Starting phenix.real_space_refine on Sat Jul 20 23:21:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/07_2024/8ucs_42139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/07_2024/8ucs_42139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/07_2024/8ucs_42139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/07_2024/8ucs_42139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/07_2024/8ucs_42139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/07_2024/8ucs_42139.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 102 5.16 5 C 8038 2.51 5 N 2087 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 25": "OD1" <-> "OD2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "D ASP 5": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "E ASP 57": "OD1" <-> "OD2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 108": "OD1" <-> "OD2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F GLU 252": "OE1" <-> "OE2" Residue "F TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 147": "OD1" <-> "OD2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G GLU 252": "OE1" <-> "OE2" Residue "H ASP 304": "OD1" <-> "OD2" Residue "I ASP 262": "OD1" <-> "OD2" Residue "I ASP 304": "OD1" <-> "OD2" Residue "J GLU 241": "OE1" <-> "OE2" Residue "J GLU 257": "OE1" <-> "OE2" Residue "J ASP 262": "OD1" <-> "OD2" Residue "J GLU 273": "OE1" <-> "OE2" Residue "J GLU 306": "OE1" <-> "OE2" Residue "J GLU 321": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12605 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Conformer: "B" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} bond proxies already assigned to first conformer: 351 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 394 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "C" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1942 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "D" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "E" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1942 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "G" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1943 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.69, per 1000 atoms: 0.69 Number of scatterers: 12605 At special positions: 0 Unit cell: (98.406, 114.345, 127.512, 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 102 16.00 O 2378 8.00 N 2087 7.00 C 8038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.13 Conformation dependent library (CDL) restraints added in 2.3 seconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 1 sheets defined 86.6% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.799A pdb=" N PHE A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'B' and resid 17 through 40 removed outlier: 4.131A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.608A pdb=" N VAL C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.571A pdb=" N VAL C 32 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 57 through 72 removed outlier: 3.799A pdb=" N LYS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 95 removed outlier: 3.609A pdb=" N ARG C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.550A pdb=" N ASN C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 123 through 174 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.671A pdb=" N GLY C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 202 through 233 removed outlier: 4.177A pdb=" N GLY C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 42 through 54 Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.608A pdb=" N PHE D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 95 removed outlier: 3.662A pdb=" N ILE D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 123 through 174 Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 177 through 202 removed outlier: 3.678A pdb=" N THR D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 233 Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.740A pdb=" N VAL D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 249 through 258 removed outlier: 4.454A pdb=" N GLN D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 24 removed outlier: 3.742A pdb=" N VAL E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.764A pdb=" N VAL E 32 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.514A pdb=" N PHE E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.603A pdb=" N PHE E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.543A pdb=" N ASN E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 123 through 174 Proline residue: E 157 - end of helix removed outlier: 3.521A pdb=" N ASN E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 202 through 234 Processing helix chain 'E' and resid 236 through 246 removed outlier: 3.649A pdb=" N SER E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'F' and resid 6 through 24 Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 35 through 54 removed outlier: 3.618A pdb=" N GLY F 44 " --> pdb=" O PHE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 76 through 95 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.548A pdb=" N ASN