Starting phenix.real_space_refine on Tue May 13 04:24:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctu_45919/05_2025/9ctu_45919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctu_45919/05_2025/9ctu_45919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctu_45919/05_2025/9ctu_45919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctu_45919/05_2025/9ctu_45919.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctu_45919/05_2025/9ctu_45919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctu_45919/05_2025/9ctu_45919.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 P 2 5.49 5 S 46 5.16 5 C 6212 2.51 5 N 1604 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9714 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Chain: "D" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain: "A" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1529 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "B" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1529 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' K': 1, '1PX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' K': 1, '1PX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Time building chain proxies: 5.70, per 1000 atoms: 0.59 Number of scatterers: 9714 At special positions: 0 Unit cell: (124.894, 80.289, 131.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 46 16.00 P 2 15.00 O 1848 8.00 N 1604 7.00 C 6212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 20 sheets defined 18.4% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.652A pdb=" N ASP C 86 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'C' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.585A pdb=" N ASP E 86 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 191' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.895A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 90 Processing helix chain 'A' and resid 18 through 37 Processing helix chain 'A' and resid 43 through 71 removed outlier: 4.281A pdb=" N TRP A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 74 through 107 Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.700A pdb=" N PHE A 112 " --> pdb=" O MET A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 37 Processing helix chain 'B' and resid 43 through 71 removed outlier: 4.267A pdb=" N TRP B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 74 through 107 removed outlier: 3.576A pdb=" N ARG B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.775A pdb=" N PHE B 112 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.537A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.104A pdb=" N SER C 135 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 185 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 137 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU C 183 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 139 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER C 181 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 141 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET C 179 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.205A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.455A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.309A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 170 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N THR D 176 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA D 168 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 178 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LYS E 111 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 13 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET E 37 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR E 53 " --> pdb=" O MET E 37 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER E 135 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU E 185 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL E 137 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 183 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N PHE E 139 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER E 181 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN E 141 " --> pdb=" O MET E 179 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET E 179 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.203A pdb=" N TRP E 152 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.676A pdb=" N GLU F 10 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 110 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.307A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 170 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR F 176 