Starting phenix.real_space_refine on Wed Jun 11 02:11:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgz_50434/06_2025/9fgz_50434.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgz_50434/06_2025/9fgz_50434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgz_50434/06_2025/9fgz_50434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgz_50434/06_2025/9fgz_50434.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgz_50434/06_2025/9fgz_50434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgz_50434/06_2025/9fgz_50434.cif" } resolution = 2.7 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= 0.039 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 66 5.16 5 C 7985 2.51 5 N 2018 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12317 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2156 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2045 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 248} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2042 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2015 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2039 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 248} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2020 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 8.40, per 1000 atoms: 0.68 Number of scatterers: 12317 At special positions: 0 Unit cell: (96.83, 105.25, 123.774, 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 66 16.00 O 2248 8.00 N 2018 7.00 C 7985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 13 sheets defined 59.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 88 through 110 removed outlier: 4.725A pdb=" N ALA A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 160 through 170 Proline residue: A 166 - end of helix Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.753A pdb=" N PHE A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 205 through 221 removed outlier: 3.894A pdb=" N PHE A 209 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.679A pdb=" N ASN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 34 through 51 Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 160 through 170 Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.741A pdb=" N PHE B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.794A pdb=" N PHE B 209 " --> pdb=" O ASN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.919A pdb=" N SER B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 Processing helix chain 'B' and resid 255 through 262 removed outlier: 3.517A pdb=" N TRP B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.550A pdb=" N ASN C 29 " --> pdb=" O ASN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 88 through 97 Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 160 through 170 Proline residue: C 166 - end of helix Processing helix chain 'C' and resid 170 through 180 removed outlier: 3.836A pdb=" N PHE C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 205 through 221 removed outlier: 3.898A pdb=" N PHE C 209 " --> pdb=" O ASN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.864A pdb=" N SER C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 262 removed outlier: 3.901A pdb=" N SER C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 256 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS C 257 " --> pdb=" O ASN C 253 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 34 through 50 removed outlier: 3.526A pdb=" N ARG D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.846A pdb=" N ILE D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 160 through 170 Proline residue: D 166 - end of helix Processing helix chain 'D' and resid 170 through 180 removed outlier: 3.690A pdb=" N PHE D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 205 through 221 removed outlier: 3.935A pdb=" N PHE D 209 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 238 removed outlier: 3.840A pdb=" N SER D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 255 removed outlier: 3.805A pdb=" N ASN D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 262 removed outlier: 3.927A pdb=" N TRP D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'E' and resid 34 through 51 Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.617A pdb=" N ILE E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 110 removed outlier: 4.978A pdb=" N ALA E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG E 100 " --> pdb=" O ASN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 160 through 170 Proline residue: E 166 - end of helix Processing helix chain 'E' and resid 170 through 180 removed outlier: 3.793A pdb=" N PHE E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 192 Processing helix chain 'E' and resid 205 through 221 Processing helix chain 'E' and resid 225 through 237 Processing helix chain 'E' and resid 240 through 262 removed outlier: 3.801A pdb=" N ASN E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'F' and resid 34 through 51 removed outlier: 3.781A pdb=" N ASN F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.514A pdb=" N ILE F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 97 removed outlier: 3.642A pdb=" N SER F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 110 Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 