 0.381 Chirality : 0.048 0.273 1708 Planarity : 0.005 0.043 1886 Dihedral : 6.640 57.699 1732 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.26 % Allowed : 12.26 % Favored : 85.48 % 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: 0.35 (0.23), residues: 1308 helix: 1.04 (0.32), residues: 252 sheet: 0.42 (0.23), residues: 414 loop : -0.11 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 222 HIS 0.005 0.001 HIS F 161 PHE 0.026 0.002 PHE C 106 TYR 0.020 0.002 TYR D 239 ARG 0.006 0.001 ARG D 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 8) link_NAG-ASN : angle 6.23338 ( 24) link_BETA1-4 : bond 0.00831 ( 6) link_BETA1-4 : angle 2.33675 ( 18) hydrogen bonds : bond 0.04771 ( 452) hydrogen bonds : angle 5.77364 ( 1266) SS BOND : bond 0.00628 ( 12) SS BOND : angle 1.64693 ( 24) covalent geometry : bond 0.00419 (10904) covalent geometry : angle 0.75564 (14902) *********************** 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 167 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 33 MET cc_start: 0.7155 (tmm) cc_final: 0.6952 (tmm) REVERT: A 109 ASN cc_start: 0.7977 (t0) cc_final: 0.7212 (t0) REVERT: A 177 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 42 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7753 (mtpp) REVERT: C 188 VAL cc_start: 0.8373 (t) cc_final: 0.8136 (t) REVERT: C 193 ILE cc_start: 0.8131 (tp) cc_final: 0.7861 (tt) REVERT: C 256 GLU cc_start: 0.6834 (tp30) cc_final: 0.6303 (tp30) REVERT: C 272 SER cc_start: 0.6702 (m) cc_final: 0.6471 (m) REVERT: D 109 ASN cc_start: 0.7860 (t0) cc_final: 0.7051 (t0) REVERT: D 296 SER cc_start: 0.7221 (m) cc_final: 0.6910 (p) REVERT: E 42 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7784 (mtpp) REVERT: F 99 GLN cc_start: 0.5954 (pm20) cc_final: 0.5414 (pm20) REVERT: F 188 VAL cc_start: 0.8471 (t) cc_final: 0.8266 (t) REVERT: F 256 GLU cc_start: 0.6777 (tp30) cc_final: 0.6322 (tp30) outliers start: 26 outliers final: 13 residues processed: 160 average time/residue: 0.2295 time to fit residues: 52.3317 Evaluate side-chains 140 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 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 59 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 F residue 183 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 55 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 HIS ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145577 restraints weight = 14541.315| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.52 r_work: 0.3819 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2818 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= 0.153 Angle : 0.733 13.934 14968 Z= 0.349 Chirality : 0.046 0.259 1708 Planarity : 0.005 0.040 1886 Dihedral : 6.171 57.086 1732 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.61 % Allowed : 13.04 % Favored : 84.35 % 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: 0.33 (0.24), residues: 1308 helix: 1.10 (0.33), residues: 252 sheet: 0.09 (0.23), residues: 426 loop : 0.08 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 222 HIS 0.003 0.001 HIS C 229 PHE 0.022 0.002 PHE C 106 TYR 0.018 0.002 TYR D 239 ARG 0.008 0.001 ARG E 118 Details of bonding type rmsd link_NAG-ASN : bond 0.01070 ( 8) link_NAG-ASN : angle 5.58227 ( 24) link_BETA1-4 : bond 0.00735 ( 6) link_BETA1-4 : angle 1.77100 ( 18) hydrogen bonds : bond 0.04117 ( 452) hydrogen bonds : angle 5.45776 ( 1266) SS BOND : bond 0.00462 ( 12) SS BOND : angle 1.63082 ( 24) covalent geometry : bond 0.00349 (10904) covalent geometry : angle 0.69369 (14902) *********************** 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 185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 33 MET cc_start: 0.7114 (tmm) cc_final: 0.6851 (tmm) REVERT: A 109 ASN cc_start: 0.8018 (t0) cc_final: 0.6912 (t0) REVERT: B 42 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7674 (mtpp) REVERT: C 114 GLN cc_start: 0.8380 (mt0) cc_final: 0.8109 (mt0) REVERT: C 188 VAL cc_start: 0.8388 (t) cc_final: 0.8135 (t) REVERT: C 193 ILE cc_start: 0.8092 (tp) cc_final: 0.7887 (tt) REVERT: C 215 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7223 (ttt90) REVERT: C 256 GLU cc_start: 0.6548 (tp30) cc_final: 0.5987 (tp30) REVERT: D 109 ASN cc_start: 0.7904 (t0) cc_final: 0.6730 (t0) REVERT: D 191 ASN cc_start: 0.8108 (t0) cc_final: 0.7893 (t0) REVERT: E 42 LYS cc_start: 0.7953 (mtpp) cc_final: 0.7700 (mtpp) REVERT: F 99 GLN cc_start: 0.6027 (pm20) cc_final: 0.5400 (pm20) REVERT: F 188 VAL cc_start: 0.8396 (t) cc_final: 0.8173 (t) REVERT: F 256 GLU cc_start: 0.6468 (tp30) cc_final: 0.6161 (tp30) outliers start: 30 outliers final: 23 residues processed: 175 average time/residue: 0.2229 time to fit residues: 55.5545 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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 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 166 THR Chi-restraints excluded: chain D residue 235 TYR 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 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 106 optimal weight: 0.0170 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 15 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 120 GLN ** 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 = 0.4217 r_free = 0.4217 target = 0.172877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.148472 restraints weight = 14495.810| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.53 r_work: 0.3858 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10930 Z= 0.126 Angle : 0.708 13.639 14968 Z= 0.334 Chirality : 0.046 0.254 1708 Planarity : 0.004 0.039 1886 Dihedral : 6.026 57.026 1732 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.43 % Allowed : 14.61 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.24), residues: 1308 helix: 1.18 (0.34), residues: 252 sheet: 0.17 (0.24), residues: 420 loop : 0.14 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 222 HIS 0.006 0.001 HIS F 229 PHE 0.023 0.002 PHE F 230 TYR 0.016 0.001 TYR D 239 ARG 0.006 0.000 ARG A 62 Details of bonding type rmsd link_NAG-ASN : bond 0.01189 ( 8) link_NAG-ASN : angle 5.52857 ( 24) link_BETA1-4 : bond 0.00792 ( 6) link_BETA1-4 : angle 1.75699 ( 18) hydrogen bonds : bond 0.03834 ( 452) hydrogen bonds : angle 5.36030 ( 1266) SS BOND : bond 0.00281 ( 12) SS BOND : angle 1.61348 ( 24) covalent geometry : bond 0.00278 (10904) covalent geometry : angle 0.66824 (14902) *********************** 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 185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7105 (tmm) cc_final: 0.6846 (tmm) REVERT: A 62 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7009 (ttm-80) REVERT: A 109 ASN cc_start: 0.7973 (t0) cc_final: 0.7204 (t0) REVERT: B 42 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7559 (mtpp) REVERT: C 215 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7332 (ttt90) REVERT: C 256 GLU cc_start: 0.6722 (tp30) cc_final: 0.6202 (tp30) REVERT: C 272 SER cc_start: 0.6368 (m) cc_final: 0.6138 (t) REVERT: D 62 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7388 (ptm160) REVERT: D 109 ASN cc_start: 0.8003 (t0) cc_final: 0.7157 (t0) REVERT: D 188 ASP cc_start: 0.7378 (m-30) cc_final: 0.7130 (t0) REVERT: E 42 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7699 (mtpp) REVERT: F 99 GLN cc_start: 0.6073 (pm20) cc_final: 0.5448 (pm20) REVERT: F 256 GLU cc_start: 0.6566 (tp30) cc_final: 0.6244 (tp30) REVERT: F 272 SER cc_start: 0.6299 (m) cc_final: 0.6099 (m) outliers start: 28 outliers final: 24 residues processed: 178 average time/residue: 0.2490 time to fit residues: 64.4958 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 : 1.270 ------------------------------------------------------------------------------- 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 B residue 41 ASP 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 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 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 72 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 39 optimal weight: 0.7980 chunk 63 optimal weight: 0.0060 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS ** D 41 ASN ** 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 = 0.4126 r_free = 0.4126 target = 0.164283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.140399 restraints weight = 14713.598| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.44 r_work: 0.3758 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10930 Z= 0.236 Angle : 0.807 12.034 14968 Z= 0.385 Chirality : 0.049 0.271 1708 Planarity : 0.005 0.042 1886 Dihedral : 6.447 56.683 1732 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.22 % Allowed : 16.52 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.33), residues: 258 sheet: -0.22 (0.24), residues: 410 loop : -0.11 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 222 HIS 0.004 0.001 HIS B 49 PHE 0.028 0.003 PHE F 106 TYR 0.017 0.002 TYR A 8 ARG 0.006 