Starting phenix.real_space_refine on Sat May 17 09:32:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ouf_17191/05_2025/8ouf_17191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouf_17191/05_2025/8ouf_17191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ouf_17191/05_2025/8ouf_17191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouf_17191/05_2025/8ouf_17191.map" model { file = "/net/cci-nas-00/data/ceres_data/8ouf_17191/05_2025/8ouf_17191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouf_17191/05_2025/8ouf_17191.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 86 5.16 5 C 9354 2.51 5 N 2681 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15230 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1849 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 37, 'rna3p_pyr': 33} Link IDs: {'rna2p': 15, 'rna3p': 70} Chain breaks: 6 Chain: "C" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3129 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain breaks: 1 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "E" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "G" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2792 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain: "I" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "J" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "K" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2724 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 23, 'TRANS': 324} Chain breaks: 3 Time building chain proxies: 9.18, per 1000 atoms: 0.60 Number of scatterers: 15230 At special positions: 0 Unit cell: (159.909, 110.136, 117.549, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 86 15.00 O 3023 8.00 N 2681 7.00 C 9354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 19 sheets defined 30.8% alpha, 21.7% beta 30 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.689A pdb=" N LEU C 62 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 138 through 141 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.685A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.518A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER C 295 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.554A pdb=" N VAL C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 383 through 395 removed outlier: 3.652A pdb=" N LYS C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.593A pdb=" N LYS D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 40 through 57 removed outlier: 3.890A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 88 through 102 removed outlier: 4.604A pdb=" N HIS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.981A pdb=" N LEU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.608A pdb=" N ARG G 81 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 138 through 141 Processing helix chain 'G' and resid 142 through 149 removed outlier: 3.543A pdb=" N ALA G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 176 removed outlier: 3.845A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 238 Processing helix chain 'G' and resid 263 through 277 Processing helix chain 'G' and resid 279 through 286 Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 304 through 311 removed outlier: 4.413A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 358 Processing helix chain 'G' and resid 383 through 395 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.586A pdb=" N PHE H 138 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 153 through 158 Processing helix chain 'I' and resid 24 through 30 removed outlier: 3.767A pdb=" N ASN I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 57 Processing helix chain 'I' and resid 63 through 73 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 93 through 102 removed outlier: 3.536A pdb=" N ARG I 101 " --> pdb=" O MET I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.629A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 149 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'K' and resid 163 through 167 Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 239 through 242 removed outlier: 3.612A pdb=" N THR K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 239 through 242' Processing sheet with id=AA1, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.539A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 297 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE C 336 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU C 299 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 333 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N MET C 345 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 335 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE C 343 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL C 369 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET C 345 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 315 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 96 current: chain 'C' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 136 current: chain 'C' and resid 195 through 207 removed outlier: 3.841A pdb=" N GLU C 201 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE C 215 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR C 207 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU C 213 " --> pdb=" O TYR C 207 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 213 through 220 current: chain 'C' and resid 254 through 255 Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 80 removed outlier: 5.374A pdb=" N PHE D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS D 87 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS D 78 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 85 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 84 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR D 124 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE D 116 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER D 126 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 111 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE D 144 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AA6, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.607A pdb=" N VAL G 300 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR G 323 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG G 298 " --> pdb=" O TYR G 323 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE G 347 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE G 366 " --> pdb=" O ILE G 347 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE G 315 " --> pdb=" O VAL G 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 96 current: chain 'G' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 129 through 136 current: chain 'G' and resid 195 through 208 removed outlier: 5.355A pdb=" N SER G 202 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER G 219 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N MET G 204 " --> pdb=" O TRP G 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP G 217 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 206 " --> pdb=" O ILE G 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 220 current: chain 'G' and resid 254 through 255 Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 79 removed outlier: 4.311A pdb=" N VAL H 85 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N PHE H 123 " --> pdb=" O CYS H 88 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 124 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE H 116 " --> pdb=" O TYR H 124 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER H 126 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 111 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE H 144 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.485A pdb=" N MET I 79 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE I 108 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU I 81 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AB3, first strand: chain 'K' and resid 155 through 160 removed outlier: 4.247A pdb=" N GLY K 159 " --> pdb=" O LEU K 514 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU K 514 " --> pdb=" O GLY K 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 172 through 177 removed outlier: 4.013A pdb=" N GLY K 174 " --> pdb=" O ASN K 187 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER K 188 " --> pdb=" O ILE K 192 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 195 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU K 218 " --> pdb=" O ILE K 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 226 through 231 removed outlier: 3.649A pdb=" N ASP K 228 " --> pdb=" O SER K 248 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE K 254 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER K 267 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE K 256 " --> pdb=" O ARG K 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 282 through 285 removed outlier: 3.889A pdb=" N SER K 282 " --> pdb=" O GLY K 295 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 318 through 319 Processing sheet with id=AB8, first strand: chain 'K' and resid 328 through 333 removed outlier: 3.556A pdb=" N CYS K 330 " --> pdb=" O GLY K 343 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER K 348 " --> pdb=" O SER K 344 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU K 349 " --> pdb=" O LEU K 362 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU K 362 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU K 351 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 370 through 375 removed outlier: 3.561A pdb=" N HIS K 372 " --> pdb=" O GLY K 385 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA K 386 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU K 391 " --> pdb=" O ALA K 386 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP K 405 " --> pdb=" O CYS K 394 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.612A pdb=" N VAL K 437 " --> pdb=" O SER K 456 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER K 456 " --> pdb=" O VAL K 437 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL K 439 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4163 1.33 - 1.46: 3172 1.46 - 1.58: 8115 1.58 - 1.70: 165 1.70 - 1.82: 125 Bond restraints: 15740 Sorted by residual: bond pdb=" CA PRO H 66 " pdb=" C PRO H 66 " ideal model delta sigma weight residual 1.514 1.530 -0.016 5.50e-03 3.31e+04 8.08e+00 bond pdb=" CA PRO G 184 " pdb=" C PRO G 184 " ideal model delta sigma weight residual 1.514 1.529 -0.014 5.50e-03 3.31e+04 6.89e+00 bond