Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 16:39:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/04_2023/8hsc_34993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/04_2023/8hsc_34993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/04_2023/8hsc_34993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/04_2023/8hsc_34993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/04_2023/8hsc_34993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsc_34993/04_2023/8hsc_34993.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.022 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 70 5.16 5 C 6469 2.51 5 N 1751 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 147": "OD1" <-> "OD2" Residue "R PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 74": "OD1" <-> "OD2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10180 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 747 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2008 Classifications: {'peptide': 273} Incomplete info: {'n_c_alpha_c_only': 11, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 259} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.66, per 1000 atoms: 0.56 Number of scatterers: 10180 At special positions: 0 Unit cell: (92.352, 121.472, 158.912, 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 70 16.00 O 1890 8.00 N 1751 7.00 C 6469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 309 " - pdb=" SG CYS E 374 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 122 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 19 sheets defined 31.7% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.659A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.162A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.579A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.820A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.897A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.514A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'F' and resid 47 through 51 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'R' and resid 33 through 43 removed outlier: 3.947A pdb=" N GLU R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 49 removed outlier: 4.294A pdb=" N THR R 48 " --> pdb=" O GLU R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 79 removed outlier: 4.346A pdb=" N VAL R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 116 Proline residue: R 107 - end of helix removed outlier: 4.291A pdb=" N PHE R 110 " --> pdb=" O LEU R 106 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA R 111 " --> pdb=" O PRO R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 129 Processing helix chain 'R' and resid 130 through 133 removed outlier: 3.686A pdb=" N ASN R 133 " --> pdb=" O TYR R 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 138 through 153 Processing helix chain 'R' and resid 162 through 183 removed outlier: 4.370A pdb=" N CYS R 166 " --> pdb=" O ARG R 162 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA R 167 " --> pdb=" O GLN R 163 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY R 179 " --> pdb=" O TRP R 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 180 " --> pdb=" O LEU R 176 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 205 removed outlier: 3.815A pdb=" N THR R 201 " --> pdb=" O VAL R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 223 removed outlier: 3.561A pdb=" N ARG R 218 " --> pdb=" O VAL R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 254 removed outlier: 3.870A pdb=" N MET R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL R 246 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 264 removed outlier: 3.812A pdb=" N HIS R 258 " --> pdb=" O PHE R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 282 removed outlier: 3.716A pdb=" N TYR R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 removed outlier: 3.733A pdb=" N ASN R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER R 290 " --> pdb=" O SER R 286 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS R 291 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 311 removed outlier: 3.906A pdb=" N ALA R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR R 307 " --> pdb=" O GLY R 303 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL R 308 " --> pdb=" O PHE R 304 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.145A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.156A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AA2, first strand: chain 'E' and resid 297 through 298 removed outlier: 6.990A pdb=" N LEU E 297 " --> pdb=" O GLU E 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 330 through 334 removed outlier: 5.095A pdb=" N LEU E 332 " --> pdb=" O GLN E 323 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N GLN E 323 " --> pdb=" O LEU E 332 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.616A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.753A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.062A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.737A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 151 removed outlier: 6.520A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.136A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.939A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AB4, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.522A pdb=" N GLU F 29 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR F 139 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE F 53 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE F 69 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.522A pdb=" N GLU F 29 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR F 139 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR F 131 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.052A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.052A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AC1, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.734A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1281 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: 3.32 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2587 1.33 - 1.46: 3257 1.46 - 1.60: 4449 1.60 - 1.73: 0 1.73 - 1.86: 98 Bond restraints: 10391 Sorted by