160 through 170 Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 170 through 180 removed outlier: 3.820A pdb=" N PHE F 180 " --> pdb=" O GLU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 192 Processing helix chain 'F' and resid 205 through 221 removed outlier: 3.825A pdb=" N PHE F 209 " --> pdb=" O ASN F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 238 removed outlier: 3.534A pdb=" N CYS F 229 " --> pdb=" O TYR F 225 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER F 238 " --> pdb=" O LYS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 262 removed outlier: 4.392A pdb=" N SER F 249 " --> pdb=" O ASN F 245 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 269 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 6.251A pdb=" N PHE A 20 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN A 60 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 22 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 197 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 removed outlier: 6.609A pdb=" N ALA A 123 " --> pdb=" O LEU A 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 16 removed outlier: 6.181A pdb=" N PHE B 20 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN B 60 " --> pdb=" O PHE B 20 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE B 22 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 137 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN B 198 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER B 139 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.591A pdb=" N ALA B 123 " --> pdb=" O LEU B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.096A pdb=" N LYS C 197 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 123 through 124 removed outlier: 6.682A pdb=" N ALA C 123 " --> pdb=" O LEU C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.222A pdb=" N PHE D 20 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN D 60 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE D 22 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 197 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.537A pdb=" N ALA D 123 " --> pdb=" O LEU D 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.252A pdb=" N THR E 57 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N CYS E 118 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE E 59 " --> pdb=" O CYS E 118 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS E 197 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 123 through 124 removed outlier: 6.630A pdb=" N ALA E 123 " --> pdb=" O LEU E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.335A pdb=" N PHE F 20 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLN F 60 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE F 22 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR F 57 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N CYS F 118 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE F 59 " --> pdb=" O CYS F 118 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS F 197 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 123 through 124 removed outlier: 6.615A pdb=" N ALA F 123 " --> pdb=" O LEU F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 641 hydrogen bonds defined for protein. 1866 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: 3.59 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3862 1.34 - 1.46: 1936 1.46 - 1.57: 6693 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 12587 Sorted by residual: bond pdb=" C GLU E 263 " pdb=" N PRO E 264 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.30e-02 5.92e+03 2.33e+00 bond pdb=" CB VAL B 102 " pdb=" CG1 VAL B 102 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" C ASN E 248 " pdb=" O ASN E 248 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 9.07e-01 bond pdb=" CA PRO F 149 " pdb=" C PRO F 149 " ideal model delta sigma weight residual 1.528 1.518 0.010 1.20e-02 6.94e+03 7.01e-01 bond pdb=" C LEU A 165 " pdb=" O LEU A 165 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.00e-02 1.00e+04 6.15e-01 ... (remaining 12582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 16487 1.23 - 2.45: 435 2.45 - 3.68: 60 3.68 - 4.90: 21 4.90 - 6.13: 8 Bond angle restraints: 17011 Sorted by residual: angle pdb=" N TYR A 55 " pdb=" CA TYR A 55 " pdb=" C TYR A 55 " ideal model delta sigma weight residual 114.56 110.23 4.33 1.27e+00 6.20e-01 1.16e+01 angle pdb=" N GLY E 125 " pdb=" CA GLY E 125 " pdb=" C GLY E 125 " ideal model delta sigma weight residual 110.95 115.40 -4.45 1.70e+00 3.46e-01 6.86e+00 angle pdb=" C VAL B 252 " pdb=" N ASN B 253 " pdb=" CA ASN B 253 " ideal model delta sigma weight residual 121.66 117.71 3.95 1.76e+00 3.23e-01 5.05e+00 angle pdb=" N GLY C 63 " pdb=" CA GLY C 63 " pdb=" C GLY C 63 " ideal model delta sigma weight residual 112.22 116.12 -3.90 1.74e+00 3.30e-01 5.02e+00 angle pdb=" CA TYR A 55 " pdb=" C TYR A 55 " pdb=" N PHE A 56 " ideal model delta sigma weight residual 119.26 116.93 2.33 1.14e+00 7.69e-01 4.19e+00 ... (remaining 17006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 6763 15.43 - 30.85: 608 30.85 - 46.28: 117 46.28 - 61.70: 23 61.70 - 77.13: 9 Dihedral angle restraints: 7520 sinusoidal: 2947 harmonic: 4573 Sorted by residual: dihedral pdb=" CA PHE E 65 " pdb=" C