pdb=" N GLY H 65 " pdb=" CA GLY H 65 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.50e+00 bond pdb=" C LEU G 317 " pdb=" O LEU G 317 " ideal model delta sigma weight residual 1.243 1.222 0.022 9.50e-03 1.11e+04 5.22e+00 bond pdb=" C ARG C 284 " pdb=" O ARG C 284 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.19e-02 7.06e+03 4.49e+00 ... (remaining 15735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 19831 1.64 - 3.27: 1546 3.27 - 4.91: 281 4.91 - 6.55: 28 6.55 - 8.19: 11 Bond angle restraints: 21697 Sorted by residual: angle pdb=" N GLY G 130 " pdb=" CA GLY G 130 " pdb=" C GLY G 130 " ideal model delta sigma weight residual 111.56 117.55 -5.99 1.01e+00 9.80e-01 3.52e+01 angle pdb=" C3' U B 416 " pdb=" C2' U B 416 " pdb=" O2' U B 416 " ideal model delta sigma weight residual 110.70 117.54 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" N PRO C 404 " pdb=" CA PRO C 404 " pdb=" C PRO C 404 " ideal model delta sigma weight residual 111.33 117.36 -6.03 1.43e+00 4.89e-01 1.78e+01 angle pdb=" N LEU D 120 " pdb=" CA LEU D 120 " pdb=" C LEU D 120 " ideal model delta sigma weight residual 111.07 115.30 -4.23 1.07e+00 8.73e-01 1.56e+01 angle pdb=" N ALA I 35 " pdb=" CA ALA I 35 " pdb=" C ALA I 35 " ideal model delta sigma weight residual 112.38 117.15 -4.77 1.22e+00 6.72e-01 1.53e+01 ... (remaining 21692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8619 17.69 - 35.38: 742 35.38 - 53.07: 150 53.07 - 70.76: 146 70.76 - 88.45: 55 Dihedral angle restraints: 9712 sinusoidal: 4841 harmonic: 4871 Sorted by residual: dihedral pdb=" CA GLY K 365 " pdb=" C GLY K 365 " pdb=" N HIS K 366 " pdb=" CA HIS K 366 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA CYS C 220 " pdb=" C CYS C 220 " pdb=" N GLU C 221 " pdb=" CA GLU C 221 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLN D 119 " pdb=" C GLN D 119 " pdb=" N LEU D 120 " pdb=" CA LEU D 120 " ideal model delta harmonic sigma weight residual -180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 9709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1590 0.059 - 0.117: 592 0.117 - 0.176: 203 0.176 - 0.235: 79 0.235 - 0.293: 8 Chirality restraints: 2472 Sorted by residual: chirality pdb=" C2' U B 416 " pdb=" C3' U B 416 " pdb=" O2' U B 416 " pdb=" C1' U B 416 " both_signs ideal model delta sigma weight residual False -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN G 99 " pdb=" N ASN G 99 " pdb=" C ASN G 99 " pdb=" CB ASN G 99 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA LYS K 321 " pdb=" N LYS K 321 " pdb=" C LYS K 321 " pdb=" CB LYS K 321 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2469 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 88 " 0.164 9.50e-02 1.11e+02 7.43e-02 4.51e+00 pdb=" NE ARG G 88 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 88 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG G 88 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 88 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 416 " 0.021 2.00e-02 2.50e+03 1.27e-02 3.62e+00 pdb=" N1 U B 416 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U B 416 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 416 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 416 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B 416 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 416 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U B 416 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 416 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 96 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.36e+00 pdb=" N PRO G 97 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 97 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 97 " -0.026 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1209 2.75 - 3.29: 14763 3.29 - 3.83: 25550 3.83 - 4.36: 32610 4.36 - 4.90: 53093 Nonbonded interactions: 127225 Sorted by model distance: nonbonded pdb=" O LYS E 130 " pdb=" OH TYR E 135 " model vdw 2.213 3.040 nonbonded pdb=" OE2 GLU K 163 " pdb=" OH TYR K 196 " model vdw 2.277 3.040 nonbonded pdb=" OG SER K 329 " pdb=" O ILE K 370 " model vdw 2.319 3.040 nonbonded pdb=" O LYS I 130 " pdb=" OH TYR I 135 " model vdw 2.359 3.040 nonbonded pdb=" O GLU G 137 " pdb=" OG1 THR G 140 " model vdw 2.420 3.040 ... (remaining 127220 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 'C' and resid 43 through 395) selection = (chain 'G' and (resid 43 through 186 or resid 192 through 395)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 66 through 159) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.220 Find NCS groups from input model: 0.460 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 : 0.006 0.038 15740 Z= 0.416 Angle : 0.993 8.185 21697 Z= 0.613 Chirality : 0.074 0.293 2472 Planarity : 0.006 0.074 2448 Dihedral : 17.150 88.452 6574 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.14 % Allowed : 0.34 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.59 (0.20), residues: 1648 helix: -0.36 (0.24), residues: 385 sheet: -1.44 (0.25), residues: 360 loop : 0.26 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP G 380 HIS 0.012 0.002 HIS H 78 PHE 0.015 0.003 PHE K 382 TYR 0.024 0.004 TYR E 91 ARG 0.022 0.002 ARG G 197 Details of bonding type rmsd hydrogen bonds : bond 