Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:30:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpg_0745/04_2023/6kpg_0745_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.004 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 67 5.16 5 C 5623 2.51 5 N 1500 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 258": "OE1" <-> "OE2" Residue "S ASP 189": "OD1" <-> "OD2" 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: 8805 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1771 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2592 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2223 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1755 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'8D0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.05, per 1000 atoms: 0.57 Number of scatterers: 8805 At special positions: 0 Unit cell: (105.04, 118.56, 105.04, 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 67 16.00 O 1615 8.00 N 1500 7.00 C 5623 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 257 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 3.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 14 sheets defined 29.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 removed outlier: 3.502A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.535A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.777A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.693A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'B' and resid 4 through 23 removed outlier: 3.779A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 23 removed outlier: 3.753A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 33 No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 37 through 47 removed outlier: 3.573A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 138 removed outlier: 3.523A pdb=" N ILE R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 131 " --> pdb=" O GLY R 127 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 151 through 162 removed outlier: 3.663A pdb=" N ILE R 156 " --> pdb=" O TYR R 153 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU R 159 " --> pdb=" O ILE R 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL R 161 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA R 162 " --> pdb=" O LEU R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 175 removed outlier: 3.704A pdb=" N TYR R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 219 removed outlier: 3.515A pdb=" N THR R 201 " --> pdb=" O THR R 197 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL R 204 " --> pdb=" O PHE R 200 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 227 removed outlier: 3.669A pdb=" N TYR R 224 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS R 225 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 245 removed outlier: 3.776A pdb=" N VAL R 234 " --> pdb=" O ARG R 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU R 239 " --> pdb=" O VAL R 235 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE R 245 " --> pdb=" O TRP R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 253 No H-bonds generated for 'chain 'R' and resid 250 through 253' Processing helix chain 'R' and resid 279 through 300 removed outlier: 5.206A pdb=" N LEU R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 289 " --> pdb=" O VAL R 285 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET R 295 " --> pdb=" O VAL R 291 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 305 No H-bonds generated for 'chain 'R' and resid 302 through 305' Processing helix chain 'R' and resid 307 through 310 No H-bonds generated for 'chain 'R' and resid 307 through 310' Processing helix chain 'R' and resid 337 through 349 removed outlier: 3.677A pdb=" N LEU R 341 " --> pdb=" O MET R 337 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS R 343 " --> pdb=" O ILE R 339 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR R 344 " --> pdb=" O GLU R 340 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 354 No H-bonds generated for 'chain 'R' and resid 351 through 354' Processing helix chain 'R' and resid 356 through 366 removed outlier: 3.538A pdb=" N MET R 363 " --> pdb=" O LEU R 359 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 373 through 380 removed outlier: 3.819A pdb=" N ALA R 380 " --> pdb=" O LYS R 376 " (cutoff:3.500A) Processing helix chain 'R' and resid 385 through 393 removed outlier: 3.731A pdb=" N SER R 390 " --> pdb=" O CYS R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 402 through 410 removed outlier: 4.536A pdb=" N ALA R 407 " --> pdb=" O ASP R 403 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.660A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 removed outlier: 6.894A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.000A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 6.088A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.620A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.654A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.877A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.557A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.828A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.261A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 4 through 6 removed outlier: 3.614A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.760A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.780A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER S 196 " --> pdb=" O ALA S 199 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.506A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 702 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: 2.52 Time building geometry restraints manager: 3.65 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: 2090 1.33 - 1.45: 2119 1.45 - 1.58: 4678 1.58 - 1.70: 3 1.70 - 1.82: 96 Bond restraints: 8986 Sorted by residual: bond pdb=" C26 8D0 R 501 " pdb=" N1 8D0 R 501 " ideal model delta sigma weight residual 1.512 1.202 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C6 8D0 R 501 " pdb=" O1 8D0 R 501 " ideal model delta sigma weight residual 1.594 1.371 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C9 8D0 R 501 " pdb=" O1 8D0 R 501 " ideal model delta sigma weight residual 1.617 1.412 