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 168 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 178 " --> pdb=" O PHE F 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 151 through 154 Processing sheet with id=AB9, first strand: chain 'A' and resid 128 through 132 removed outlier: 7.339A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 175 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 201 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR A 179 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N TYR A 199 " --> pdb=" O TYR A 179 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A 181 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 197 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 183 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 195 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 157 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE A 151 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N HIS A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.302A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 175 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 142 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE B 151 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N HIS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.302A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 175 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1185 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: 3.18 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3040 1.34 - 1.46: 2448 1.46 - 1.58: 4396 1.58 - 1.70: 2 1.70 - 1.82: 66 Bond restraints: 9952 Sorted by residual: bond pdb=" CBJ 1PX B 301 " pdb=" OBL 1PX B 301 " ideal model delta sigma weight residual 1.416 1.348 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CBJ 1PX A 301 " pdb=" OBL 1PX A 301 " ideal model delta sigma weight residual 1.416 1.348 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N ILE C 110 " pdb=" CA ILE C 110 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.00e+00 bond pdb=" N ARG E 112 " pdb=" CA ARG E 112 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.23e-02 6.61e+03 7.94e+00 bond pdb=" N ARG C 112 " pdb=" CA ARG C 112 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.87e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 13457 2.88 - 5.75: 55 5.75 - 8.63: 18 8.63 - 11.50: 12 11.50 - 14.38: 6 Bond angle restraints: 13548 Sorted by residual: angle pdb=" OAD 1PX B 301 " pdb=" PBP 1PX B 301 " pdb=" OBL 1PX B 301 " ideal model delta sigma weight residual 102.13 87.75 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" OAD 1PX A 301 " pdb=" PBP 1PX A 301 " pdb=" OBL 1PX A 301 " ideal model delta sigma weight residual 102.13 87.91 14.22 3.00e+00 1.11e-01 2.25e+01 angle pdb=" CBJ 1PX B 301 " pdb=" CBO 1PX B 301 " pdb=" NBK 1PX B 301 " ideal model delta sigma weight residual 108.38 94.45 13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CBO 1PX A 301 " pdb=" CBJ 1PX A 301 " pdb=" OBL 1PX A 301 " ideal model delta sigma weight residual 112.59 99.43 13.16 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CBJ 1PX A 301 " pdb=" CBO 1PX A 301 " pdb=" NBK 1PX A 301 " ideal model delta sigma weight residual 108.38 95.23 13.15 3.00e+00 1.11e-01 1.92e+01 ... (remaining 13543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 5729 24.39 - 48.77: 167 48.77 - 73.16: 17 73.16 - 97.54: 2 97.54 - 121.93: 1 Dihedral angle restraints: 5916 sinusoidal: 2312 harmonic: 3604 Sorted by residual: dihedral pdb=" CB CYS F 140 " pdb=" SG CYS F 140 " pdb=" SG CYS F 195 " pdb=" CB CYS F 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.01 39.99 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.03 39.97 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CAV 1PX B 301 " pdb=" CAY 1PX B 301 " pdb=" CBA 1PX B 301 " pdb=" CAX 1PX B 301 " ideal model delta sinusoidal sigma weight residual 59.41 -62.52 121.93 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1477 0.105 - 0.210: 51 0.210 - 0.315: 2 0.315 - 0.420: 0 0.420 - 0.525: 2 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CBO 1PX A 301 " pdb=" CBJ 1PX A 301 " pdb=" CBN 1PX A 301 " pdb=" NBK 1PX A 301 " both_signs ideal model delta sigma weight residual False -2.50 -3.02 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" CBO 1PX B 301 " pdb=" CBJ 1PX B 301 " pdb=" CBN 1PX B 301 " pdb=" NBK 1PX B 301 " both_signs ideal model delta sigma weight residual False -2.50 -3.01 0.52 2.00e-01 2.50e+01 6.65e+00 chirality pdb=" CBN 1PX B 301 " pdb=" CAI 1PX B 301 " pdb=" CBO 1PX B 301 " pdb=" OAE 1PX B 301 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1529 