PHE E 65 " pdb=" N PHE E 66 " pdb=" CA PHE E 66 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE B 65 " pdb=" C PHE B 65 " pdb=" N PHE B 66 " pdb=" CA PHE B 66 " ideal model delta harmonic sigma weight residual 180.00 164.15 15.85 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LYS D 266 " pdb=" CB LYS D 266 " pdb=" CG LYS D 266 " pdb=" CD LYS D 266 " ideal model delta sinusoidal sigma weight residual -60.00 -119.73 59.73 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1134 0.033 - 0.066: 523 0.066 - 0.099: 163 0.099 - 0.132: 62 0.132 - 0.165: 9 Chirality restraints: 1891 Sorted by residual: chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CB VAL F 221 " pdb=" CA VAL F 221 " pdb=" CG1 VAL F 221 " pdb=" CG2 VAL F 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE F 22 " pdb=" N ILE F 22 " pdb=" C ILE F 22 " pdb=" CB ILE F 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1888 not shown) Planarity restraints: 2161 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 94 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C VAL E 94 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL E 94 " 0.012 2.00e-02 2.50e+03 pdb=" N SER E 95 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 94 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C VAL A 94 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL A 94 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 95 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 226 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO F 227 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 227 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 227 " 0.023 5.00e-02 4.00e+02 ... (remaining 2158 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 158 2.68 - 3.24: 11450 3.24 - 3.79: 19200 3.79 - 4.35: 28615 4.35 - 4.90: 46249 Nonbonded interactions: 105672 Sorted by model distance: nonbonded pdb=" OG SER A 228 " pdb=" O LEU B 155 " model vdw 2.125 3.040 nonbonded pdb=" OG SER E 228 " pdb=" O LEU F 155 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP F 49 " pdb=" OG SER F 112 " model vdw 2.179 3.040 nonbonded pdb=" OG SER D 228 " pdb=" O LEU E 155 " model vdw 2.188 3.040 nonbonded pdb=" O LYS E 266 " pdb=" NE2 GLN E 270 " model vdw 2.217 3.120 ... (remaining 105667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 45 or (resid 46 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 47 through 49 or (resid 5 \ 0 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 51 or (resid 52 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 53 through 63 or (resid 64 and (name N or name CA or name \ C or name O or name CB )) or resid 65 through 71 or (resid 72 through 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 or (resid 75 thro \ ugh 76 and (name N or name CA or name C or name O or name CB )) or resid 77 or r \ esid 86 through 190 or (resid 191 and (name N or name CA or name C or name O or \ name CB or name CG )) or resid 192 through 204 or (resid 205 through 208 and (na \ me N or name CA or name C or name O or name CB )) or resid 209 through 211 or (r \ esid 212 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 213 through 214 or (resid 215 and (name N or name CA or name C or name O o \ r name CB or name CG )) or resid 216 through 218 or (resid 219 and (name N or na \ me CA or name C or name O or name CB )) or resid 220 through 256 or (resid 257 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ resid 258 through 265 or (resid 266 and (name N or name CA or name C or name O \ or name CB )) or resid 267 through 269 or (resid 270 and (name N or name CA or n \ ame C or name O or name CB )))) selection = (chain 'B' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD )) or resid \ 51 through 63 or (resid 64 and (name N or name CA or name C or name O or name CB \ )) or resid 65 through 71 or (resid 72 through 73 and (name N or name CA or nam \ e C or name O or name CB )) or resid 74 or (resid 75 through 76 and (name N or n \ ame CA or name C or name O or name CB )) or resid 77 or resid 86 through 204 or \ (resid 205 through 208 and (name N or name CA or name C or name O or name CB )) \ or resid 209 through 211 or (resid 212 and (name N or name CA or name C or name \ O or name CB or name CG )) or resid 213 through 214 or (resid 215 and (name N or \ name CA or name C or name O or name CB or name CG )) or resid 216 through 218 o \ r (resid 219 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 20 through 253 or (resid 254 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 255 through 256 or (resid 257 and (name N or name CA o \ r name C or name O or name CB or name CG or name CD )) or resid 258 through 265 \ or (resid 266 and (name N or name CA or name C or name O or name CB )) or resid \ 267 through 269 or (resid 270 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'C' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 49 or (resid 50 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 51 or (resid 5 \ 2 and (name N or name CA or name C or name O or name CB or name CG )) or resid 5 \ 3 through 63 or (resid 64 and (name N or name CA or name C or name O or name CB \ )) or resid 65 through 74 or (resid 75 through 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 or resid 86 