F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 123 through 174 Proline residue: F 157 - end of helix removed outlier: 3.580A pdb=" N ASN F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 202 removed outlier: 3.654A pdb=" N THR F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 234 Processing helix chain 'F' and resid 238 through 245 removed outlier: 3.611A pdb=" N GLU F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 249 through 254 removed outlier: 4.193A pdb=" N GLN F 254 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 removed outlier: 3.745A pdb=" N GLY G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 55 through 72 removed outlier: 3.581A pdb=" N PHE G 70 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 94 Processing helix chain 'G' and resid 95 through 98 removed outlier: 3.589A pdb=" N SER G 98 " --> pdb=" O GLY G 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 98' Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 111 through 120 removed outlier: 3.643A pdb=" N VAL G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 174 Proline residue: G 157 - end of helix Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 189 through 202 Processing helix chain 'G' and resid 202 through 233 Processing helix chain 'G' and resid 236 through 246 removed outlier: 3.884A pdb=" N SER G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 260 removed outlier: 3.520A pdb=" N GLN G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 255 Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.531A pdb=" N ALA H 264 " --> pdb=" O THR H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 280 Processing helix chain 'H' and resid 283 through 295 Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 239 through 244 removed outlier: 4.130A pdb=" N ILE I 244 " --> pdb=" O GLU I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 256 removed outlier: 3.539A pdb=" N ARG I 253 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 254 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 256 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 268 removed outlier: 3.835A pdb=" N LYS I 268 " --> pdb=" O ALA I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 281 removed outlier: 3.665A pdb=" N ALA I 275 " --> pdb=" O SER I 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL I 277 " --> pdb=" O GLU I 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN I 281 " --> pdb=" O VAL I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 296 Processing helix chain 'I' and resid 301 through 319 removed outlier: 3.573A pdb=" N GLN I 310 " --> pdb=" O GLU I 306 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 311 " --> pdb=" O LYS I 307 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE I 316 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG I 317 " --> pdb=" O VAL I 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 256 removed outlier: 3.787A pdb=" N GLN J 252 " --> pdb=" O ASP J 248 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 253 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 268 removed outlier: 3.562A pdb=" N LYS J 268 " --> pdb=" O ALA J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 279 Processing helix chain 'J' and resid 283 through 298 removed outlier: 3.733A pdb=" N SER J 288 " --> pdb=" O LYS J 284 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 292 " --> pdb=" O SER J 288 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY J 298 " --> pdb=" O ILE J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 319 removed outlier: 4.138A pdb=" N GLU J 306 " --> pdb=" O ILE J 302 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS J 307 " --> pdb=" O MET J 303 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 316 " --> pdb=" O ILE J 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 991 hydrogen bonds defined for protein. 2928 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: 3.86 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4116 1.34 - 1.46: 2682 1.46 - 1.58: 5786 1.58 - 1.70: 0 1.70 - 1.81: 199 Bond restraints: 12783 Sorted by residual: bond pdb=" CB GLU I 292 " pdb=" CG GLU I 292 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB ASP J 293 " pdb=" CG ASP J 293 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.72e-01 bond pdb=" CB MET H 303 " pdb=" CG MET H 303 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.62e-01 bond pdb=" CB ASP F 86 " pdb=" CG ASP F 86 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.39e-01 bond pdb=" CB ASP I 262 " pdb=" CG ASP I 262 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.26e-01 ... (remaining 12778 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.98: 238 105.98 - 113.02: 7030 113.02 - 120.05: 4397 120.05 - 127.08: 5484 127.08 - 134.11: 76 Bond angle restraints: 17225 Sorted by residual: angle pdb=" CA MET H 303 " pdb=" CB MET H 303 " pdb=" CG MET H 303 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CB MET H 303 " pdb=" CG MET H 303 " pdb=" SD MET H 303 " ideal model delta sigma weight residual 112.70 121.76 -9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" N ILE