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP F 188 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO F 189 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 188 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO D 189 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 189 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 189 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 109 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.88e+00 pdb=" C GLU C 109 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU C 109 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 110 " -0.010 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 2915 2.83 - 3.40: 9836 3.40 - 3.98: 19041 3.98 - 4.56: 25612 4.56 - 5.14: 40041 Nonbonded interactions: 97445 Sorted by model distance: nonbonded pdb=" OG SER D 190 " pdb=" OE1 GLU D 191 " model vdw 2.246 3.040 nonbonded pdb=" OG SER F 190 " pdb=" OE1 GLU F 191 " model vdw 2.247 3.040 nonbonded pdb=" O TYR C 190 " pdb=" OH TYR C 196 " model vdw 2.255 3.040 nonbonded pdb=" O TYR E 190 " pdb=" OH TYR E 196 " model vdw 2.256 3.040 nonbonded pdb=" O GLU A 137 " pdb=" OH TYR A 179 " model vdw 2.267 3.040 ... (remaining 97440 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.610 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.230 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.003 0.068 9960 Z= 0.188 Angle : 0.723 14.381 13564 Z= 0.338 Chirality : 0.048 0.525 1532 Planarity : 0.004 0.048 1698 Dihedral : 11.157 121.930 3584 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.03 % Allowed : 2.52 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: -0.53 (0.24), residues: 1228 helix: -0.64 (0.33), residues: 190 sheet: -0.09 (0.23), residues: 518 loop : -0.32 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.002 0.000 HIS B 154 PHE 0.007 0.001 PHE E 122 TYR 0.009 0.001 TYR A 199 ARG 0.002 0.000 ARG B 198 Details of bonding type rmsd hydrogen bonds : bond 0.19775 ( 434) hydrogen bonds : angle 9.00661 ( 1185) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.50012 ( 16) covalent geometry : bond 0.00348 ( 9952) covalent geometry : angle 0.72356 (13548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.981 Fit side-chains REVERT: C 97 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7348 (tt0) REVERT: C 179 MET cc_start: 0.8494 (ttp) cc_final: 0.8062 (ttp) REVERT: D 11 LEU cc_start: 0.8542 (tp) cc_final: 0.8323 (tp) REVERT: D 170 LEU cc_start: 0.7635 (tp) cc_final: 0.7389 (tp) REVERT: E 24 LYS cc_start: 0.7809 (mttt) cc_final: 0.7596 (tttp) REVERT: E 30 ASP cc_start: 0.7699 (m-30) cc_final: 0.6961 (p0) REVERT: E 97 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7372 (tt0) REVERT: E 171 ASP cc_start: 0.7917 (t0) cc_final: 0.7422 (t0) REVERT: E 179 MET cc_start: 0.8053 (ttp) cc_final: 0.7160 (ttt) REVERT: A 35 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.5953 (mt) REVERT: A 134 LEU cc_start: 0.9136 (mt) cc_final: 0.8860 (mm) REVERT: A 150 ARG cc_start: 0.8149 (ptm160) cc_final: 0.7200 (ptp-170) REVERT: A 185 GLN cc_start: 0.6863 (tt0) cc_final: 0.6321 (pt0) REVERT: B 35 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6495 (tt) REVERT: B 84 MET cc_start: 0.7860 (mmt) cc_final: 0.7467 (mmt) REVERT: B 150 ARG cc_start: 0.8252 (ptm160) cc_final: 0.6934 (ptp-170) REVERT: B 185 GLN cc_start: 0.7483 (tt0) cc_final: 0.6816 (pt0) outliers start: 11 outliers final: 6 residues processed: 167 average time/residue: 0.2169 time to fit residues: 50.6831 Evaluate side-chains 131 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 57 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain B residue 35 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 100 ASN E 38 ASN E 95 ASN F 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.213650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.157612 restraints weight = 10050.511| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.07 r_work: 0.3497 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9960 Z= 0.254 Angle : 0.612 7.400 13564 Z= 0.319 Chirality : 0.046 0.150 1532 Planarity : 0.005 0.079 1698 Dihedral : 8.527 86.866 1423 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.68 % Allowed : 9.14 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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 (0.24), residues: 1228 helix: 0.19 (0.35), residues: 194 sheet: -0.03 (0.23), residues: 490 loop : -0.23 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 47 HIS 0.005 0.001 HIS A 125 PHE 0.014 0.002 PHE A 193 TYR 0.019 0.002 TYR C 36 ARG 0.005 0.001 ARG B 146 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 434) hydrogen bonds : angle 6.24972 ( 