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 192 th \ rough 204 or (resid 205 through 208 and (name N or name CA or name C or name O o \ r name CB )) or resid 209 through 211 or (resid 212 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 213 through 214 or (resid 215 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 216 \ through 253 or (resid 254 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 255 through 256 or (resid 257 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD )) or resid 258 through 265 or \ (resid 266 and (name N or name CA or name C or name O or name CB )) or resid 267 \ through 270)) selection = (chain 'D' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 51 or (resid 52 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 53 through 63 or (resid 6 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 65 through 7 \ 1 or (resid 72 through 73 and (name N or name CA or name C or name O or name CB \ )) or resid 74 through 204 or (resid 205 through 208 and (name N or name CA or n \ ame C or name O or name CB )) or resid 209 through 211 or (resid 212 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 213 through 21 \ 8 or (resid 219 and (name N or name CA or name C or name O or name CB )) or resi \ d 220 through 265 or (resid 266 and (name N or name CA or name C or name O or na \ me CB )) or resid 267 through 269 or (resid 270 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'E' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 45 or (resid 46 and (name N or name C \ A or name C or name O or name CB or name CG )) or resid 47 through 49 or (resid \ 50 and (name N or name CA or name C or name O or name CB or name CG or name CD ) \ ) or resid 51 or (resid 52 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 53 through 71 or (resid 72 through 73 and (name N or nam \ e CA or name C or name O or name CB )) or resid 74 or (resid 75 through 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 85 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 192 through 214 or (resid 215 and (name N or name CA or name C or name O \ or name CB or name CG )) or resid 216 through 253 or (resid 254 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 255 through 256 or \ (resid 257 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD )) or resid 258 through 265 or (resid 266 and (name N or name CA or name \ C or name O or name CB )) or resid 267 through 269 or (resid 270 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 63 or (resid 64 and (name N or name CA \ or name C or name O or name CB )) or resid 65 through 71 or (resid 72 through 7 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 74 or (resid \ 75 through 76 and (name N or name CA or name C or name O or name CB )) or resid \ 85 through 204 or (resid 205 through 208 and (name N or name CA or name C or na \ me O or name CB )) or resid 209 through 211 or (resid 212 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 213 through 214 or (resid \ 215 and (name N or name CA or name C or name O or name CB or name CG )) or resi \ d 216 through 218 or (resid 219 and (name N or name CA or name C or name O or na \ me CB )) or resid 220 through 253 or (resid 254 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 255 through 256 or (resid 257 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD )) or res \ id 258 through 269 or (resid 270 and (name N or name CA or name C or name O or n \ ame CB )))) } 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: 4.610 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.140 Find NCS groups from input model: 0.680 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 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 0.035 12587 Z= 0.136 Angle : 0.506 6.130 17011 Z= 0.290 Chirality : 0.043 0.165 1891 Planarity : 0.004 0.041 2161 Dihedral : 12.421 77.128 4580 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1543 helix: -1.02 (0.16), residues: 816 sheet: -0.84 (0.34), residues: 190 loop : -1.68 (0.23), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 93 HIS 0.001 0.000 HIS C 111 PHE 0.013 0.001 PHE E 97 TYR 0.007 0.001 TYR B 186 ARG 0.003 0.000 ARG B 100 Details of bonding type rmsd hydrogen bonds : bond 0.16286 ( 641) hydrogen bonds : angle 6.74733 ( 1866) covalent geometry : bond 0.00303 (12587) covalent geometry : angle 0.50617 (17011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.539 Fit side-chains REVERT: A 257 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8248 (ptpt) REVERT: C 218 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8396 (mtm110) REVERT: C 234 LYS cc_start: 0.8549 (tttm) cc_final: 0.8130 (ttpt) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 1.7018 time to fit residues: 388.2209 Evaluate side-chains 141 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 181 ASN C 96 ASN D 245 ASN F 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.089353 restraints weight = 15630.382| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.34 r_work: 0.2795 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12587 Z= 0.173 Angle : 0.544 5.633 17011 Z= 0.289 Chirality : 0.046 0.226 1891 Planarity : 0.004 0.049 2161 Dihedral : 4.370 16.343 1681 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.36 % Allowed : 7.86 