0.17897 ( 515) hydrogen bonds : angle 7.46710 ( 1293) covalent geometry : bond 0.00617 (15740) covalent geometry : angle 0.99309 (21697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7653 (tttt) cc_final: 0.7229 (mmmt) REVERT: C 164 GLU cc_start: 0.7602 (tt0) cc_final: 0.7096 (mm-30) REVERT: C 183 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7309 (mtp180) REVERT: C 195 ARG cc_start: 0.6750 (mtp180) cc_final: 0.6404 (mtm180) REVERT: C 203 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6747 (mmtm) REVERT: C 258 ASP cc_start: 0.6441 (t0) cc_final: 0.5977 (t0) REVERT: C 280 SER cc_start: 0.7658 (t) cc_final: 0.7423 (p) REVERT: C 284 ARG cc_start: 0.7457 (mmt-90) cc_final: 0.7006 (mmm-85) REVERT: C 372 GLU cc_start: 0.8051 (tt0) cc_final: 0.7520 (tp30) REVERT: C 414 GLN cc_start: 0.8166 (tp40) cc_final: 0.7810 (tm-30) REVERT: D 97 TYR cc_start: 0.7201 (m-10) cc_final: 0.6713 (m-80) REVERT: D 108 GLU cc_start: 0.7881 (tt0) cc_final: 0.7505 (pt0) REVERT: D 144 PHE cc_start: 0.7386 (m-80) cc_final: 0.7106 (m-80) REVERT: D 150 LYS cc_start: 0.6916 (mttp) cc_final: 0.6527 (mttp) REVERT: E 36 GLN cc_start: 0.7203 (mt0) cc_final: 0.6862 (mm-40) REVERT: E 62 ARG cc_start: 0.6387 (ptt90) cc_final: 0.5969 (ttp-170) REVERT: E 66 GLU cc_start: 0.7615 (tt0) cc_final: 0.7297 (tt0) REVERT: E 101 ARG cc_start: 0.5883 (mtt-85) cc_final: 0.5623 (mmm-85) REVERT: E 144 GLU cc_start: 0.7130 (tt0) cc_final: 0.6588 (tm-30) REVERT: F 21 ASP cc_start: 0.5405 (p0) cc_final: 0.4858 (p0) REVERT: F 25 GLN cc_start: 0.7341 (pt0) cc_final: 0.6458 (pm20) REVERT: F 36 SER cc_start: 0.8105 (p) cc_final: 0.7859 (p) REVERT: G 81 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8252 (mtt180) REVERT: G 144 LYS cc_start: 0.8094 (tttm) cc_final: 0.7788 (mptt) REVERT: G 161 ASN cc_start: 0.8646 (t0) cc_final: 0.8443 (t0) REVERT: G 164 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7222 (tm-30) REVERT: G 316 MET cc_start: 0.8854 (mmt) cc_final: 0.8215 (mmt) REVERT: G 328 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8095 (mm-30) REVERT: G 372 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7428 (tp30) REVERT: H 108 GLU cc_start: 0.7624 (tt0) cc_final: 0.7274 (tt0) REVERT: H 130 SER cc_start: 0.8125 (m) cc_final: 0.7619 (m) REVERT: H 133 MET cc_start: 0.7506 (mmt) cc_final: 0.7086 (mmm) REVERT: H 139 LYS cc_start: 0.6997 (mtpt) cc_final: 0.6322 (pttm) REVERT: I 36 GLN cc_start: 0.6576 (mt0) cc_final: 0.6338 (mp10) REVERT: I 41 ARG cc_start: 0.6720 (ttt-90) cc_final: 0.6384 (ttt180) REVERT: I 52 LYS cc_start: 0.7895 (tttt) cc_final: 0.7537 (mmtt) REVERT: I 89 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7962 (mp0) REVERT: I 113 ASP cc_start: 0.8476 (m-30) cc_final: 0.8219 (m-30) REVERT: I 145 GLU cc_start: 0.7589 (tt0) cc_final: 0.7272 (tp30) REVERT: J 40 LYS cc_start: 0.8684 (mttt) cc_final: 0.8412 (mmmt) REVERT: J 53 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8351 (mmtm) REVERT: K 147 ASN cc_start: 0.5952 (t0) cc_final: 0.5686 (t0) REVERT: K 182 SER cc_start: 0.8772 (t) cc_final: 0.8331 (m) REVERT: K 273 HIS cc_start: 0.8686 (p-80) cc_final: 0.8387 (p90) REVERT: K 274 LEU cc_start: 0.8845 (mt) cc_final: 0.8587 (mt) REVERT: K 307 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7233 (tpt170) outliers start: 2 outliers final: 2 residues processed: 295 average time/residue: 0.3276 time to fit residues: 133.4953 Evaluate side-chains 224 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain I residue 91 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN E 68 GLN F 10 GLN F 44 HIS G 160 HIS G 168 GLN G 259 HIS G 270 GLN G 296 HIS G 395 GLN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN J 31 HIS J 44 HIS J 58 GLN K 197 ASN K 366 HIS K 515 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102693 restraints weight = 21571.308| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.59 r_work: 0.3087 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15740 Z= 0.163 Angle : 0.666 8.683 21697 Z= 0.348 Chirality : 0.045 0.240 2472 Planarity : 0.005 0.045 2448 Dihedral : 16.870 87.626 3206 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.01 % Allowed : 6.16 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.21 (0.20), residues: 1648 helix: 0.52 (0.26), residues: 389 sheet: -1.38 (0.24), residues: 366 loop : 0.30 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 380 HIS 0.008 0.001 HIS E 132 PHE 0.016 0.002 PHE K 382 TYR 0.028 0.002 TYR C 281 ARG 0.009 0.001 ARG I 42 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 515) hydrogen bonds : angle 5.62868 ( 1293) covalent geometry : bond 0.00381 (15740) covalent geometry : angle 0.66614 (21697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 1.485 Fit side-chains REVERT: C 164 GLU cc_start: 0.7680 (tt0) cc_final: 0.7347 (mm-30) REVERT: C 203 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7374 (mttp) REVERT: C 284 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7812 (mmt180) REVERT: E 44 THR cc_start: 0.8290 (m) cc_final: 0.8051 (p) REVERT: E 57 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7487 (mm-40) REVERT: F 21 ASP cc_start: 0.6676 (p0) cc_final: 0.6405 (p0) REVERT: F 25 GLN cc_start: 0.7995 (pt0) cc_final: 0.7490 (pm20) REVERT: F 36 SER cc_start: 0.8903 (p) cc_final: 0.8656 (t) REVERT: G 243 MET cc_start: 0.8648 (ttp) cc_final: 0.8320 (ttp) REVERT: G 316 MET cc_start: 0.8663 (mmt) cc_final: 0.8326 (mmt) REVERT: H 130 SER cc_start: 0.8267 (m) cc_final: 0.8047 (m) REVERT: I 113 ASP cc_start: 0.8996 (m-30) cc_final: 0.8715 (m-30) REVERT: K 265 ARG cc_start: 0.8486 (ttt180) cc_final: 0.7686 (ttp80) REVERT: K 274 LEU cc_start: 0.9184 (mt) cc_final: 0.8946 (mt) outliers start: 15 outliers final: 8 residues processed: 243 average time/residue: 0.3298 time to fit residues: 110.7070 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 135 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 168 GLN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN K 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102358 restraints weight = 21403.199| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.59 r_work: 0.3091 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15740 Z= 0.159 Angle : 0.614 8.483 21697 Z= 0.318 Chirality : 0.043 0.209 2472 Planarity : 0.004 0.044 2448 Dihedral : 16.732 85.942 3206 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.62 % Allowed : 8.66 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.22 (0.20), residues: 1648 helix: 0.72 (0.27), residues: 392 sheet: -1.47 (0.24), residues: 393 loop : 0.29 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 380 HIS 0.005 0.001 HIS E 132 PHE 0.014 0.002 PHE H 138 TYR 0.020 0.002 TYR C 281 ARG 0.006 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 515) hydrogen bonds : angle 5.20288 ( 1293) covalent geometry : bond 0.00377 (15740) covalent geometry : angle 0.61415 (21697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.707 Fit side-chains REVERT: C 164 GLU cc_start: 0.7839 (tt0) cc_final: 0.7494 (mm-30) REVERT: C 203 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7328 (mttm) REVERT: C 284 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7774 (mmt180) REVERT: C 421 GLU cc_start: 0.4263 (mm-30) cc_final: 0.3570 (pt0) REVERT: D 143 LYS cc_start: 0.7575 (mtmt) cc_final: 0.6757 (mmmm) REVERT: E 44 THR cc_start: 0.8252 (m) cc_final: 0.8040 (p) REVERT: E 57 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7271 (mm-40) REVERT: F 21 ASP cc_start: 0.6587 (p0) cc_final: 0.6268 (p0) REVERT: F 25 GLN cc_start: 0.7999 (pt0) cc_final: 0.7469 (pm20) REVERT: F 36 SER cc_start: 0.8937 (p) cc_final: 0.8714 (t) REVERT: G 243 MET cc_start: 0.8579 (ttp) cc_final: 0.8201 (ttp) REVERT: H 108 GLU cc_start: 0.7421 (tt0) cc_final: 0.7211 (tt0) REVERT: H 115 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7993 (mm-30) REVERT: I 113 ASP cc_start: 0.8990 (m-30) cc_final: 0.8762 (m-30) REVERT: J 58 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: K 265 ARG cc_start: 0.8539 (ttt180) cc_final: 0.7770 (ttp80) outliers start: 24 outliers final: 14 residues processed: 229 average time/residue: 0.3204 time to fit residues: 103.2569 Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 146 ILE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 273 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 360 HIS H 106 ASN I 57 GLN K 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101449 restraints weight = 21324.550| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.58 r_work: 0.3083 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15740 Z= 0.159 Angle : 0.600 8.314 21697 Z= 0.308 Chirality : 0.042 0.201 2472 Planarity : 0.004 0.047 2448 Dihedral : 16.665 83.717 3206 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.69 % Allowed : 10.15 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.23 (0.21), residues: 1648 helix: 0.85 (0.27), residues: 392 sheet: -1.55 (0.23), residues: 404 loop : 0.29 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 380 HIS 0.012 0.001 HIS K 273 PHE 0.013 0.002 PHE K 382 TYR 0.014 0.001 TYR G 281 ARG 0.008 0.000 ARG E 62 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 515) hydrogen bonds : angle 5.08625 ( 1293) covalent geometry : bond 0.00379 (15740) covalent geometry : angle 0.60046 (21697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.538 Fit side-chains REVERT: C 164 GLU cc_start: 0.7804 (tt0) cc_final: 0.7428 (mm-30) REVERT: C 203 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7347 (mttp) REVERT: C 284 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7789 (mmt180) REVERT: C 421 GLU cc_start: 0.4327 (mm-30) cc_final: 0.3542 (pt0) REVERT: E 44 THR cc_start: 0.8205 (m) cc_final: 0.8003 (p) REVERT: E 57 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7292 (mm-40) REVERT: F 21 ASP cc_start: 0.6571 (p0) cc_final: 0.6230 (p0) REVERT: F 25 GLN cc_start: 0.8010 (pt0) cc_final: 0.7439 (pm20) REVERT: G 243 MET cc_start: 0.8605 (ttp) cc_final: 0.8137 (ttp) REVERT: H 108 GLU cc_start: 0.7518 (tt0) cc_final: 0.7305 (tt0) REVERT: H 115 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7940 (mm-30) REVERT: I 113 ASP cc_start: 0.8951 (m-30) cc_final: 0.8746 (m-30) REVERT: I 145 GLU cc_start: 0.8127 (tp30) cc_final: 0.7745 (tp30) REVERT: J 58 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: K 265 ARG cc_start: 0.8576 (ttt180) cc_final: 0.7812 (ttp80) outliers start: 25 outliers final: 21 residues processed: 213 average time/residue: 0.3136 time to fit residues: 94.3188 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 339 