Starting phenix.real_space_refine on Mon Aug 5 05:01:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/08_2024/8ucs_42139.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/08_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_42139/08_2024/8ucs_42139.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/08_2024/8ucs_42139.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/08_2024/8ucs_42139.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ucs_42139/08_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-5409/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: 8.66, 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: 5.06 Conformation dependent library (CDL) restraints added in 2.1 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: 1.03 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: 3.74 Time building geometry restraints manager: 5.55 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 3.120 nonbonded pdb=" O GLY G 95 " pdb=" OG SER G 98 " model vdw 2.260 3.040 nonbonded pdb=" O GLY F 95 " pdb=" OG SER F 98 " model vdw 2.271 3.040 nonbonded pdb=" O ARG H 253 " pdb=" NH1 ARG H 253 " model vdw 2.274 3.120 nonbonded pdb=" O GLY D 22 " pdb=" OG SER D 25 " model vdw 2.281 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 12.030 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.030 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.600 ------------------------------------------------------------------------------- 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 : 1.396 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: 1.3166 time to fit residues: 360.0922 Evaluate side-chains 237 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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: 0.9980 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 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: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 D 29 ASN F 254 GLN J 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12783 Z= 0.218 Angle : 0.553 7.793 17225 Z= 0.301 Chirality : 0.040 0.167 2012 Planarity : 0.005 0.049 2184 Dihedral : 4.836 52.581 1743 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.73 % Allowed : 24.75 % Favored : 70.52 % 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: 1.60 (0.21), residues: 1613 helix: 1.44 (0.14), residues: 1379 sheet: None (None), residues: 0 loop : -0.98 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 19 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 0.004 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 322 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 258 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.7800 (tmtt) cc_final: 0.7176 (mttm) REVERT: B 56 GLN cc_start: 0.7463 (mt0) cc_final: 0.7256 (mm-40) REVERT: C 68 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6646 (tm-30) REVERT: C 72 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.4851 (p0) REVERT: C 187 LYS cc_start: 0.8314 (mppt) cc_final: 0.7487 (mmtm) REVERT: D 243 LYS cc_start: 0.6833 (ptpt) cc_final: 0.6622 (pttt) REVERT: F 14 LEU cc_start: 0.8435 (mt) cc_final: 0.8101 (tp) REVERT: F 108 ASP cc_start: 0.7584 (t70) cc_final: 0.7095 (t70) REVERT: G 56 MET cc_start: 0.7510 (tpt) cc_final: 0.7291 (mmp) REVERT: G 141 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7583 (mtm110) outliers start: 64 outliers final: 19 residues processed: 293 average time/residue: 1.2842 time to fit residues: 406.7955 Evaluate side-chains 259 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 239 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP 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 136 ASP Chi-restraints excluded: chain G residue 183 SER 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: 1.9990 chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 C 200 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1482 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= 0.271 Angle : 0.568 8.351 17225 Z= 0.307 Chirality : 0.041 0.167 2012 Planarity : 0.005 0.049 2184 Dihedral : 4.679 56.279 1737 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.88 % Allowed : 24.60 % Favored : 70.52 % 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: 1.66 (0.21), residues: 1613 helix: 1.49 (0.14), residues: 1383 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 PHE 0.025 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 305 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7943 (tp40) REVERT: B 47 LYS cc_start: 0.7826 (tmtt) cc_final: 0.7195 (mttm) REVERT: B 56 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7269 (mm-40) REVERT: C 68 GLN cc_start: 0.7134 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 72 ASP cc_start: 0.5476 (OUTLIER) cc_final: 0.4675 (p0) REVERT: C 185 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7977 (mpt) REVERT: C 187 LYS cc_start: 0.8375 (mppt) cc_final: 0.7514 (mmtm) REVERT: D 185 MET cc_start: 0.8845 (tpt) cc_final: 0.8640 (tpt) REVERT: E 112 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6711 (mtpp) REVERT: F 14 LEU cc_start: 0.8435 (mt) cc_final: 0.8101 (tp) REVERT: F 108 ASP cc_start: 0.7599 (t70) cc_final: 0.7117 (t70) REVERT: G 129 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: G 141 ARG cc_start: 0.7934 (mtm-85) cc_final: 0.7580 (mtm110) REVERT: J 241 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.4179 (pm20) outliers start: 66 outliers final: 32 residues processed: 283 average time/residue: 1.3900 time to fit residues: 423.8657 Evaluate side-chains 272 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 42 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 59 MET 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 185 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 232 GLN 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 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU 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 245 VAL 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 241 GLU 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: 1.9990 chunk 15 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12783 Z= 0.195 Angle : 0.517 7.664 17225 Z= 0.280 Chirality : 0.039 0.161 2012 Planarity : 0.005 0.050 2184 Dihedral : 4.521 53.324 1737 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.37 % Allowed : 24.89 % 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: 1.95 (0.21), residues: 1613 helix: 1.70 (0.14), residues: 1383 sheet: None (None), residues: 0 loop : -1.10 (0.41), residues: 230 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 0.022 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.004 0.000 ARG C 61 *********************** 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 302 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 243 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7934 (tp40) REVERT: B 47 LYS cc_start: 0.7806 (tmtt) cc_final: 0.7216 (mttm) REVERT: B 56 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7217 (mm-40) REVERT: C 68 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6638 (tm-30) REVERT: C 72 ASP cc_start: 0.5290 (OUTLIER) cc_final: 0.4537 (p0) REVERT: C 187 LYS cc_start: 0.8353 (mppt) cc_final: 0.7510 (mmtm) REVERT: F 14 LEU cc_start: 0.8463 (mt) cc_final: 0.8119 (tp) REVERT: F 129 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7152 (pp20) REVERT: G 56 MET cc_start: 0.7531 (tpt) cc_final: 0.7322 (mmp) REVERT: G 92 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.4612 (ttm-80) REVERT: G 129 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6518 (mp0) REVERT: G 141 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7541 (mtm110) outliers start: 59 outliers final: 25 residues processed: 281 average time/residue: 1.3613 time to fit residues: 412.4145 Evaluate side-chains 264 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 234 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 42 SER 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 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR 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 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU 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 92 ARG 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 245 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 321 GLU 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: 0.2980 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12783 Z= 0.207 Angle : 0.524 8.006 17225 Z= 0.282 Chirality : 0.039 0.165 2012 Planarity : 0.005 0.051 2184 Dihedral : 4.539 55.108 1737 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.59 % Allowed : 24.67 % 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: 2.02 (0.21), residues: 1613 helix: 1.75 (0.14), residues: 1383 sheet: None (None), residues: 0 loop : -1.10 (0.41), residues: 230 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 0.023 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.005 0.000 ARG C 61 *********************** 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 297 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: B 47 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7247 (mttm) REVERT: B 55 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7839 (ttm) REVERT: B 56 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7225 (mm-40) REVERT: C 68 GLN cc_start: 0.7042 (tm-30) cc_final: 0.6633 (tm-30) REVERT: C 72 ASP cc_start: 0.5257 (OUTLIER) cc_final: 0.4486 (p0) REVERT: C 187 LYS cc_start: 0.8382 (mppt) cc_final: 0.7525 (mmtm) REVERT: F 14 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8121 (tp) REVERT: F 129 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7162 (pp20) REVERT: G 56 MET cc_start: 0.7569 (tpt) cc_final: 0.7351 (mmp) REVERT: G 129 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: G 141 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7543 (mtm110) outliers start: 62 outliers final: 32 residues processed: 277 average time/residue: 1.3224 time to fit residues: 395.1507 Evaluate side-chains 272 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain B residue 55 MET 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 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 143 LYS 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 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 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU 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 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 321 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12783 Z= 0.236 Angle : 0.543 8.525 17225 Z= 0.292 Chirality : 0.040 0.170 2012 Planarity : 0.005 0.052 2184 Dihedral : 4.606 55.947 1737 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.66 % Allowed : 24.60 % 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: 1.96 (0.21), residues: 1613 helix: 1.69 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.03 (0.41), 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 0.001 TYR F 110 ARG 0.005 0.000 ARG C 61 *********************** 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 296 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 233 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: B 47 LYS cc_start: 0.7824 (tmtt) cc_final: 0.7226 (mttm) REVERT: B 55 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7862 (ttm) REVERT: B 56 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7248 (mm-40) REVERT: C 68 GLN cc_start: 0.7090 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 72 ASP cc_start: 0.5293 (OUTLIER) cc_final: 0.4513 (p0) REVERT: C 187 LYS cc_start: 0.8372 (mppt) cc_final: 0.7501 (mmtt) REVERT: F 14 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8123 (tp) REVERT: F 108 ASP cc_start: 0.7615 (t70) cc_final: 0.7150 (t70) REVERT: F 129 