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1543 helix: 0.26 (0.18), residues: 813 sheet: -0.41 (0.36), residues: 192 loop : -1.23 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 93 HIS 0.002 0.000 HIS C 111 PHE 0.014 0.002 PHE A 65 TYR 0.008 0.001 TYR F 55 ARG 0.004 0.000 ARG B 267 Details of bonding type rmsd hydrogen bonds : bond 0.05738 ( 641) hydrogen bonds : angle 5.18715 ( 1866) covalent geometry : bond 0.00421 (12587) covalent geometry : angle 0.54447 (17011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: A 257 LYS cc_start: 0.8569 (ptpp) cc_final: 0.8273 (ptpt) REVERT: B 34 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: B 46 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 50 ARG cc_start: 0.8385 (mtp180) cc_final: 0.8145 (mtp180) REVERT: D 16 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8156 (mt-10) outliers start: 18 outliers final: 8 residues processed: 156 average time/residue: 1.6677 time to fit residues: 277.8591 Evaluate side-chains 135 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 255 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.091557 restraints weight = 15918.486| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.38 r_work: 0.2831 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12587 Z= 0.124 Angle : 0.481 5.491 17011 Z= 0.256 Chirality : 0.043 0.202 1891 Planarity : 0.004 0.049 2161 Dihedral : 4.160 15.535 1681 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.28 % Allowed : 9.52 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1543 helix: 0.85 (0.19), residues: 811 sheet: -0.30 (0.36), residues: 192 loop : -0.98 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 93 HIS 0.001 0.000 HIS C 111 PHE 0.010 0.001 PHE E 97 TYR 0.007 0.001 TYR E 145 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 641) hydrogen bonds : angle 4.85632 ( 1866) covalent geometry : bond 0.00290 (12587) covalent geometry : angle 0.48077 (17011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 257 LYS cc_start: 0.8560 (ptpp) cc_final: 0.8281 (ptpt) REVERT: B 46 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 53 ASP cc_start: 0.8645 (m-30) cc_final: 0.8434 (m-30) REVERT: E 190 CYS cc_start: 0.7882 (m) cc_final: 0.7618 (t) outliers start: 17 outliers final: 10 residues processed: 155 average time/residue: 1.6310 time to fit residues: 271.6616 Evaluate side-chains 137 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 255 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.089442 restraints weight = 15832.724| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.38 r_work: 0.2844 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12587 Z= 0.132 Angle : 0.487 5.492 17011 Z= 0.259 Chirality : 0.044 0.207 1891 Planarity : 0.004 0.049 2161 Dihedral : 4.134 15.368 1681 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.12 % Allowed : 10.05 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1543 helix: 1.06 (0.19), residues: 811 sheet: -0.24 (0.36), residues: 192 loop : -0.90 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 93 HIS 0.001 0.000 HIS F 240 PHE 0.011 0.001 PHE F 20 TYR 0.007 0.001 TYR E 145 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 641) hydrogen bonds : angle 4.77954 ( 1866) covalent geometry : bond 0.00316 (12587) covalent geometry : angle 0.48720 (17011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: B 34 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: B 46 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: B 182 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7932 (mttm) REVERT: B 185 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8604 (mttp) REVERT: E 190 CYS cc_start: 0.7921 (m) cc_final: 0.7630 (t) outliers start: 28 outliers final: 10 residues processed: 162 average time/residue: 1.6220 time to fit residues: 281.5316 Evaluate side-chains 140 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 255 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 111 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.101674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089053 restraints weight = 15649.760| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.35 r_work: 0.2790 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12587 Z= 0.191 Angle : 0.551 5.615 17011 Z= 0.291 Chirality : 0.046 0.218 1891 Planarity : 0.004 0.049 2161 Dihedral : 4.321 16.606 1681 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.81 % Allowed : 11.34 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1543 helix: 0.93 (0.19), residues: 813 sheet: -0.22 (0.36), residues: 192 loop : -0.92 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 93 HIS 0.002 0.000 HIS C 111 PHE 0.013 0.002 PHE F 20 TYR 0.009 0.002 TYR E 103 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.05713 ( 641) hydrogen bonds : angle 4.94496 ( 1866) covalent geometry : bond 0.00472 (12587) covalent geometry : angle 0.55064 (17011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.405 Fit side-chains REVERT: A 7 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: B 34 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: B 46 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: B 182 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7950 (mttm) REVERT: B 185 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8629 (mttp) REVERT: E 6 ARG cc_start: 0.8287 (ptt90) cc_final: 0.7593 (ptt180) REVERT: E 190 CYS cc_start: 0.7918 (m) cc_final: 0.7644 (t) REVERT: E 191 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: F 100 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7311 (ptt-90) REVERT: F 142 ASP cc_start: 0.8833 (p0) cc_final: 0.8557 (p0) outliers start: 24 outliers final: 11 residues processed: 151 average time/residue: 1.7461 time to fit residues: 281.3523 Evaluate side-chains 136 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 255 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 29 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.090106 restraints weight = 16036.912| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.39 r_work: 0.2816 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12587 Z= 0.123 Angle : 0.479 5.478 17011 Z= 0.254 Chirality : 0.043 0.202 1891 Planarity : 0.004 0.049 2161 Dihedral : 4.119 15.367 1681 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.66 % Allowed : 11.87 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.21), residues: 1543 helix: 1.25 (0.19), residues: 811 sheet: -0.19 (0.36), residues: 192 loop : -0.83 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 93 HIS 0.001 0.000 HIS C 111 PHE 0.010 0.001 PHE E 97 TYR 0.006 0.001 TYR B 103 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 641) hydrogen bonds : angle 4.72770 ( 1866) covalent geometry : bond 0.00289 (12587) covalent geometry : angle 0.47916 (17011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: A 233 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8779 (tttt) REVERT: B 34 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: B 46 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 185 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: E 6 ARG cc_start: 0.8242 (ptt90) cc_final: 0.7520 (ptt180) REVERT: E 190 CYS cc_start: 0.7853 (m) cc_final: 0.7595 (t) outliers start: 22 outliers final: 11 residues processed: 150 average time/residue: 2.1178 time to fit residues: 340.5809 Evaluate side-chains 136 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 255 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 89 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 138 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.091128 restraints weight = 15819.725| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.38 r_work: 0.2854 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12587 Z= 0.106 Angle : 0.457 5.423 17011 Z= 0.243 Chirality : 0.043 0.192 1891 Planarity : 0.004 0.048 2161 Dihedral : 3.998 14.609 1681 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.51 % Allowed : 12.32 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1543 helix: 1.41 (0.19), residues: 813 sheet: -0.16 (0.36), residues: 192 loop : -0.80 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 93 HIS 0.001 0.000 HIS B 111 PHE 0.009 0.001 PHE E 97 TYR 0.006 0.001 TYR C 145 ARG 0.003 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 641) hydrogen bonds : angle 4.59224 ( 1866) covalent geometry : bond 0.00240 (12587) covalent geometry : angle 0.45656 (17011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: A 233 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8774 (tttt) REVERT: B 34 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: B 46 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: B 185 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8505 (mttp) REVERT: E 6 ARG cc_start: 0.8235 (ptt90) cc_final: 0.7494 (ptt180) REVERT: E 190 CYS cc_start: 0.7917 (m) cc_final: 0.7673 (t) REVERT: F 245 ASN cc_start: 0.7986 (p0) cc_final: 0.6835 (m110) outliers start: 20 outliers final: 8 residues processed: 150 average time/residue: 1.6596 time to fit residues: 266.0232 Evaluate side-chains 135 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3103 r_free = 0.3103 target = 0.103004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.090212 restraints weight = 15928.057| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.38 r_work: 0.2834 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12587 Z= 0.131 Angle : 0.487 5.474 17011 Z= 0.259 Chirality : 0.044 0.197 1891 Planarity : 0.004 0.048 2161 Dihedral : 4.074 15.101 1681 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.44 % Allowed : 12.55 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1543 helix: 1.40 (0.19), residues: 804 sheet: -0.14 (0.36), residues: 192 loop : -0.83 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 93 HIS 0.001 0.000 HIS F 240 PHE 0.011 0.001 PHE E 97 TYR 0.007 0.001 TYR E 145 ARG 0.004 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 641) hydrogen bonds : angle 4.66901 ( 1866) covalent geometry : bond 0.00312 (12587) covalent geometry : angle 0.48738 (17011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: A 233 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8803 (tttt) REVERT: A 279 ARG cc_start: 0.4014 (OUTLIER) cc_final: 0.1254 (ptm-80) REVERT: B 34 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: B 46 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: B 185 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8573 (mttp) REVERT: E 6 ARG cc_start: 0.8248 (ptt90) cc_final: 0.7508 (ptt180) REVERT: E 190 CYS cc_start: 