F 6 " pdb=" CA ILE F 6 " pdb=" C ILE F 6 " ideal model delta sigma weight residual 113.10 110.36 2.74 9.70e-01 1.06e+00 7.98e+00 angle pdb=" CA GLU J 273 " pdb=" CB GLU J 273 " pdb=" CG GLU J 273 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.62e+00 angle pdb=" C ASP E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 ... (remaining 17220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6588 17.83 - 35.66: 852 35.66 - 53.48: 260 53.48 - 71.31: 55 71.31 - 89.14: 19 Dihedral angle restraints: 7774 sinusoidal: 3122 harmonic: 4652 Sorted by residual: dihedral pdb=" CA GLY C 227 " pdb=" C GLY C 227 " pdb=" N VAL C 228 " pdb=" CA VAL C 228 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL D 202 " pdb=" C VAL D 202 " pdb=" N PHE D 203 " pdb=" CA PHE D 203 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL F 202 " pdb=" C VAL F 202 " pdb=" N PHE F 203 " pdb=" CA PHE F 203 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1473 0.037 - 0.074: 450 0.074 - 0.111: 81 0.111 - 0.148: 7 0.148 - 0.185: 1 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA THR F 8 " pdb=" N THR F 8 " pdb=" C THR F 8 " pdb=" CB THR F 8 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CG LEU E 172 " pdb=" CB LEU E 172 " pdb=" CD1 LEU E 172 " pdb=" CD2 LEU E 172 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 122 " pdb=" N ILE C 122 " pdb=" C ILE C 122 " pdb=" CB ILE C 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 2009 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 303 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C MET H 303 " -0.040 2.00e-02 2.50e+03 pdb=" O MET H 303 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP H 304 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 236 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 237 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 237 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 237 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 250 " 0.028 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 251 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 251 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 251 " 0.024 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2490 2.77 - 3.30: 12723 3.30 - 3.83: 22411 3.83 - 4.37: 26233 4.37 - 4.90: 43397 Nonbonded interactions: 107254 Sorted by model distance: nonbonded pdb=" NH2 ARG C 238 " pdb=" OD2 ASP D 120 " model vdw 2.235 2.520 nonbonded pdb=" O GLY G 95 " pdb=" OG SER G 98 " model vdw 2.260 2.440 nonbonded pdb=" O GLY F 95 " pdb=" OG SER F 98 " model vdw 2.271 2.440 nonbonded pdb=" O ARG H 253 " pdb=" NH1 ARG H 253 " model vdw 2.274 2.520 nonbonded pdb=" O GLY D 22 " pdb=" OG SER D 25 " model vdw 2.281 2.440 ... (remaining 107249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 32 or resid 34 through 60)) selection = (chain 'B' and (resid 16 through 32 or resid 34 through 60)) } ncs_group { reference = (chain 'C' and resid 8 through 259) selection = (chain 'D' and resid 8 through 259) selection = (chain 'E' and resid 8 through 259) selection = (chain 'F' and resid 8 through 259) selection = (chain 'G' and resid 8 through 259) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 7.230 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: 0.000 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 38.040 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.060 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 0.032 12783 Z= 0.164 Angle : 0.485 9.064 17225 Z= 0.253 Chirality : 0.036 0.185 2012 Planarity : 0.004 0.051 2184 Dihedral : 18.156 89.141 4778 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.36 % Allowed : 28.89 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1613 helix: 0.70 (0.14), residues: 1354 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 21 HIS 0.001 0.000 HIS D 142 PHE 0.016 0.001 PHE C 59 TYR 0.006 0.001 TYR F 256 ARG 0.005 0.000 ARG I 317 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: D 223 MET cc_start: 0.8604 (ptm) cc_final: 0.8391 (ptt) REVERT: F 104 ASN cc_start: 0.7700 (m-40) cc_final: 0.7267 (m110) REVERT: F 108 ASP cc_start: 0.7627 (t70) cc_final: 0.7171 (t70) outliers start: 4 outliers final: 4 residues processed: 253 average time/residue: 1.3314 time to fit residues: 363.8690 Evaluate side-chains 237 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 29 ASN C 200 ASN D 29 ASN D 174 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12783 Z= 0.262 Angle : 0.574 7.948 17225 Z= 0.313 Chirality : 0.041 0.172 2012 Planarity : 0.005 0.050 2184 Dihedral : 4.949 53.952 1743 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.02 % Allowed : 24.60 % Favored : 70.38 % 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: 1.52 (0.21), residues: 1613 helix: 1.37 (0.14), residues: 1381 sheet: None (None), residues: 0 loop : -0.88 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 21 HIS 0.002 0.001 HIS G 142 PHE 0.024 0.002 PHE B 48 TYR 0.009 0.001 TYR E 110 ARG 0.004 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 245 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.7804 (tmtt) cc_final: 0.7198 (mttm) REVERT: C 68 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 72 ASP cc_start: 0.5707 (OUTLIER) cc_final: 0.4898 (p0) REVERT: C 187 LYS cc_start: 0.8354 (mppt) cc_final: 0.7519 (mmtt) REVERT: D 243 LYS cc_start: 0.6921 (ptpt) cc_final: 0.6704 (pttt) REVERT: F 14 LEU cc_start: 0.8428 (mt) cc_final: 0.8090 (tp) REVERT: F 108 ASP cc_start: 0.7598 (t70) cc_final: 0.7106 (t70) REVERT: G 141 ARG cc_start: 0.7998 (mtm-85) cc_final: 0.7638 (mtm110) outliers start: 68 outliers final: 23 residues processed: 282 average time/residue: 1.2949 time to fit residues: 394.9136 Evaluate side-chains 267 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN D 29 ASN D 209 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN I 310 GLN J 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12783 Z= 0.281 Angle : 0.566 8.733 17225 Z= 0.308 Chirality : 0.042 0.171 2012 Planarity : 0.005 0.051 2184 Dihedral : 4.716 55.522 1737 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.53 % Allowed : 23.80 % Favored : 70.67 % 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: 1.63 (0.21), residues: 1613 helix: 1.47 (0.14), residues: 1381 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 19 HIS 0.002 0.001 HIS G 142 PHE 0.026 0.002 PHE B 48 TYR 0.008 0.002 TYR E 110 ARG 0.004 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 240 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7946 (tp40) REVERT: B 47 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7199 (mttm) REVERT: C 68 GLN cc_start: 0.7167 (tm-30) cc_final: 0.6663 (tm-30) REVERT: C 72 ASP cc_start: 0.5532 (OUTLIER) cc_final: 0.4729 (p0) REVERT: C 81 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8329 (mm) REVERT: C 187 LYS cc_start: 0.8359 (mppt) cc_final: 0.7509 (mmtm) REVERT: E 112 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6960 (mtpt) REVERT: F 14 LEU cc_start: 0.8452 (mt) cc_final: 0.8090 (tp) REVERT: F 108 ASP cc_start: 0.7612 (t70) cc_final: 0.7131 (t70) REVERT: F 129 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7245 (pt0) REVERT: G 129 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: G 141 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7635 (mtm110) outliers start: 75 outliers final: 32 residues processed: 286 average time/residue: 1.3131 time to fit residues: 406.2789 Evaluate side-chains 274 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 10.0000 chunk 108 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 0.0470 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 0.0000 chunk 41 optimal weight: 0.9980 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 29 ASN C 105 ASN D 29 ASN F 254 GLN G 68 GLN G 236 ASN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12783 Z= 0.153 Angle : 0.481 7.930 17225 Z= 0.261 Chirality : 0.037 0.157 2012 Planarity : 0.004 0.050 2184 Dihedral : 4.383 49.143 1737 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.78 % Allowed : 25.91 % Favored : 70.31 % 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: 2.21 (0.22), residues: 1613 helix: 1.85 (0.14), residues: 1386 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.001 0.000 HIS D 142 PHE 0.020 0.001 PHE B 48 TYR 0.010 0.001 TYR E 110 ARG 0.003 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 249 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7917 (tp40) REVERT: B 47 LYS cc_start: 0.7781 (tmtt) cc_final: 0.7186 (mttm) REVERT: B 55 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7786 (ttm) REVERT: C 68 GLN cc_start: 0.7109 (tm-30) cc_final: 0.6696 (tm-30) REVERT: C 187 LYS cc_start: 0.8379 (mppt) cc_final: 0.7485 (mmtm) REVERT: F 14 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8098 (tp) REVERT: F 108 ASP cc_start: 0.7595 (t70) cc_final: 0.7122 (t70) outliers start: 51 outliers final: 14 residues processed: 278 average time/residue: 1.2697 time to fit residues: 382.6158 Evaluate side-chains 257 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 2 optimal weight: 0.0070 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12783 Z= 0.148 Angle : 0.469 7.651 17225 Z= 0.254 Chirality : 0.037 0.158 2012 Planarity : 0.004 0.049 2184 Dihedral : 4.286 47.196 1737 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.71 % Allowed : 25.69 % Favored : 70.60 % 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: 2.45 (0.22), residues: 1613 helix: 2.02 (0.14), residues: 1386 sheet: None (None), residues: 0 loop : -0.81 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 19 HIS 0.001 0.000 HIS G 142 PHE 0.020 0.001 PHE B 33 TYR 0.009 0.001 TYR F 110 ARG 0.003 0.000 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7929 (tp40) REVERT: B 56 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7094 (mt0) REVERT: C 68 GLN cc_start: 0.7025 (tm-30) cc_final: 0.6686 (tm-30) REVERT: C 92 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7354 (mtt-85) REVERT: C 187 LYS cc_start: 0.8379 (mppt) cc_final: 0.7480 (mmtm) REVERT: D 185 MET cc_start: 0.8838 (tpt) cc_final: 0.8630 (tpt) REVERT: F 14 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8103 (tp) REVERT: F 108 ASP cc_start: 0.7593 (t70) cc_final: 