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 360 HIS H 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101005 restraints weight = 21866.780| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.58 r_work: 0.3074 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15740 Z= 0.177 Angle : 0.596 8.255 21697 Z= 0.306 Chirality : 0.042 0.199 2472 Planarity : 0.004 0.052 2448 Dihedral : 16.626 82.426 3206 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.17 % Allowed : 11.23 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.26 (0.21), residues: 1648 helix: 0.87 (0.27), residues: 391 sheet: -1.54 (0.24), residues: 396 loop : 0.20 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 380 HIS 0.005 0.001 HIS C 259 PHE 0.014 0.002 PHE K 382 TYR 0.013 0.002 TYR E 135 ARG 0.007 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 515) hydrogen bonds : angle 5.04426 ( 1293) covalent geometry : bond 0.00423 (15740) covalent geometry : angle 0.59637 (21697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 1.562 Fit side-chains REVERT: C 164 GLU cc_start: 0.7565 (tt0) cc_final: 0.7336 (mm-30) REVERT: C 203 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7350 (mttp) REVERT: C 284 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7785 (mmt180) REVERT: C 421 GLU cc_start: 0.4492 (mm-30) cc_final: 0.3624 (pt0) REVERT: F 21 ASP cc_start: 0.6538 (p0) cc_final: 0.6214 (p0) REVERT: F 25 GLN cc_start: 0.7853 (pt0) cc_final: 0.7393 (pm20) REVERT: F 59 GLN cc_start: 0.5678 (mt0) cc_final: 0.5369 (mm-40) REVERT: G 243 MET cc_start: 0.8655 (ttp) cc_final: 0.8151 (ttp) REVERT: H 108 GLU cc_start: 0.7567 (tt0) cc_final: 0.7337 (tt0) REVERT: H 115 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7956 (mm-30) REVERT: I 145 GLU cc_start: 0.8145 (tp30) cc_final: 0.7758 (tp30) REVERT: J 58 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: K 265 ARG cc_start: 0.8606 (ttt180) cc_final: 0.7827 (ttp80) REVERT: K 321 LYS cc_start: 0.7649 (pttt) cc_final: 0.6903 (mttt) outliers start: 32 outliers final: 26 residues processed: 220 average time/residue: 0.3114 time to fit residues: 97.0159 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104064 restraints weight = 21595.345| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.58 r_work: 0.3112 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15740 Z= 0.113 Angle : 0.542 8.417 21697 Z= 0.277 Chirality : 0.040 0.171 2472 Planarity : 0.004 0.051 2448 Dihedral : 16.506 80.061 3206 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.89 % Allowed : 11.50 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.08 (0.21), residues: 1648 helix: 1.00 (0.27), residues: 392 sheet: -1.44 (0.24), residues: 382 loop : 0.29 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 380 HIS 0.004 0.001 HIS F 44 PHE 0.011 0.001 PHE K 382 TYR 0.012 0.001 TYR G 281 ARG 0.005 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 515) hydrogen bonds : angle 4.85836 ( 1293) covalent geometry : bond 0.00264 (15740) covalent geometry : angle 0.54177 (21697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: C 60 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8393 (p0) REVERT: C 164 GLU cc_start: 0.7677 (tt0) cc_final: 0.7369 (mm-30) REVERT: C 203 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7350 (mttp) REVERT: C 284 ARG cc_start: 0.8043 (mmt-90) cc_final: 0.7808 (mmm-85) REVERT: C 421 GLU cc_start: 0.4590 (mm-30) cc_final: 0.3719 (pt0) REVERT: F 2 PHE cc_start: 0.8154 (m-80) cc_final: 0.7900 (m-80) REVERT: F 21 ASP cc_start: 0.6427 (p0) cc_final: 0.6138 (p0) REVERT: F 25 GLN cc_start: 0.7757 (pt0) cc_final: 0.7428 (pm20) REVERT: G 66 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7924 (t) REVERT: G 243 MET cc_start: 0.8518 (ttp) cc_final: 0.8033 (ttp) REVERT: H 108 GLU cc_start: 0.7554 (tt0) cc_final: 0.7299 (tt0) REVERT: H 115 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7889 (mm-30) REVERT: I 145 GLU cc_start: 0.8169 (tp30) cc_final: 0.7751 (tp30) REVERT: K 265 ARG cc_start: 0.8474 (ttt180) cc_final: 0.7820 (ttp80) REVERT: K 321 LYS cc_start: 0.7631 (pttt) cc_final: 0.6754 (mttt) REVERT: K 360 LEU cc_start: 0.8522 (mt) cc_final: 0.8294 (mt) outliers start: 28 outliers final: 19 residues processed: 233 average time/residue: 0.3083 time to fit residues: 102.3613 Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 5 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 147 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 126 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 ASN C 360 HIS H 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104646 restraints weight = 21687.924| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.83 r_work: 0.3109 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15740 Z= 0.101 Angle : 0.527 9.086 21697 Z= 0.267 Chirality : 0.039 0.165 2472 Planarity : 0.004 0.051 2448 Dihedral : 16.418 79.440 3206 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.89 % Allowed : 12.58 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.06 (0.21), residues: 1648 helix: 1.12 (0.27), residues: 392 sheet: -1.31 (0.25), residues: 376 loop : 0.34 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 380 HIS 0.006 0.001 HIS E 132 PHE 0.010 0.001 PHE K 382 TYR 0.012 0.001 TYR F 41 ARG 0.006 