0.7945 (m) cc_final: 0.7701 (t) REVERT: F 245 ASN cc_start: 0.8084 (p0) cc_final: 0.6944 (m110) outliers start: 19 outliers final: 7 residues processed: 142 average time/residue: 1.6780 time to fit residues: 254.7798 Evaluate side-chains 134 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3096 r_free = 0.3096 target = 0.102457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.089654 restraints weight = 15881.681| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.38 r_work: 0.2827 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12587 Z= 0.140 Angle : 0.498 5.510 17011 Z= 0.264 Chirality : 0.044 0.214 1891 Planarity : 0.004 0.048 2161 Dihedral : 4.124 15.380 1681 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.36 % Allowed : 12.85 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1543 helix: 1.36 (0.19), residues: 804 sheet: -0.13 (0.36), residues: 192 loop : -0.82 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 93 HIS 0.001 0.000 HIS C 111 PHE 0.011 0.001 PHE E 97 TYR 0.007 0.001 TYR E 145 ARG 0.005 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 641) hydrogen bonds : angle 4.71452 ( 1866) covalent geometry : bond 0.00337 (12587) covalent geometry : angle 0.49828 (17011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: A 279 ARG cc_start: 0.4097 (OUTLIER) cc_final: 0.1285 (ptm-80) REVERT: B 34 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8018 (mt-10) REVERT: B 46 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: B 185 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8585 (mttp) REVERT: E 6 ARG cc_start: 0.8258 (ptt90) cc_final: 0.7519 (ptt180) REVERT: E 190 CYS cc_start: 0.7938 (m) cc_final: 0.7693 (t) REVERT: E 246 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8086 (ttmm) REVERT: F 100 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7392 (ptt-90) REVERT: F 245 ASN cc_start: 0.8118 (p0) cc_final: 0.6974 (m110) outliers start: 18 outliers final: 8 residues processed: 136 average time/residue: 1.6506 time to fit residues: 239.9990 Evaluate side-chains 133 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3093 r_free = 0.3093 target = 0.102249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.089465 restraints weight = 15813.422| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.38 r_work: 0.2821 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12587 Z= 0.145 Angle : 0.505 5.527 17011 Z= 0.268 Chirality : 0.045 0.213 1891 Planarity : 0.004 0.048 2161 Dihedral : 4.151 15.658 1681 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.74 % Allowed : 12.55 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1543 helix: 1.32 (0.19), residues: 809 sheet: -0.12 (0.36), residues: 192 loop : -0.80 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 93 HIS 0.001 0.000 HIS C 111 PHE 0.011 0.001 PHE E 97 TYR 0.007 0.001 TYR B 103 ARG 0.005 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.04872 ( 641) hydrogen bonds : angle 4.74105 ( 1866) covalent geometry : bond 0.00351 (12587) covalent geometry : angle 0.50500 (17011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: A 233 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8802 (tttt) REVERT: A 279 ARG cc_start: 0.4198 (OUTLIER) cc_final: 0.1327 (ptm-80) REVERT: B 34 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 46 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: B 182 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7886 (mttm) REVERT: B 185 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8552 (mttp) REVERT: E 6 ARG cc_start: 0.8254 (ptt90) cc_final: 0.7513 (ptt180) REVERT: E 190 CYS cc_start: 0.7939 (m) cc_final: 0.7711 (t) REVERT: E 246 LYS cc_start: 0.8478 (ttmt) cc_final: 0.8046 (ttmm) REVERT: F 100 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7382 (ptt-90) REVERT: F 245 ASN cc_start: 0.8133 (p0) cc_final: 0.6970 (m110) outliers start: 23 outliers final: 9 residues processed: 142 average time/residue: 1.6926 time to fit residues: 256.6932 Evaluate side-chains 136 residues out of total 1373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 221 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 118 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 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 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090802 restraints weight = 15857.930| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.39 r_work: 0.2851 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12587 Z= 0.116 Angle : 0.472 5.461 17011 Z= 0.251 Chirality : 0.043 0.207 1891 Planarity : 0.004 0.048 2161 Dihedral : 4.042 15.017 1681 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.36 % Allowed : 13.00 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1543 helix: 1.45 (0.19), residues: 806 sheet: -0.11 (0.36), residues: 192 loop : -0.79 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 93 HIS 0.001 0.000 HIS F 111 PHE 0.009 0.001 PHE E 97 TYR 0.006 0.001 TYR E 145 ARG 0.005 0.000 ARG E 50 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 641) hydrogen bonds : angle 4.62420 ( 1866) covalent geometry : bond 0.00271 (12587) covalent geometry : angle 0.47246 (17011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8410.33 seconds wall clock time: 146 minutes 16.36 seconds (8776.36 seconds total)