residual: bond pdb=" CG ASN R 94 " pdb=" OD1 ASN R 94 " ideal model delta sigma weight residual 1.231 1.199 0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " ideal model delta sigma weight residual 1.808 1.861 -0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" C THR R 86 " pdb=" N PRO R 87 " ideal model delta sigma weight residual 1.334 1.357 -0.023 1.51e-02 4.39e+03 2.31e+00 bond pdb=" CG ASN R 94 " pdb=" ND2 ASN R 94 " ideal model delta sigma weight residual 1.328 1.297 0.031 2.10e-02 2.27e+03 2.18e+00 bond pdb=" CG ARG C 62 " pdb=" CD ARG C 62 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.84e+00 ... (remaining 10386 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.48: 158 105.48 - 112.64: 5427 112.64 - 119.80: 3409 119.80 - 126.95: 4969 126.95 - 134.11: 125 Bond angle restraints: 14088 Sorted by residual: angle pdb=" C LYS S 76 " pdb=" N ASN S 77 " pdb=" CA ASN S 77 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CA CYS R 119 " pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " ideal model delta sigma weight residual 114.40 123.17 -8.77 2.30e+00 1.89e-01 1.45e+01 angle pdb=" CG ARG C 62 " pdb=" CD ARG C 62 " pdb=" NE ARG C 62 " ideal model delta sigma weight residual 112.00 119.76 -7.76 2.20e+00 2.07e-01 1.24e+01 angle pdb=" CB MET C 21 " pdb=" CG MET C 21 " pdb=" SD MET C 21 " ideal model delta sigma weight residual 112.70 122.98 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA GLN E 375 " pdb=" CB GLN E 375 " pdb=" CG GLN E 375 " ideal model delta sigma weight residual 114.10 120.94 -6.84 2.00e+00 2.50e-01 1.17e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5142 17.94 - 35.88: 732 35.88 - 53.82: 197 53.82 - 71.75: 42 71.75 - 89.69: 13 Dihedral angle restraints: 6126 sinusoidal: 2271 harmonic: 3855 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA ASN R 133 " pdb=" C ASN R 133 " pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA ARG R 117 " pdb=" C ARG R 117 " pdb=" N GLY R 118 " pdb=" CA GLY R 118 " ideal model delta harmonic sigma weight residual -180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1334 0.057 - 0.115: 245 0.115 - 0.172: 26 0.172 - 0.229: 8 0.229 - 0.287: 1 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CG LEU B 210 " pdb=" CB LEU B 210 " pdb=" CD1 LEU B 210 " pdb=" CD2 LEU B 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR R 98 " pdb=" CA THR R 98 " pdb=" OG1 THR R 98 " pdb=" CG2 THR R 98 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU R 132 " pdb=" CB LEU R 132 " pdb=" CD1 LEU R 132 " pdb=" CD2 LEU R 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1611 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 86 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO R 87 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 87 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 87 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 140 " -0.023 2.00e-02 2.50e+03 1.77e-02 5.50e+00 pdb=" CG PHE R 140 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE R 140 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE R 140 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE R 140 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE R 140 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE R 140 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 173 " 0.010 2.00e-02 2.50e+03 1.51e-02 3.97e+00 pdb=" CG PHE R 173 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE R 173 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 173 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 173 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 173 " -0.000 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 400 2.71 - 3.26: 9543 3.26 - 3.80: 16632 3.80 - 4.35: 20168 4.35 - 4.90: 35260 Nonbonded interactions: 82003 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.228 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.234 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.247 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.264 2.440 ... (remaining 81998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.980 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.120 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: 0.010 Load rotamer database and sin/cos tables:4.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.053 10391 Z= 0.232 Angle : 0.696 10.276 14088 Z= 0.365 Chirality : 0.047 0.287 1614 Planarity : 0.005 0.067 1783 Dihedral : 18.311 89.693 3639 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.27 (0.23), residues: 1323 helix: -0.69 (0.26), residues: 361 sheet: -0.45 (0.26), residues: 390 loop : -1.08 (0.26), residues: 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 1.388 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 173 average time/residue: 0.2437 time to fit residues: 58.7815 Evaluate side-chains 173 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0987 time to fit residues: 2.4811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN R 272 HIS R 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 10391 Z= 0.349 Angle : 0.590 6.943 14088 Z= 0.316 Chirality : 0.043 0.177 1614 Planarity : 0.004 0.058 1783 Dihedral : 4.710 23.389 1447 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 6.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.96 (0.23), residues: 1323 helix: 0.13 (0.28), residues: 371 sheet: -0.52 (0.26), residues: 386 loop : -1.12 (0.27), residues: 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 177 time to evaluate : 1.319 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 36 residues processed: 223 average time/residue: 0.2347 time to fit residues: 72.9150 Evaluate side-chains 208 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.0977 time to fit residues: 8.1284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 331 ASN A 347 ASN C 11 GLN R 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10391 Z= 0.249 Angle : 0.541 6.828 14088 Z= 0.288 Chirality : 0.042 0.154 1614 Planarity : 0.004 0.049 1783 Dihedral : 4.472 23.768 1447 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 3.