1185) SS BOND : bond 0.00209 ( 8) SS BOND : angle 0.65961 ( 16) covalent geometry : bond 0.00604 ( 9952) covalent geometry : angle 0.61243 (13548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: C 179 MET cc_start: 0.8562 (ttp) cc_final: 0.8320 (ttp) REVERT: D 13 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7831 (mmmt) REVERT: D 170 LEU cc_start: 0.7790 (tp) cc_final: 0.7420 (tp) REVERT: E 24 LYS cc_start: 0.7686 (mttt) cc_final: 0.7448 (tttp) REVERT: E 30 ASP cc_start: 0.7831 (m-30) cc_final: 0.7201 (p0) REVERT: E 32 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: E 97 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7508 (tt0) REVERT: E 179 MET cc_start: 0.8346 (ttp) cc_final: 0.7304 (ttt) REVERT: A 150 ARG cc_start: 0.8465 (ptm160) cc_final: 0.7812 (ptp-170) REVERT: A 185 GLN cc_start: 0.7708 (tt0) cc_final: 0.7270 (pt0) REVERT: B 84 MET cc_start: 0.8216 (mmt) cc_final: 0.7932 (mmt) REVERT: B 150 ARG cc_start: 0.8247 (ptm160) cc_final: 0.7610 (ptp-170) REVERT: B 185 GLN cc_start: 0.7730 (tt0) cc_final: 0.7363 (pt0) outliers start: 18 outliers final: 12 residues processed: 148 average time/residue: 0.2082 time to fit residues: 43.6800 Evaluate side-chains 132 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 61 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN C 141 ASN D 39 GLN D 164 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.214512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.159370 restraints weight = 10076.178| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.10 r_work: 0.3541 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9960 Z= 0.144 Angle : 0.513 6.354 13564 Z= 0.268 Chirality : 0.043 0.149 1532 Planarity : 0.005 0.078 1698 Dihedral : 7.959 89.291 1413 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.15 % Allowed : 12.41 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: -0.10 (0.24), residues: 1228 helix: 0.44 (0.35), residues: 206 sheet: 0.10 (0.23), residues: 508 loop : -0.28 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 31 HIS 0.004 0.001 HIS A 154 PHE 0.012 0.001 PHE F 146 TYR 0.018 0.001 TYR D 60 ARG 0.002 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 434) hydrogen bonds : angle 5.66883 ( 1185) SS BOND : bond 0.00256 ( 8) SS BOND : angle 0.58163 ( 16) covalent geometry : bond 0.00335 ( 9952) covalent geometry : angle 0.51264 (13548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.040 Fit side-chains REVERT: D 13 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7893 (mmmt) REVERT: E 30 ASP cc_start: 0.7777 (m-30) cc_final: 0.7125 (p0) REVERT: E 32 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: E 179 MET cc_start: 0.8426 (ttp) cc_final: 0.7680 (ttp) REVERT: A 150 ARG cc_start: 0.8362 (ptm160) cc_final: 0.7708 (ptp-170) REVERT: A 185 GLN cc_start: 0.7730 (tt0) cc_final: 0.7437 (pt0) REVERT: B 84 MET cc_start: 0.8231 (mmt) cc_final: 0.7901 (mmt) REVERT: B 150 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7433 (ptp-170) REVERT: B 185 GLN cc_start: 0.7640 (tt0) cc_final: 0.7302 (pt0) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.1911 time to fit residues: 39.0999 Evaluate side-chains 139 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.211254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157601 restraints weight = 10055.516| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.31 r_work: 0.3499 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9960 Z= 0.203 Angle : 0.556 6.807 13564 Z= 0.287 Chirality : 0.044 0.147 1532 Planarity : 0.005 0.078 1698 Dihedral : 7.882 86.926 1413 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.43 % Allowed : 13.81 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 1228 helix: 0.67 (0.36), residues: 194 sheet: 0.10 (0.23), residues: 504 loop : -0.15 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 47 HIS 0.003 0.001 HIS A 125 PHE 0.014 0.001 PHE A 193 TYR 0.023 0.002 TYR D 60 ARG 0.002 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 434) hydrogen bonds : angle 5.69100 ( 1185) SS BOND : bond 0.00228 ( 8) SS BOND : angle 0.68789 ( 16) covalent geometry : bond 0.00481 ( 9952) covalent geometry : angle 0.55541 (13548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 1.005 Fit side-chains REVERT: C 171 ASP cc_start: 0.7819 (t0) cc_final: 0.7579 (t0) REVERT: D 13 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7982 (mmmt) REVERT: E 30 ASP cc_start: 0.7816 (m-30) cc_final: 0.7196 (p0) REVERT: E 32 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6800 (m-30) REVERT: E 179 MET cc_start: 0.8531 (ttp) cc_final: 0.7774 (ttp) REVERT: A 115 GLU cc_start: 0.7881 (pt0) cc_final: 0.7633 (pt0) REVERT: A 