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 515) hydrogen bonds : angle 4.68040 ( 1293) covalent geometry : bond 0.00234 (15740) covalent geometry : angle 0.52734 (21697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 2.408 Fit side-chains revert: symmetry clash REVERT: C 60 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8481 (p0) REVERT: C 164 GLU cc_start: 0.7768 (tt0) cc_final: 0.7435 (mm-30) REVERT: C 203 LYS cc_start: 0.8001 (mtmt) cc_final: 0.7405 (mttp) REVERT: C 273 TYR cc_start: 0.9256 (t80) cc_final: 0.9019 (t80) REVERT: C 284 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7824 (mmm-85) REVERT: F 2 PHE cc_start: 0.8195 (m-80) cc_final: 0.7957 (m-80) REVERT: F 21 ASP cc_start: 0.6366 (p0) cc_final: 0.6047 (p0) REVERT: F 25 GLN cc_start: 0.7751 (pt0) cc_final: 0.7462 (pm20) REVERT: F 61 ARG cc_start: 0.6641 (mtm180) cc_final: 0.6066 (mtp180) REVERT: G 66 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7972 (t) REVERT: G 243 MET cc_start: 0.8507 (ttp) cc_final: 0.8029 (ttp) REVERT: H 108 GLU cc_start: 0.7558 (tt0) cc_final: 0.7349 (tt0) REVERT: I 145 GLU cc_start: 0.8174 (tp30) cc_final: 0.7810 (tp30) REVERT: K 265 ARG cc_start: 0.8513 (ttt180) cc_final: 0.7960 (ttp80) REVERT: K 321 LYS cc_start: 0.7431 (pttt) cc_final: 0.6734 (mttt) outliers start: 28 outliers final: 24 residues processed: 226 average time/residue: 0.3187 time to fit residues: 101.0387 Evaluate side-chains 215 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 347 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 0.0170 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 149 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 10 GLN J 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105246 restraints weight = 21413.400| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.54 r_work: 0.3156 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15740 Z= 0.098 Angle : 0.522 9.097 21697 Z= 0.264 Chirality : 0.039 0.157 2472 Planarity : 0.004 0.050 2448 Dihedral : 16.374 79.097 3206 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.23 % Allowed : 12.86 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.15 (0.21), residues: 1648 helix: 1.17 (0.27), residues: 392 sheet: -1.09 (0.25), residues: 362 loop : 0.30 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 380 HIS 0.004 0.001 HIS E 132 PHE 0.010 0.001 PHE K 382 TYR 0.010 0.001 TYR F 41 ARG 0.005 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 515) hydrogen bonds : angle 4.59055 ( 1293) covalent geometry : bond 0.00226 (15740) covalent geometry : angle 0.52153 (21697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.478 Fit side-chains REVERT: C 116 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7138 (pt0) REVERT: C 164 GLU cc_start: 0.7629 (tt0) cc_final: 0.7412 (mm-30) REVERT: C 203 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7365 (mttp) REVERT: C 273 TYR cc_start: 0.9233 (t80) cc_final: 0.8999 (t80) REVERT: C 284 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.7762 (mmm-85) REVERT: D 133 MET cc_start: 0.7392 (tpp) cc_final: 0.7024 (tpt) REVERT: E 132 HIS cc_start: 0.5192 (OUTLIER) cc_final: 0.4911 (t70) REVERT: F 2 PHE cc_start: 0.8222 (m-80) cc_final: 0.7983 (m-80) REVERT: F 8 ASN cc_start: 0.6571 (p0) cc_final: 0.6252 (p0) REVERT: F 21 ASP cc_start: 0.6342 (p0) cc_final: 0.6054 (p0) REVERT: F 25 GLN cc_start: 0.7851 (pt0) cc_final: 0.7433 (pm20) REVERT: F 61 ARG cc_start: 0.6515 (mtm180) cc_final: 0.6053 (mtp180) REVERT: G 66 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7970 (t) REVERT: H 108 GLU cc_start: 0.7521 (tt0) cc_final: 0.7315 (tt0) REVERT: K 265 ARG cc_start: 0.8449 (ttt180) cc_final: 0.7930 (ttp80) REVERT: K 321 LYS cc_start: 0.7460 (pttt) cc_final: 0.6791 (mttt) REVERT: K 461 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8229 (mtmm) outliers start: 33 outliers final: 27 residues processed: 223 average time/residue: 0.3084 time to fit residues: 96.8137 Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 347 ARG Chi-restraints excluded: chain K residue 461 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 79 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 120 HIS C 161 ASN F 10 GLN H 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102014 restraints weight = 21609.192| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.84 r_work: 0.3079 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15740 Z= 0.164 Angle : 0.577 7.870 21697 Z= 0.293 Chirality : 0.042 0.201 2472 Planarity : 0.004 0.051 2448 Dihedral : 16.450 78.853 3206 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.23 % Allowed : 13.06 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1648 helix: 1.12 (0.27), residues: 394 sheet: -1.22 (0.25), residues: 376 loop : 0.27 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 380 HIS 0.010 0.001 HIS C 259 PHE 0.014 0.002 PHE D 98 TYR 0.019 0.001 TYR F 41 ARG 0.007 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 515) hydrogen bonds : angle 4.75889 ( 1293) covalent geometry : bond 0.00393 (15740) covalent geometry : angle 0.57656 (21697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 1.618 Fit side-chains REVERT: C 116 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7324 (pt0) REVERT: C 164 GLU cc_start: 0.7694 (tt0) cc_final: 0.7330 (mm-30) REVERT: C 183 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7858 (mtp180) REVERT: C 203 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7352 (mttp) REVERT: C 260 MET cc_start: 0.8162 (mtp) cc_final: 0.7915 (ttp) REVERT: C 284 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7803 (mmt180) REVERT: D 115 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6646 (tt0) REVERT: D 133 MET cc_start: 0.7408 (tpp) cc_final: 0.7043 (tpt) REVERT: E 132 HIS cc_start: 0.5108 (OUTLIER) cc_final: 0.4715 (t-90) REVERT: F 2 PHE cc_start: 0.8244 (m-80) cc_final: 0.7994 (m-80) REVERT: F 8 ASN cc_start: 0.6446 (p0) cc_final: 0.6144 (p0) REVERT: F 21 ASP cc_start: 0.6397 (p0) cc_final: 0.6092 (p0) REVERT: F 25 GLN cc_start: 0.7930 (pt0) cc_final: 0.7474 (pm20) REVERT: F 59 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6970 (mm-40) REVERT: G 180 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8825 (mt) REVERT: H 108 GLU cc_start: 0.7641 (tt0) cc_final: 0.7388 (tt0) REVERT: K 265 ARG cc_start: 0.8599 (ttt180) cc_final: 0.7976 (ttp80) REVERT: K 321 LYS cc_start: 0.7472 (pttt) cc_final: 0.6768 (mttt) REVERT: K 461 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8214 (mtmm) outliers start: 33 outliers final: 28 residues processed: 205 average time/residue: 0.3207 time to fit residues: 92.4328 Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 347 ARG Chi-restraints excluded: chain K residue 461 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 141 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN F 10 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104741 restraints weight = 21581.818| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.74 r_work: 0.3100 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15740 Z= 0.110 Angle : 0.541 9.106 21697 Z= 0.274 Chirality : 0.040 0.171 2472 Planarity : 0.004 0.050 2448 Dihedral : 16.373 79.016 3206 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.10 % Allowed : 13.19 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.09 (0.21), residues: 1648 helix: 1.19 (0.27), residues: 392 sheet: -1.06 (0.25), residues: 378 loop : 0.21 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 405 HIS 0.004 0.001 HIS E 93 PHE 0.010 0.001 PHE K 382 TYR 0.014 0.001 TYR F 41 ARG 0.008 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 515) hydrogen bonds : angle 4.64292 ( 1293) covalent geometry : bond 0.00259 (15740) covalent geometry : angle 0.54072 (21697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.690 Fit side-chains REVERT: C 116 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7232 (pt0) REVERT: C 164 GLU cc_start: 0.7617 (tt0) cc_final: 0.7341 (mm-30) REVERT: C 203 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7359 (mttp) REVERT: C 273 TYR cc_start: 0.9276 (t80) cc_final: 0.9033 (t80) REVERT: C 284 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7794 (mmt180) REVERT: D 133 MET cc_start: 0.7312 (tpp) cc_final: 0.6965 (tpt) REVERT: E 132 HIS cc_start: 0.5025 (OUTLIER) cc_final: 0.4623 (t-90) REVERT: F 2 PHE cc_start: 0.8227 (m-80) cc_final: 0.7984 (m-80) REVERT: F 8 ASN cc_start: 0.6466 (p0) cc_final: 0.6160 (p0) REVERT: F 25 GLN cc_start: 0.7893 (pt0) cc_final: 0.7310 (pm20) REVERT: F 39 ASP cc_start: 0.8064 (t0) cc_final: 0.7762 (t0) REVERT: F 61 ARG cc_start: 0.6561 (mtm180) cc_final: 0.5912 (mtp180) REVERT: G 66 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7993 (t) REVERT: H 108 GLU cc_start: 0.7601 (tt0) cc_final: 0.7370 (tt0) REVERT: H 115 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7605 (mm-30) REVERT: K 265 ARG cc_start: 0.8566 (ttt180) cc_final: 0.7959 (ttp80) REVERT: K 321 LYS cc_start: 0.7433 (pttt) cc_final: 0.6760 (mttt) REVERT: K 381 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.7624 (ptm160) REVERT: K 461 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8236 (mtmm) outliers start: 31 outliers final: 26 residues processed: 208 average time/residue: 0.3333 time to fit residues: 97.9081 Evaluate side-chains 214 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 347 ARG Chi-restraints excluded: chain K residue 461 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 161 ASN F 10 GLN G 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101477 restraints weight = 21622.508| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.61 r_work: 0.3081 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 15740 Z= 0.201 Angle : 0.612 12.108 21697 Z= 0.311 Chirality : 0.043 0.208 2472 Planarity : 0.005 0.051 2448 Dihedral : 16.422 78.845 3206 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.30 % Allowed : 13.26 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.07 (0.21), residues: 1648 helix: 1.07 (0.27), residues: 393 sheet: -1.22 (0.24), residues: 388 loop : 0.17 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 380 HIS 0.004 0.001 HIS E 132 PHE 0.014 0.002 PHE K 382 TYR 0.019 0.002 TYR F 41 ARG 0.008 0.000 ARG I 41 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 515) hydrogen bonds : angle 4.85216 ( 1293) covalent geometry : bond 0.00484 (15740) covalent geometry : angle 0.61229 (21697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9130.28 seconds wall clock time: 158 minutes 18.09 seconds (9498.09 seconds total)