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.74 (0.23), residues: 1323 helix: 0.51 (0.28), residues: 373 sheet: -0.45 (0.26), residues: 381 loop : -1.10 (0.27), residues: 569 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 1.293 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 214 average time/residue: 0.2291 time to fit residues: 68.7629 Evaluate side-chains 201 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0984 time to fit residues: 5.9412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 269 ASN C 11 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 10391 Z= 0.380 Angle : 0.613 11.992 14088 Z= 0.325 Chirality : 0.044 0.183 1614 Planarity : 0.004 0.048 1783 Dihedral : 4.698 24.073 1447 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 5.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.89 (0.23), residues: 1323 helix: 0.59 (0.28), residues: 374 sheet: -0.74 (0.25), residues: 397 loop : -1.19 (0.27), residues: 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 175 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 28 residues processed: 207 average time/residue: 0.2376 time to fit residues: 68.2537 Evaluate side-chains 199 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.222 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.0963 time to fit residues: 6.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN F 62 GLN R 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.068 10391 Z= 0.590 Angle : 0.716 7.953 14088 Z= 0.382 Chirality : 0.049 0.199 1614 Planarity : 0.004 0.045 1783 Dihedral : 5.156 24.899 1447 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.24 % Favored : 91.69 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.28 (0.23), residues: 1323 helix: 0.31 (0.28), residues: 373 sheet: -1.03 (0.25), residues: 381 loop : -1.40 (0.26), residues: 569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 1.292 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 28 residues processed: 216 average time/residue: 0.2351 time to fit residues: 71.0300 Evaluate side-chains 207 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1164 time to fit residues: 7.2579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN A 306 GLN C 11 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10391 Z= 0.176 Angle : 0.547 7.528 14088 Z= 0.286 Chirality : 0.042 0.151 1614 Planarity : 0.004 0.046 1783 Dihedral : 4.527 23.687 1447 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.77 (0.23), residues: 1323 helix: 0.70 (0.28), residues: 372 sheet: -0.57 (0.26), residues: 371 loop : -1.20 (0.26), residues: 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 203 average time/residue: 0.2411 time to fit residues: 67.7639 Evaluate side-chains 190 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0961 time to fit residues: 3.1087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 10391 Z= 0.383 Angle : 0.634 10.332 14088 Z= 0.334 Chirality : 0.046 0.238 1614 Planarity : 0.004 0.045 1783 Dihedral : 4.745 24.205 1447 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.94 (0.23), residues: 1323 helix: 0.61 (0.29), residues: 373 sheet: -0.88 (0.26), residues: 375 loop : -1.17 (0.26), residues: 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 201 average time/residue: 0.2441 time to fit residues: 69.7486 Evaluate side-chains 193 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1033 time to fit residues: 3.6844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 86 optimal weight: 0.0470 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 0.0370 chunk 114 optimal weight: 5.9990 overall best weight: 1.0958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 ASN C 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10391 Z= 0.208 Angle : 0.571 9.821 14088 Z= 0.296 Chirality : 0.042 0.193 1614 Planarity : 0.004 0.042 1783 Dihedral : 4.496 23.817 1447 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.70 (0.24), residues: 1323 helix: 0.77 (0.29), residues: 372 sheet: -0.57 (0.26), residues: 371 loop : -1.12 (0.27), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 1.317 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 188 average time/residue: 0.2380 time to fit residues: 62.4489 Evaluate side-chains 186 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0988 time to fit residues: 3.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 10391 Z= 0.260 Angle : 0.593 9.697 14088 Z= 0.310 Chirality : 0.043 0.158 1614 Planarity : 0.004 0.044 1783 Dihedral : 4.521 23.331 1447 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.67 (0.24), residues: 1323 helix: 0.74 (0.28), residues: 373 sheet: -0.60 (0.26), residues: 384 loop : -1.04 (0.27), residues: 566 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.128 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 186 average time/residue: 0.2367 time to fit residues: 61.4215 Evaluate side-chains 184 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0964 time to fit residues: 2.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10391 Z= 0.263 Angle : 0.598 9.576 14088 Z= 0.313 Chirality : 0.043 0.170 1614 Planarity : 0.004 0.045 1783 Dihedral : 4.550 23.668 1447 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.71 (0.24), residues: 1323 helix: 0.72 (0.28), residues: 373 sheet: -0.62 (0.26), residues: 378 loop : -1.07 (0.27), residues: 572 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 1.203 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 174 average time/residue: 0.2486 time to fit residues: 59.9906 Evaluate side-chains 173 residues out of total 1140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0936 time to fit residues: 2.0308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.165507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.112224 restraints weight = 14202.222| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.06 r_work: 0.3372 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10391 Z= 0.224 Angle : 0.576 9.550 14088 Z= 0.301 Chirality : 0.042 0.157 1614 Planarity : 0.004 0.045 1783 Dihedral : 4.430 23.154 1447 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.64 (0.24), residues: 1323 helix: 0.77 (0.28), residues: 373 sheet: -0.60 (0.26), residues: 380 loop : -1.02 (0.27), residues: 570 =============================================================================== Job complete usr+sys time: 2502.88 seconds wall clock time: 46 minutes 10.87 seconds (2770.87 seconds total)