0.001 ARG D 276 Details of bonding type rmsd link_NAG-ASN : bond 0.00706 ( 8) link_NAG-ASN : angle 5.63297 ( 24) link_BETA1-4 : bond 0.00861 ( 6) link_BETA1-4 : angle 1.89839 ( 18) hydrogen bonds : bond 0.04402 ( 452) hydrogen bonds : angle 5.49963 ( 1266) SS BOND : bond 0.00390 ( 12) SS BOND : angle 1.66322 ( 24) covalent geometry : bond 0.00555 (10904) covalent geometry : angle 0.77069 (14902) *********************** 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 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8064 (t0) cc_final: 0.6947 (t0) REVERT: C 215 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7318 (ttt90) REVERT: C 256 GLU cc_start: 0.6751 (tp30) cc_final: 0.6241 (tp30) REVERT: D 62 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7287 (ttm-80) REVERT: D 109 ASN cc_start: 0.7976 (t0) cc_final: 0.6744 (t0) REVERT: E 42 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7622 (mtpp) REVERT: F 99 GLN cc_start: 0.6124 (pm20) cc_final: 0.5496 (pm20) REVERT: F 256 GLU cc_start: 0.6431 (tp30) cc_final: 0.6143 (tp30) REVERT: F 272 SER cc_start: 0.6439 (m) cc_final: 0.6225 (m) outliers start: 37 outliers final: 29 residues processed: 168 average time/residue: 0.2047 time to fit residues: 49.5952 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 41 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 VAL 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 131 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 26 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 3 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: ** 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 = 0.4171 r_free = 0.4171 target = 0.168312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.143860 restraints weight = 14827.944| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.54 r_work: 0.3801 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10930 Z= 0.149 Angle : 0.736 11.840 14968 Z= 0.351 Chirality : 0.046 0.285 1708 Planarity : 0.005 0.039 1886 Dihedral : 6.208 56.937 1732 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.78 % Allowed : 17.39 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.24), residues: 1308 helix: 0.77 (0.34), residues: 258 sheet: -0.22 (0.24), residues: 412 loop : -0.03 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 222 HIS 0.003 0.001 HIS F 229 PHE 0.031 0.002 PHE F 230 TYR 0.017 0.002 TYR D 8 ARG 0.006 0.000 ARG A 128 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 8) link_NAG-ASN : angle 5.25958 ( 24) link_BETA1-4 : bond 0.00733 ( 6) link_BETA1-4 : angle 1.73229 ( 18) hydrogen bonds : bond 0.03959 ( 452) hydrogen bonds : angle 5.37925 ( 1266) SS BOND : bond 0.00279 ( 12) SS BOND : angle 1.74401 ( 24) covalent geometry : bond 0.00343 (10904) covalent geometry : angle 0.70104 (14902) *********************** 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 173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6650 (tmm) cc_final: 0.6409 (tmm) REVERT: A 109 ASN cc_start: 0.8039 (t0) cc_final: 0.6928 (t0) REVERT: B 29 LEU cc_start: 0.8736 (tt) cc_final: 0.8202 (tt) REVERT: C 215 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7386 (ttt90) REVERT: C 256 GLU cc_start: 0.6682 (tp30) cc_final: 0.6171 (tp30) REVERT: D 33 MET cc_start: 0.6849 (tmm) cc_final: 0.6568 (tmm) REVERT: D 62 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7570 (ttm-80) REVERT: D 109 ASN cc_start: 0.7974 (t0) cc_final: 0.6772 (t0) REVERT: E 42 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7524 (mtpp) REVERT: F 99 GLN cc_start: 0.6149 (pm20) cc_final: 0.5496 (pm20) REVERT: F 256 GLU cc_start: 0.6502 (tp30) cc_final: 0.6167 (tp30) outliers start: 32 outliers final: 28 residues processed: 166 average time/residue: 0.2312 time to fit residues: 54.4349 Evaluate side-chains 159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 41 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 VAL 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 72 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 5 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.4187 r_free = 0.4187 target = 0.169503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144747 restraints weight = 14468.663| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.51 r_work: 0.3811 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10930 Z= 0.146 Angle : 0.730 11.405 14968 Z= 0.349 Chirality : 0.046 0.276 1708 Planarity : 0.005 0.038 1886 Dihedral : 6.185 56.699 1732 