0.7135 (t70) REVERT: F 129 GLU cc_start: 0.7510 (pt0) cc_final: 0.7136 (pp20) REVERT: G 131 MET cc_start: 0.7405 (mtm) cc_final: 0.7202 (mmm) outliers start: 50 outliers final: 21 residues processed: 285 average time/residue: 1.2592 time to fit residues: 389.5143 Evaluate side-chains 270 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.0370 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12783 Z= 0.180 Angle : 0.501 11.822 17225 Z= 0.270 Chirality : 0.038 0.165 2012 Planarity : 0.004 0.050 2184 Dihedral : 4.360 50.213 1737 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.29 % Allowed : 25.55 % Favored : 70.16 % 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: 2.42 (0.22), residues: 1613 helix: 2.00 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.001 0.000 HIS G 142 PHE 0.021 0.002 PHE B 33 TYR 0.010 0.001 TYR F 110 ARG 0.004 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 243 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7930 (tp40) REVERT: B 56 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7180 (mt0) REVERT: C 68 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 72 ASP cc_start: 0.5292 (OUTLIER) cc_final: 0.4534 (p0) REVERT: C 92 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7383 (mtt-85) REVERT: C 187 LYS cc_start: 0.8387 (mppt) cc_final: 0.7514 (mmtm) REVERT: F 14 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8104 (tp) REVERT: F 108 ASP cc_start: 0.7597 (t70) cc_final: 0.7144 (t70) REVERT: F 123 GLU cc_start: 0.7124 (mp0) cc_final: 0.6913 (mp0) REVERT: F 125 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: F 129 GLU cc_start: 0.7524 (pt0) cc_final: 0.7161 (pp20) REVERT: H 303 MET cc_start: 0.5659 (tmm) cc_final: 0.5208 (tmm) outliers start: 58 outliers final: 29 residues processed: 276 average time/residue: 1.3034 time to fit residues: 388.9292 Evaluate side-chains 270 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12783 Z= 0.195 Angle : 0.509 10.114 17225 Z= 0.274 Chirality : 0.039 0.166 2012 Planarity : 0.004 0.053 2184 Dihedral : 4.411 51.753 1737 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.71 % Allowed : 26.13 % Favored : 70.16 % 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: 2.38 (0.22), residues: 1613 helix: 1.97 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : -0.88 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.001 0.001 HIS G 142 PHE 0.021 0.002 PHE F 70 TYR 0.010 0.001 TYR F 110 ARG 0.005 0.000 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7936 (tp40) REVERT: B 56 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7153 (mt0) REVERT: C 68 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6634 (tm-30) REVERT: C 72 ASP cc_start: 0.5353 (OUTLIER) cc_final: 0.4603 (p0) REVERT: C 92 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7364 (mtt-85) REVERT: C 187 LYS cc_start: 0.8390 (mppt) cc_final: 0.7529 (mmtm) REVERT: E 111 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7392 (mtm) REVERT: F 14 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8111 (tp) REVERT: F 108 ASP cc_start: 0.7602 (t70) cc_final: 0.7139 (t70) REVERT: F 123 GLU cc_start: 0.7146 (mp0) cc_final: 0.6923 (mp0) REVERT: F 125 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7148 (mm-30) REVERT: F 129 GLU cc_start: 0.7568 (pt0) cc_final: 0.7212 (pp20) REVERT: G 129 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: H 303 MET cc_start: 0.5591 (tmm) cc_final: 0.5134 (tmm) outliers start: 50 outliers final: 30 residues processed: 272 average time/residue: 1.2760 time to fit residues: 377.2136 Evaluate side-chains 276 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 174 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12783 Z= 0.260 Angle : 0.560 8.960 17225 Z= 0.300 Chirality : 0.041 0.173 2012 Planarity : 0.005 0.057 2184 Dihedral : 4.599 56.052 1737 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.22 % Allowed : 25.69 % Favored : 70.09 % 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: 2.11 (0.21), residues: 1613 helix: 1.78 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.88 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 PHE 0.024 0.002 PHE B 48 TYR 0.009 0.002 TYR F 110 ARG 0.007 0.000 ARG I 318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7746 (tp40) REVERT: B 47 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7236 (mttm) REVERT: C 68 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 72 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.4596 (p0) REVERT: C 92 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7357 (mtt-85) REVERT: C 187 LYS cc_start: 0.8366 (mppt) cc_final: 0.7510 (mmtt) REVERT: E 111 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7405 (mtm) REVERT: F 14 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8108 (tp) REVERT: F 108 ASP cc_start: 0.7625 (t70) cc_final: 0.7144 (t70) REVERT: F 129 GLU cc_start: 0.7554 (pt0) cc_final: 0.7220 (pp20) REVERT: G 129 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: H 303 MET cc_start: 0.5628 (tmm) cc_final: 0.5236 (tmm) outliers start: 57 outliers final: 29 residues processed: 272 average