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7176 (pp20) REVERT: G 56 MET cc_start: 0.7572 (tpt) cc_final: 0.7349 (mmp) REVERT: G 129 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: G 141 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.7521 (mtm110) outliers start: 63 outliers final: 39 residues processed: 274 average time/residue: 1.2880 time to fit residues: 381.3341 Evaluate side-chains 272 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 227 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 42 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET 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 192 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 143 LYS 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 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 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU 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 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 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 284 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 Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 288 SER Chi-restraints excluded: chain J residue 321 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 128 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12783 Z= 0.196 Angle : 0.532 12.584 17225 Z= 0.283 Chirality : 0.039 0.164 2012 Planarity : 0.005 0.052 2184 Dihedral : 4.514 54.534 1737 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.37 % Allowed : 25.04 % 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: 2.12 (0.21), residues: 1613 helix: 1.81 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 226 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 0.022 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.005 0.000 ARG C 61 *********************** 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: 59 poor density : 234 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7936 (tp40) REVERT: B 47 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7238 (mttm) REVERT: B 55 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7860 (ttm) REVERT: B 56 GLN cc_start: 0.7497 (mm-40) cc_final: 0.7198 (mm-40) REVERT: C 68 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6637 (tm-30) REVERT: C 72 ASP cc_start: 0.5184 (OUTLIER) cc_final: 0.4411 (p0) REVERT: C 92 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7366 (mtt-85) REVERT: C 187 LYS cc_start: 0.8390 (mppt) cc_final: 0.7538 (mmtm) REVERT: F 14 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8120 (tp) REVERT: F 108 ASP cc_start: 0.7615 (t70) cc_final: 0.7151 (t70) REVERT: F 125 GLU cc_start: 0.7264 (pm20) cc_final: 0.6936 (pm20) REVERT: F 129 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7172 (pp20) REVERT: G 129 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: G 141 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7477 (mtm110) REVERT: H 303 MET cc_start: 0.5615 (tmm) cc_final: 0.5143 (tmm) outliers start: 59 outliers final: 36 residues processed: 277 average time/residue: 1.3652 time to fit residues: 408.7763 Evaluate side-chains 271 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 228 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET 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 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 228 VAL 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 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 72 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU 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 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12783 Z= 0.218 Angle : 0.548 11.524 17225 Z= 0.292 Chirality : 0.039 0.168 2012 Planarity : 0.005 0.052 2184 Dihedral : 4.551 55.698 1737 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.73 % Allowed : 24.96 % 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: 2.07 (0.21), residues: 1613 helix: 1.77 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 226 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 0.022 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.006 0.000 ARG C 238 *********************** 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 296 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 232 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7943 (tp40) REVERT: B 47 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7239 (mttm) REVERT: B 55 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7846 (ttm) REVERT: B 56 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7229 (mm-40) REVERT: C 68 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6638 (tm-30) REVERT: C 72 ASP cc_start: 0.5203 (OUTLIER) cc_final: 0.4419 (p0) REVERT: C 92 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7349 (mtt-85) REVERT: C 187 LYS cc_start: 0.8383 (mppt) cc_final: 0.7510 (mmtt) REVERT: F 14 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8123 (tp) REVERT: F 92 ARG cc_start: 0.7179 (mtp85) cc_final: 0.6885 (mtt-85) REVERT: F 108 ASP cc_start: 0.7621 (t70) cc_final: 0.7157 (t70) REVERT: F 129 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7188 (pp20) REVERT: G 129 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: G 141 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7485 (mtm110) REVERT: H 303 MET cc_start: 0.5617 (tmm) cc_final: 0.5202 (tmm) outliers start: 64 outliers final: 42 residues processed: 274 average time/residue: 1.3268 time to fit residues: 392.3802 Evaluate side-chains 278 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 229 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET 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 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 228 VAL 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 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 72 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU 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 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 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 321 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1884 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= 0.200 Angle : 0.542 10.788 17225 Z= 0.288 Chirality : 0.039 0.165 2012 Planarity : 0.005 0.056 2184 Dihedral : 4.505 54.784 1737 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.15 % Allowed : 25.18 % 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: 2.15 (0.21), residues: 1613 helix: 1.82 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 226 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 0.023 0.002 PHE F 70 TYR 0.009 0.001 TYR F 110 ARG 0.005 0.000 ARG C 61 *********************** 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 288 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 232 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7933 (tp40) REVERT: B 47 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7316 (mttm) REVERT: B 55 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7846 (ttm) REVERT: B 56 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7216 (mm-40) REVERT: C 61 ARG cc_start: 0.7375 (ttp80) cc_final: 0.7115 (ttt180) REVERT: C 68 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6642 (tm-30) REVERT: C 72 ASP cc_start: 0.5144 (OUTLIER) cc_final: 0.4363 (p0) REVERT: C 92 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7355 (mtt-85) REVERT: C 187 LYS cc_start: 0.8367 (mppt) cc_final: 0.7500 (mmtt) REVERT: F 14 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8116 (tp) REVERT: F 92 ARG cc_start: 0.7162 (mtp85) cc_final: 0.6876 (mtt-85) REVERT: F 108 ASP cc_start: 0.7616 (t70) cc_final: 0.7149 (t70) REVERT: F 125 GLU cc_start: 0.7278 (pm20) cc_final: 0.6932 (pm20) REVERT: F 129 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: G 129 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: G 141 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7458 (mtm110) REVERT: H 303 MET cc_start: 0.5602 (tmm) cc_final: 0.5141 (tmm) outliers start: 56 outliers final: 36 residues processed: 271 average time/residue: 1.3279 time to fit residues: 388.3327 Evaluate side-chains 273 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP 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 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 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 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 129 GLU 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 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 228 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.0020 chunk 99 optimal weight: 0.0970 chunk 133 optimal weight: 0.9980 overall best weight: 0.2884 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12783 Z= 0.155 Angle : 0.511 10.759 17225 Z= 0.271 Chirality : 0.038 0.159 2012 Planarity : 0.004 0.061 2184 Dihedral : 4.310 49.266 1737 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.13 % Allowed : 26.35 % Favored : 70.52 % 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: 2.02 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 21 HIS 0.001 0.000 HIS C 142 PHE 0.019 0.002 PHE B 33 TYR 0.009 0.001 TYR F 110 ARG 0.004 0.000 ARG C 61 ********************** 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 298 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 256 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7945 (tp40) REVERT: B 47 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7237 (mttm) REVERT: B 56 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7074 (tp40) REVERT: C 61 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6978 (ttp-170) REVERT: C 68 GLN cc_start: 0.7040 (tm-30) cc_final: 0.6684 (tm-30) REVERT: C 92 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7330 (mtt-85) REVERT: C 187 LYS cc_start: 0.8358 (mppt) cc_final: 0.7484 (mmtm) REVERT: C 249 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7796 (m) REVERT: F 14 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8092 (tp) REVERT: F 70 PHE cc_start: 0.6326 (m-80) cc_final: 0.5916 (m-80) REVERT: F 125 GLU cc_start: 0.7247 (pm20) cc_final: 0.6905 (pm20) REVERT: F 129 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7209 (pp20) REVERT: F 226 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6901 (mm-30) REVERT: G 141 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7473 (mtm110) REVERT: H 303 MET cc_start: 0.5514 (tmm) cc_final: 0.5090 (tmm) outliers start: 42 outliers final: 20 residues processed: 284 average time/residue: 1.3697 time to fit residues: 419.0683 Evaluate side-chains 269 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 191 THR 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 F residue 129 GLU 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 H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 128 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 82 GLN C 105 ASN D 29 ASN ** F 254 GLN ** 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 = 0.4189 r_free = 0.4189 target = 0.199401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131582 restraints weight = 16267.546| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.62 r_work: 0.3222 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12783 Z= 0.188 Angle : 0.535 10.230 17225 Z= 0.285 Chirality : 0.039 0.165 2012 Planarity : 0.005 0.061 2184 Dihedral : 4.400 52.702 1737 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.62 % Allowed : 27.07 % 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: 2.33 (0.22), residues: 1613 helix: 1.94 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 21 HIS 0.001 0.000 HIS D 142 PHE 0.022 0.002 PHE C 59 TYR 0.009 0.001 TYR F 110 ARG 0.005 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6539.04 seconds wall clock time: 114 minutes 43.27 seconds (6883.27 seconds total)