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C26 8D0 R 501 " pdb=" S1 8D0 R 501 " ideal model delta sigma weight residual 1.787 1.583 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C23 8D0 R 501 " pdb=" C24 8D0 R 501 " ideal model delta sigma weight residual 1.346 1.538 -0.192 2.00e-02 2.50e+03 9.18e+01 ... (remaining 8981 not shown) Histogram of bond angle deviations from ideal: 98.39 - 114.53: 5497 114.53 - 130.68: 6626 130.68 - 146.82: 49 146.82 - 162.96: 0 162.96 - 179.10: 1 Bond angle restraints: 12173 Sorted by residual: angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 109.81 123.06 -13.25 2.21e+00 2.05e-01 3.59e+01 angle pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " pdb=" CG TYR S 223 " ideal model delta sigma weight residual 113.90 104.72 9.18 1.80e+00 3.09e-01 2.60e+01 angle pdb=" N VAL R 249 " pdb=" CA VAL R 249 " pdb=" C VAL R 249 " ideal model delta sigma weight residual 112.29 107.67 4.62 9.40e-01 1.13e+00 2.41e+01 angle pdb=" C CYS A 3 " pdb=" N THR A 4 " pdb=" CA THR A 4 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C ILE A 285 " pdb=" CA ILE A 285 " pdb=" CB ILE A 285 " ideal model delta sigma weight residual 111.81 106.61 5.20 1.25e+00 6.40e-01 1.73e+01 ... (remaining 12168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 4971 22.69 - 45.38: 322 45.38 - 68.07: 22 68.07 - 90.77: 6 90.77 - 113.46: 2 Dihedral angle restraints: 5323 sinusoidal: 2031 harmonic: 3292 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 148.40 31.60 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA THR B 86 " pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta harmonic sigma weight residual -180.00 -149.90 -30.10 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA LEU R 276 " pdb=" C LEU R 276 " pdb=" N MET R 277 " pdb=" CA MET R 277 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 5320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1219 0.093 - 0.186: 166 0.186 - 0.280: 13 0.280 - 0.373: 0 0.373 - 0.466: 1 Chirality restraints: 1399 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1396 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 230 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO R 231 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR S 223 " 0.015 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C TYR S 223 " -0.050 2.00e-02 2.50e+03 pdb=" O TYR S 223 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO S 224 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 140 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C ALA B 140 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA B 140 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY B 141 " 0.016 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1704 2.76 - 3.29: 7974 3.29 - 3.83: 14872 3.83 - 4.36: 18267 4.36 - 4.90: 31354 Nonbonded interactions: 74171 Sorted by model distance: nonbonded pdb=" O ILE R 247 " pdb=" OH TYR R 275 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.249 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 2.440 ... (remaining 74166 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.370 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.920 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.014 0.310 8986 Z= 0.940 Angle : 1.090 13.246 12173 Z= 0.580 Chirality : 0.063 0.466 1399 Planarity : 0.007 0.078 1522 Dihedral : 14.618 113.457 3191 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.09 % 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: -5.14 (0.19), residues: 1119 helix: -4.49 (0.12), residues: 372 sheet: -3.37 (0.25), residues: 243 loop : -2.33 (0.24), residues: 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 207 average time/residue: 1.1261 time to fit residues: 249.4257 Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0788 time to fit residues: 1.5032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.2980 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 195 HIS A 213 HIS ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 306 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 62 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 119 ASN B 175 GLN B 259 GLN B 340 ASN C 24 ASN R 270 HIS R 406 HIS S 82 GLN S 113 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8986 Z= 0.232 Angle : 0.617 8.710 12173 Z= 0.318 Chirality : 0.042 0.289 1399 Planarity : 0.004 0.058 1522 Dihedral : 7.546 101.041 1233 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 4.88 % 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: -3.93 (0.21), residues: 1119 helix: -2.97 (0.20), residues: 379 sheet: -3.10 (0.25), residues: 257 loop : -1.74 (0.27), residues: 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 1.026 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 203 average time/residue: 1.0661 time to fit residues: 232.8410 Evaluate side-chains 169 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 10 residues processed: 11 average time/residue: 0.2795 time to fit residues: 5.3142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8986 Z= 0.219 Angle : 0.605 8.347 12173 Z= 0.306 Chirality : 0.042 0.270 1399 Planarity : 0.004 0.042 1522 Dihedral : 7.091 97.926 1233 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 6.16 % 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: -3.24 (0.23), residues: 1119 helix: -1.99 (0.24), residues: 384 sheet: -3.00 (0.25), residues: 251 loop : -1.55 (0.28), residues: 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 168 time to evaluate : 1.081 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 24 residues processed: 195 average time/residue: 1.0205 time to fit residues: 214.8401 Evaluate side-chains 172 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 148 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 11 average time/residue: 0.2966 time to fit residues: 5.5192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 306 GLN B 88 ASN C 18 GLN S 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.061 8986 Z= 0.518 Angle : 0.723 9.713 12173 Z= 0.373 Chirality : 0.048 0.343 1399 Planarity : 0.005 0.049 1522 Dihedral : 7.380 97.724 1233 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 7.32 % 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: -3.17 (0.23), residues: 1119 helix: -1.78 (0.24), residues: 394 sheet: -2.97 (0.26), residues: 248 loop : -1.65 (0.28), residues: 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 152 time to evaluate : 1.033 Fit side-chains outliers start: 69 outliers final: 40 residues processed: 199 average time/residue: 0.9727 time to fit residues: 209.4591 Evaluate side-chains 177 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 27 residues processed: 14 average time/residue: 0.4466 time to fit residues: 8.7948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 241 ASN A 256 ASN B 75 GLN S 113 GLN S 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8986 Z= 0.192 Angle : 0.605 8.239 12173 Z= 0.306 Chirality : 0.042 0.258 1399 Planarity : 0.004 0.038 1522 Dihedral : 6.807 98.238 1233 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 5.73 % 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: -2.63 (0.24), residues: 1119 helix: -1.17 (0.26), residues: 379 sheet: -2.71 (0.26), residues: 278 loop : -1.34 (0.29), residues: 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 157 time to evaluate : 1.058 Fit side-chains outliers start: 54 outliers final: 33 residues processed: 193 average time/residue: 0.9805 time to fit residues: 204.8671 Evaluate side-chains 178 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 11 average time/residue: 0.2513 time to fit residues: 5.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.199 Angle : 0.580 9.218 12173 Z= 0.295 Chirality : 0.042 0.278 1399 Planarity : 0.004 0.046 1522 Dihedral : 6.568 96.714 1233 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 5.94 % 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: -2.27 (0.24), residues: 1119 helix: -0.76 (0.27), residues: 379 sheet: -2.47 (0.28), residues: 261 loop : -1.35 (0.28), residues: 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 1.072 Fit side-chains revert: symmetry clash outliers start: 56 outliers final: 32 residues processed: 191 average time/residue: 0.9461 time to fit residues: 196.8211 Evaluate side-chains 180 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 9 average time/residue: 0.3272 time to fit residues: 4.9950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 241 ASN A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN S 113 GLN S 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.188 Angle : 0.586 9.646 12173 Z= 0.295 Chirality : 0.042 0.272 1399 Planarity : 0.004 0.056 1522 Dihedral : 6.404 95.721 1233 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 5.20 % 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: -2.04 (0.25), residues: 1119 helix: -0.48 (0.28), residues: 379 sheet: -2.29 (0.28), residues: 259 loop : -1.34 (0.28), residues: 481 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 165 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 32 residues processed: 197 average time/residue: 0.8859 time to fit residues: 190.7771 Evaluate side-chains 182 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 25 residues processed: 7 average time/residue: 0.1645 time to fit residues: 3.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8986 Z= 0.243 Angle : 0.622 9.765 12173 Z= 0.310 Chirality : 0.042 0.278 1399 Planarity : 0.004 0.057 1522 Dihedral : 6.413 95.546 1233 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 5.31 % 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: -1.94 (0.25), residues: 1119 helix: -0.32 (0.28), residues: 380 sheet: -2.29 (0.28), residues: 267 loop : -1.29 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 0.944 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 36 residues processed: 184 average time/residue: 1.0178 time to fit residues: 202.8198 Evaluate side-chains 180 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 24 residues processed: 12 average time/residue: 0.1458 time to fit residues: 4.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.208 Angle : 0.630 10.135 12173 Z= 0.311 Chirality : 0.042 0.262 1399 Planarity : 0.004 0.053 1522 Dihedral : 6.333 94.609 1233 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 4.25 % 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: -1.76 (0.25), residues: 1119 helix: -0.17 (0.28), residues: 380 sheet: -2.16 (0.28), residues: 264 loop : -1.23 (0.29), residues: 475 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 188 average time/residue: 0.9508 time to fit residues: 194.1158 Evaluate side-chains 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.2092 time to fit residues: 2.1741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8986 Z= 0.281 Angle : 0.653 11.505 12173 Z= 0.325 Chirality : 0.043 0.283 1399 Planarity : 0.004 0.060 1522 Dihedral : 6.290 94.931 1233 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 3.82 % 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: -1.85 (0.25), residues: 1119 helix: -0.31 (0.27), residues: 393 sheet: -2.12 (0.30), residues: 244 loop : -1.37 (0.29), residues: 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 0.994 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 29 residues processed: 174 average time/residue: 0.9311 time to fit residues: 175.9221 Evaluate side-chains 170 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.1556 time to fit residues: 2.3684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.0070 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 188 HIS A 241 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** R 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.178390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.131407 restraints weight = 11358.080| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.49 r_work: 0.3733 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8986 Z= 0.194 Angle : 0.641 11.622 12173 Z= 0.316 Chirality : 0.042 0.249 1399 Planarity : 0.004 0.051 1522 Dihedral : 5.998 91.959 1233 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 3.29 % 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: -1.70 (0.25), residues: 1119 helix: -0.14 (0.28), residues: 396 sheet: -2.02 (0.30), residues: 245 loop : -1.33 (0.28), residues: 478 =============================================================================== Job complete usr+sys time: 3848.08 seconds wall clock time: 69 minutes 11.81 seconds (4151.81 seconds total)