150 ARG cc_start: 0.8398 (ptm160) cc_final: 0.7810 (ptp-170) REVERT: A 185 GLN cc_start: 0.7789 (tt0) cc_final: 0.7502 (pt0) REVERT: B 84 MET cc_start: 0.8224 (mmt) cc_final: 0.7933 (mmt) REVERT: B 150 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7526 (ptp-170) REVERT: B 185 GLN cc_start: 0.7779 (tt0) cc_final: 0.7439 (pt0) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 0.1970 time to fit residues: 40.9005 Evaluate side-chains 141 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 116 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.161703 restraints weight = 10023.380| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.05 r_work: 0.3552 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9960 Z= 0.128 Angle : 0.501 7.531 13564 Z= 0.259 Chirality : 0.042 0.150 1532 Planarity : 0.004 0.078 1698 Dihedral : 7.585 84.647 1413 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.43 % Allowed : 14.65 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.21 (0.25), residues: 1228 helix: 1.03 (0.37), residues: 194 sheet: 0.14 (0.23), residues: 508 loop : -0.04 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 58 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 193 TYR 0.023 0.001 TYR D 60 ARG 0.002 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.02986 ( 434) hydrogen bonds : angle 5.34349 ( 1185) SS BOND : bond 0.00261 ( 8) SS BOND : angle 0.61498 ( 16) covalent geometry : bond 0.00300 ( 9952) covalent geometry : angle 0.50110 (13548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.944 Fit side-chains REVERT: D 13 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7948 (mmmt) REVERT: E 30 ASP cc_start: 0.7686 (m-30) cc_final: 0.7066 (p0) REVERT: E 32 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6774 (m-30) REVERT: E 179 MET cc_start: 0.8537 (ttp) cc_final: 0.7750 (ttp) REVERT: A 115 GLU cc_start: 0.7864 (pt0) cc_final: 0.7627 (pt0) REVERT: A 150 ARG cc_start: 0.8324 (ptm160) cc_final: 0.7686 (ptp-170) REVERT: A 185 GLN cc_start: 0.7789 (tt0) cc_final: 0.7421 (pt0) REVERT: B 84 MET cc_start: 0.8218 (mmt) cc_final: 0.7948 (mmt) REVERT: B 150 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7716 (ptt90) REVERT: B 185 GLN cc_start: 0.7637 (tt0) cc_final: 0.7301 (pt0) outliers start: 26 outliers final: 16 residues processed: 140 average time/residue: 0.1765 time to fit residues: 36.6129 Evaluate side-chains 136 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.0170 chunk 62 optimal weight: 30.0000 chunk 119 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.217104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157431 restraints weight = 10076.192| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.01 r_work: 0.3608 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9960 Z= 0.122 Angle : 0.497 7.389 13564 Z= 0.257 Chirality : 0.042 0.138 1532 Planarity : 0.004 0.078 1698 Dihedral : 7.473 83.605 1413 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.24 % Allowed : 15.39 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.31 (0.25), residues: 1228 helix: 1.17 (0.37), residues: 194 sheet: 0.21 (0.23), residues: 508 loop : -0.01 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 193 TYR 0.020 0.001 TYR D 60 ARG 0.001 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 434) hydrogen bonds : angle 5.22323 ( 1185) SS BOND : bond 0.00234 ( 8) SS BOND : angle 0.56442 ( 16) covalent geometry : bond 0.00284 ( 9952) covalent geometry : angle 0.49713 (13548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.946 Fit side-chains REVERT: D 13 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7936 (mmmt) REVERT: E 30 ASP cc_start: 0.7648 (m-30) cc_final: 0.7062 (p0) REVERT: E 32 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: E 179 MET cc_start: 0.8543 (ttp) cc_final: 0.8125 (ttp) REVERT: F 60 TYR cc_start: 0.9177 (m-80) cc_final: 0.8892 (m-80) REVERT: A 115 GLU cc_start: 0.7830 (pt0) cc_final: 0.7381 (pt0) REVERT: A 150 ARG cc_start: 0.8243 (ptm160) cc_final: 0.7672 (ptp-170) REVERT: A 185 GLN cc_start: 0.7731 (tt0) cc_final: 0.7390 (pt0) REVERT: B 84 MET cc_start: 0.8163 (mmt) cc_final: 0.7863 (mmt) REVERT: B 150 ARG cc_start: 0.7930 (ptm160) cc_final: 0.7644 (ptt90) REVERT: B 185 GLN cc_start: 0.7573 (tt0) cc_final: 0.7276 (pt0) outliers start: 24 outliers final: 16 residues processed: 138 average time/residue: 0.1732 time to fit residues: 35.4890 Evaluate side-chains 137 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN C 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.215893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159836 restraints weight = 10074.609| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.18 