time/residue: 1.3310 time to fit residues: 391.4726 Evaluate side-chains 271 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 0.0670 chunk 134 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 174 ASN D 209 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12783 Z= 0.250 Angle : 0.562 8.649 17225 Z= 0.300 Chirality : 0.040 0.172 2012 Planarity : 0.005 0.059 2184 Dihedral : 4.618 54.942 1737 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.93 % Allowed : 26.13 % Favored : 69.94 % 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: 2.02 (0.21), residues: 1613 helix: 1.72 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.92 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.002 0.001 HIS G 142 PHE 0.026 0.002 PHE F 70 TYR 0.009 0.001 TYR F 110 ARG 0.008 0.000 ARG I 318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 239 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7747 (tp40) REVERT: B 47 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7245 (mttm) REVERT: B 56 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7105 (mt0) REVERT: C 68 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6636 (tm-30) REVERT: C 72 ASP cc_start: 0.5292 (OUTLIER) cc_final: 0.4516 (p0) REVERT: C 92 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7345 (mtt-85) REVERT: C 129 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7543 (pp20) REVERT: C 187 LYS cc_start: 0.8365 (mppt) cc_final: 0.7510 (mmtt) REVERT: E 111 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7382 (mtm) REVERT: E 112 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6754 (mtpp) REVERT: F 14 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8110 (tp) REVERT: F 108 ASP cc_start: 0.7625 (t70) cc_final: 0.7147 (t70) REVERT: F 129 GLU cc_start: 0.7542 (pt0) cc_final: 0.7219 (pp20) REVERT: G 129 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: H 303 MET cc_start: 0.5540 (tmm) cc_final: 0.5185 (tmm) outliers start: 53 outliers final: 28 residues processed: 269 average time/residue: 1.3195 time to fit residues: 383.0981 Evaluate side-chains 273 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN G 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12783 Z= 0.210 Angle : 0.546 9.123 17225 Z= 0.290 Chirality : 0.039 0.166 2012 Planarity : 0.005 0.061 2184 Dihedral : 4.543 53.289 1737 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.28 % Allowed : 27.07 % Favored : 69.65 % 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: 2.13 (0.21), residues: 1613 helix: 1.80 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.91 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 21 HIS 0.001 0.001 HIS G 142 PHE 0.022 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.007 0.000 ARG I 318 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7752 (tp40) REVERT: B 47 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7248 (mttm) REVERT: B 55 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7617 (mtt) REVERT: B 56 GLN cc_start: 0.7340 (mm-40) cc_final: 0.7088 (mt0) REVERT: B 59 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7742 (mtt) REVERT: C 68 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6689 (tm-30) REVERT: C 92 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7391 (mtt-85) REVERT: C 129 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: C 187 LYS cc_start: 0.8364 (mppt) cc_final: 0.7480 (mmtt) REVERT: E 111 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7376 (mtm) REVERT: E 112 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6732 (mtpp) REVERT: F 14 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8121 (tp) REVERT: F 108 ASP cc_start: 0.7622 (t70) cc_final: 0.7146 (t70) REVERT: F 129 GLU cc_start: 0.7567 (pt0) cc_final: 0.7221 (pp20) REVERT: G 129 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: H 303 MET cc_start: 0.5548 (tmm) cc_final: 0.5204 (tmm) outliers start: 44 outliers final: 30 residues processed: 261 average time/residue: 1.3192 time to fit residues: 373.0855 Evaluate side-chains 274 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 249 SER Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 247 ASP Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 174 ASN D 209 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.196516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130031 restraints weight = 15769.887| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.55 r_work: 0.3143 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12783 Z= 0.271 Angle : 0.583 8.130 17225 Z= 0.311 Chirality : 0.041 0.175 2012 Planarity : 0.005 0.061 2184 Dihedral : 4.667 55.708 1737 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.93 % Allowed : 26.35 % Favored : 69.72 % 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: 1.92 (0.21), residues: 1613 helix: 1.65 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 21 HIS 0.002 0.001 HIS G 142 PHE 0.032 0.002 PHE D 70 TYR 0.009 0.002 TYR F 110 ARG 0.007 0.000 ARG I 318 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6443.82 seconds wall clock time: 113 minutes 4.93 seconds (6784.93 seconds total)