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.04 % Allowed : 17.39 % Favored : 79.57 % 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: 0.02 (0.24), residues: 1308 helix: 0.82 (0.34), residues: 258 sheet: -0.25 (0.24), residues: 404 loop : 0.01 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 222 HIS 0.003 0.001 HIS F 229 PHE 0.029 0.002 PHE F 230 TYR 0.016 0.002 TYR A 8 ARG 0.006 0.000 ARG A 128 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 8) link_NAG-ASN : angle 5.17482 ( 24) link_BETA1-4 : bond 0.00730 ( 6) link_BETA1-4 : angle 1.68666 ( 18) hydrogen bonds : bond 0.03891 ( 452) hydrogen bonds : angle 5.31113 ( 1266) SS BOND : bond 0.00309 ( 12) SS BOND : angle 1.60420 ( 24) covalent geometry : bond 0.00337 (10904) covalent geometry : angle 0.69600 (14902) *********************** 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 174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6698 (tmm) cc_final: 0.6441 (tmm) REVERT: A 109 ASN cc_start: 0.8018 (t0) cc_final: 0.6885 (t0) REVERT: B 29 LEU cc_start: 0.8766 (tt) cc_final: 0.8230 (tt) REVERT: C 215 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7393 (ttt90) REVERT: C 256 GLU cc_start: 0.6572 (tp30) cc_final: 0.5899 (tp30) REVERT: D 62 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7586 (ttm-80) REVERT: D 109 ASN cc_start: 0.8055 (t0) cc_final: 0.6803 (t0) REVERT: F 99 GLN cc_start: 0.6111 (pm20) cc_final: 0.5423 (pm20) REVERT: F 256 GLU cc_start: 0.6552 (tp30) cc_final: 0.6244 (tp30) outliers start: 35 outliers final: 30 residues processed: 168 average time/residue: 0.2979 time to fit residues: 71.4972 Evaluate side-chains 160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 41 ASP 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 96 VAL Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 VAL 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 72 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 0.0040 chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.5854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 ASN ** 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 = 0.4204 r_free = 0.4204 target = 0.171061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.145903 restraints weight = 14676.219| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.59 r_work: 0.3824 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3688 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= 0.137 Angle : 0.737 14.142 14968 Z= 0.349 Chirality : 0.047 0.316 1708 Planarity : 0.004 0.037 1886 Dihedral : 6.155 56.607 1732 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.78 % Allowed : 18.00 % Favored : 79.22 % 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: 0.09 (0.24), residues: 1308 helix: 0.83 (0.33), residues: 258 sheet: -0.16 (0.24), residues: 404 loop : 0.04 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 282 HIS 0.002 0.001 HIS F 229 PHE 0.030 0.002 PHE C 230 TYR 0.015 0.001 TYR A 8 ARG 0.007 0.000 ARG C 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 8) link_NAG-ASN : angle 5.77627 ( 24) link_BETA1-4 : bond 0.00729 ( 6) link_BETA1-4 : angle 1.59737 ( 18) hydrogen bonds : bond 0.03781 ( 452) hydrogen bonds : angle 5.20993 ( 1266) SS BOND : bond 0.00299 ( 12) SS BOND : angle 1.58459 ( 24) covalent geometry : bond 0.00312 (10904) covalent geometry : angle 0.69641 (14902) *********************** 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 171 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6851 (tmm) cc_final: 0.6604 (tmm) REVERT: A 109 ASN cc_start: 0.7994 (t0) cc_final: 0.6867 (t0) REVERT: B 29 LEU cc_start: 0.8760 (tt) cc_final: 0.8206 (tt) REVERT: C 215 ARG cc_start: 0.7947 (ttp80) cc_final: 0.7578 (ttt90) REVERT: C 256 GLU cc_start: 0.6562 (tp30) cc_final: 0.5858 (tp30) REVERT: D 33 MET cc_start: 0.6854 (tmm) cc_final: 0.6598 (tmm) REVERT: D 62 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7681 (ttm-80) REVERT: D 109 ASN cc_start: 0.8030 (t0) cc_final: 0.6789 (t0) REVERT: E 38 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8293 (tt0) REVERT: F 99 GLN cc_start: 0.5952 (pm20) cc_final: 0.5268 (pm20) REVERT: F 121 ARG cc_start: 0.6379 (ttp80) cc_final: 0.6077 (ttp-110) REVERT: F 256 GLU cc_start: 0.6570 (tp30) cc_final: 0.6254 (tp30) outliers start: 32 outliers final: 27 residues processed: 165 average time/residue: 0.2579 time to fit residues: 60.8713 Evaluate side-chains 158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 41 ASP