r_work: 0.3524 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9960 Z= 0.149 Angle : 0.514 7.612 13564 Z= 0.264 Chirality : 0.043 0.139 1532 Planarity : 0.004 0.078 1698 Dihedral : 7.435 82.199 1413 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.15 % Allowed : 15.21 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.34 (0.25), residues: 1228 helix: 1.10 (0.37), residues: 194 sheet: 0.26 (0.23), residues: 504 loop : 0.03 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 31 HIS 0.002 0.001 HIS A 154 PHE 0.012 0.001 PHE A 193 TYR 0.022 0.001 TYR D 60 ARG 0.001 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 434) hydrogen bonds : angle 5.24206 ( 1185) SS BOND : bond 0.00267 ( 8) SS BOND : angle 0.63675 ( 16) covalent geometry : bond 0.00354 ( 9952) covalent geometry : angle 0.51361 (13548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.953 Fit side-chains REVERT: C 171 ASP cc_start: 0.7726 (t0) cc_final: 0.7495 (t0) REVERT: D 13 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7972 (mmmt) REVERT: D 60 TYR cc_start: 0.9154 (m-80) cc_final: 0.8865 (m-80) REVERT: E 30 ASP cc_start: 0.7722 (m-30) cc_final: 0.7095 (p0) REVERT: E 32 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: E 179 MET cc_start: 0.8610 (ttp) cc_final: 0.8181 (ttp) REVERT: F 60 TYR cc_start: 0.9246 (m-80) cc_final: 0.8982 (m-80) REVERT: A 115 GLU cc_start: 0.7942 (pt0) cc_final: 0.7499 (pt0) REVERT: A 150 ARG cc_start: 0.8276 (ptm160) cc_final: 0.7666 (ptp-170) REVERT: A 185 GLN cc_start: 0.7815 (tt0) cc_final: 0.7430 (pt0) REVERT: B 84 MET cc_start: 0.8231 (mmt) cc_final: 0.7973 (mmt) REVERT: B 185 GLN cc_start: 0.7688 (tt0) cc_final: 0.7326 (pt0) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.1722 time to fit residues: 34.8142 Evaluate side-chains 136 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 ASN F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.217722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163483 restraints weight = 10071.026| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.30 r_work: 0.3561 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9960 Z= 0.117 Angle : 0.498 7.951 13564 Z= 0.255 Chirality : 0.042 0.140 1532 Planarity : 0.004 0.078 1698 Dihedral : 7.187 80.248 1413 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.15 % Allowed : 15.58 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.45 (0.25), residues: 1228 helix: 1.29 (0.37), residues: 194 sheet: 0.30 (0.23), residues: 508 loop : 0.09 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.002 0.000 HIS B 154 PHE 0.009 0.001 PHE A 193 TYR 0.020 0.001 TYR D 60 ARG 0.001 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 434) hydrogen bonds : angle 5.04012 ( 1185) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.71948 ( 16) covalent geometry : bond 0.00275 ( 9952) covalent geometry : angle 0.49803 (13548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.061 Fit side-chains REVERT: C 171 ASP cc_start: 0.7847 (t0) cc_final: 0.7588 (t0) REVERT: D 13 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7965 (mmmt) REVERT: D 60 TYR cc_start: 0.9141 (m-80) cc_final: 0.8840 (m-80) REVERT: E 30 ASP cc_start: 0.7684 (m-30) cc_final: 0.7102 (p0) REVERT: E 32 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: E 179 MET cc_start: 0.8601 (ttp) cc_final: 0.8184 (ttp) REVERT: F 60 TYR cc_start: 0.9227 (m-80) cc_final: 0.8945 (m-80) REVERT: A 84 MET cc_start: 0.8566 (tpp) cc_final: 0.8181 (mmt) REVERT: A 150 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7610 (ptp-170) REVERT: A 185 GLN cc_start: 0.7794 (tt0) cc_final: 0.7408 (pt0) REVERT: B 84 MET cc_start: 0.8245 (mmt) cc_final: 0.7940 (mmt) REVERT: B 150 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7676 (ptt90) REVERT: B 185 GLN cc_start: 0.7661 (tt0) cc_final: 0.7324 (pt0) outliers start: 23 outliers final: 17 residues processed: 136 average time/residue: 0.1920 time to fit residues: 38.9249 Evaluate side-chains 134 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.0040 chunk 116 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS F 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.217715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162215 restraints weight = 10046.911| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.18 r_work: 0.3549 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9960 Z= 0.118 Angle : 0.505 7.707 13564 Z= 0.257 Chirality : 0.042 0.137 1532 Planarity : 0.004 0.081 1698 Dihedral : 7.127 79.651 1413 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.77 % Allowed : 15.49 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.49 (0.25), residues: 1228 helix: 1.33 (0.37), residues: 194 sheet: 0.32 (0.23), residues: 508 loop : 0.12 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.002 0.000 HIS A 154 PHE 0.010 0.001 PHE A 193 TYR 0.020 0.001 TYR D 60 ARG 0.001 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.02826 ( 434) hydrogen bonds : angle 5.00468 ( 1185) SS BOND : bond 0.00269 ( 8) SS BOND : angle 0.69524 ( 16) covalent geometry : bond 0.00278 ( 9952) covalent geometry : angle 0.50454 (13548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.958 Fit side-chains REVERT: C 37 MET cc_start: 0.8517 (tpt) cc_final: 0.8016 (tpt) REVERT: C 171 ASP cc_start: 0.7922 (t0) cc_final: 0.7662 (t0) REVERT: D 60 TYR cc_start: 0.9118 (m-80) cc_final: 0.8867 (m-80) REVERT: E 30 ASP cc_start: 0.7699 (m-30) cc_final: 0.7142 (p0) REVERT: E 32 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: E 179 MET cc_start: 0.8689 (ttp) cc_final: 0.8161 (ttp) REVERT: F 60 TYR cc_start: 0.9214 (m-80) cc_final: 0.8938 (m-80) REVERT: A 84 MET cc_start: 0.8564 (tpp) cc_final: 0.8197 (mmt) REVERT: A 150 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7697 (ptp-170) REVERT: A 185 GLN cc_start: 0.7847 (tt0) cc_final: 0.7494 (pt0) REVERT: B 84 MET cc_start: 0.8247 (mmt) cc_final: 0.7982 (mmt) REVERT: B 185 GLN cc_start: 0.7678 (tt0) cc_final: 0.7384 (pt0) outliers start: 19 outliers final: 16 residues processed: 126 average time/residue: 0.1779 time to fit residues: 33.6093 Evaluate side-chains 127 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 48 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.216487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162245 restraints weight = 10131.353| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.38 r_work: 0.3570 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9960 Z= 0.140 Angle : 0.516 7.694 13564 Z= 0.263 Chirality : 0.042 0.138 1532 Planarity : 0.004 0.081 1698 Dihedral : 7.124 79.282 1413 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.77 % Allowed : 15.58 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.49 (0.25), residues: 1228 helix: 1.25 (0.37), residues: 194 sheet: 0.30 (0.23), residues: 508 loop : 0.16 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.002 0.001 HIS B 125 PHE 0.011 0.001 PHE A 193 TYR 0.021 0.001 TYR D 60 ARG 0.002 0.000 ARG B 200 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 434) hydrogen bonds : angle 5.04977 ( 1185) SS BOND : bond 0.00249 ( 8) SS BOND : angle 0.69521 ( 16) covalent geometry : bond 0.00333 ( 9952) covalent geometry : angle 0.51550 (13548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.919 Fit side-chains REVERT: C 171 ASP cc_start: 0.7919 (t0) cc_final: 0.7623 (t0) REVERT: D 60 TYR cc_start: 0.9139 (m-80) cc_final: 0.8882 (m-80) REVERT: E 30 ASP cc_start: 0.7697 (m-30) cc_final: 0.7085 (p0) REVERT: E 32 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: E 179 MET cc_start: 0.8640 (ttp) cc_final: 0.7761 (ttp) REVERT: A 150 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7659 (ptp-170) REVERT: A 185 GLN cc_start: 0.7812 (tt0) cc_final: 0.7435 (pt0) REVERT: B 84 MET cc_start: 0.8227 (mmt) cc_final: 0.7950 (mmt) REVERT: B 185 GLN cc_start: 0.7655 (tt0) cc_final: 0.7329 (pt0) outliers start: 19 outliers final: 16 residues processed: 124 average time/residue: 0.1765 time to fit residues: 32.5585 Evaluate side-chains 122 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 35 ASN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.216484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.161923 restraints weight = 9975.958| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.32 r_work: 0.3555 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9960 Z= 0.135 Angle : 0.514 7.720 13564 Z= 0.263 Chirality : 0.042 0.138 1532 Planarity : 0.004 0.080 1698 Dihedral : 6.912 78.480 1411 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.87 % Allowed : 15.58 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.58 % 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: 0.53 (0.25), residues: 1228 helix: 1.27 (0.37), residues: 194 sheet: 0.33 (0.23), residues: 508 loop : 0.19 (0.30), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 31 HIS 0.002 0.001 HIS A 154 PHE 0.012 0.001 PHE A 193 TYR 0.020 0.001 TYR D 60 ARG 0.001 0.000 ARG E 65 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 434) hydrogen bonds : angle 5.02344 ( 1185) SS BOND : bond 0.00236 ( 8) SS BOND : angle 0.67198 ( 16) covalent geometry : bond 0.00321 ( 9952) covalent geometry : angle 0.51368 (13548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5870.37 seconds wall clock time: 102 minutes 14.54 seconds (6134.54 seconds total)