Chi-restraints excluded: chain B residue 69 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 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 VAL 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 72 VAL 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 57 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 97 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4183 r_free = 0.4183 target = 0.168792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144131 restraints weight = 14629.927| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.52 r_work: 0.3809 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10930 Z= 0.167 Angle : 0.791 19.609 14968 Z= 0.373 Chirality : 0.052 0.693 1708 Planarity : 0.005 0.066 1886 Dihedral : 6.287 56.400 1732 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.70 % Allowed : 18.35 % Favored : 78.96 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.03 (0.24), residues: 1308 helix: 0.77 (0.33), residues: 258 sheet: -0.28 (0.24), residues: 404 loop : -0.02 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 282 HIS 0.003 0.001 HIS E 49 PHE 0.036 0.002 PHE C 230 TYR 0.021 0.002 TYR C 122 ARG 0.007 0.000 ARG A 128 Details of bonding type rmsd link_NAG-ASN : bond 0.01024 ( 8) link_NAG-ASN : angle 6.76766 ( 24) link_BETA1-4 : bond 0.00749 ( 6) link_BETA1-4 : angle 1.64964 ( 18) hydrogen bonds : bond 0.03888 ( 452) hydrogen bonds : angle 5.26688 ( 1266) SS BOND : bond 0.00314 ( 12) SS BOND : angle 1.68695 ( 24) covalent geometry : bond 0.00388 (10904) covalent geometry : angle 0.73921 (14902) ********************** 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 166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.7006 (tmm) cc_final: 0.6713 (tmm) REVERT: A 109 ASN cc_start: 0.8000 (t0) cc_final: 0.6872 (t0) REVERT: B 29 LEU cc_start: 0.8797 (tt) cc_final: 0.8278 (tt) REVERT: B 157 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7711 (pp) REVERT: C 215 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7399 (ttt90) REVERT: C 256 GLU cc_start: 0.6552 (tp30) cc_final: 0.5883 (tp30) REVERT: D 33 MET cc_start: 0.6967 (tmm) cc_final: 0.6693 (tmm) REVERT: D 62 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7635 (ttm-80) REVERT: D 109 ASN cc_start: 0.8064 (t0) cc_final: 0.6826 (t0) REVERT: F 99 GLN cc_start: 0.6008 (pm20) cc_final: 0.5375 (pm20) REVERT: F 121 ARG cc_start: 0.6487 (ttp80) cc_final: 0.6174 (ttp-110) REVERT: F 256 GLU cc_start: 0.6537 (tp30) cc_final: 0.6238 (tp30) REVERT: F 257 VAL cc_start: 0.7666 (OUTLIER) cc_final: 0.6866 (m) outliers start: 31 outliers final: 28 residues processed: 162 average time/residue: 0.2645 time to fit residues: 60.8532 Evaluate side-chains 156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 41 ASP Chi-restraints excluded: chain B residue 69 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 131 VAL Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 188 VAL 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 72 VAL Chi-restraints excluded: chain F residue 131 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 Chi-restraints excluded: chain F residue 257 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4204 r_free = 0.4204 target = 0.170799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.146564 restraints weight = 14378.778| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.42 r_work: 0.3838 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10930 Z= 0.143 Angle : 0.753 13.794 14968 Z= 0.356 Chirality : 0.047 0.297 1708 Planarity : 0.005 0.037 1886 Dihedral : 6.025 56.502 1732 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.70 % Allowed : 18.96 % Favored : 78.35 % 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: 0.79 (0.33), residues: 258 sheet: -0.28 (0.24), residues: 404 loop : 0.02 (0.27), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 291 HIS 0.002 0.001 HIS B 161 PHE 0.032 0.002 PHE C 230 TYR 0.017 0.002 TYR C 122 ARG 0.007 0.000 ARG A 128 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 8) link_NAG-ASN : angle 5.34995 ( 24) link_BETA1-4 : bond 0.00680 ( 6) link_BETA1-4 : angle 1.56170 ( 18) hydrogen bonds : bond 0.03814 ( 452) hydrogen bonds : angle 5.21684 ( 1266) SS BOND : bond 0.00304 ( 12) SS BOND : angle 1.62958 ( 24) covalent geometry : bond 0.00326 (10904) covalent geometry : angle 0.71852 (14902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6227.71 seconds wall clock time: 113 minutes 35.47 seconds (6815.47 seconds total)