Starting phenix.real_space_refine on Tue Sep 24 15:48:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/09_2024/6wi9_21683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/09_2024/6wi9_21683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/09_2024/6wi9_21683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/09_2024/6wi9_21683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/09_2024/6wi9_21683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi9_21683/09_2024/6wi9_21683.cif" } resolution = 4.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5410 2.51 5 N 1526 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1646 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain breaks: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2706 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 11, 'TRANS': 356} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 189 Time building chain proxies: 5.46, per 1000 atoms: 0.64 Number of scatterers: 8550 At special positions: 0 Unit cell: (78.26, 173.72, 97.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1561 8.00 N 1526 7.00 C 5410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 75 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.03 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: 2.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 40.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.503A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.720A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.761A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.685A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.962A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.187A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.796A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.756A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 31 through 46 removed outlier: 4.010A pdb=" N ASP R 43 " --> pdb=" O TRP R 39 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN R 44 " --> pdb=" O GLU R 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS R 45 " --> pdb=" O GLU R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 93 through 97 Processing helix chain 'R' and resid 131 through 165 removed outlier: 3.509A pdb=" N ARG R 135 " --> pdb=" O SER R 131 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 200 removed outlier: 3.541A pdb=" N TYR R 176 " --> pdb=" O CYS R 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N HIS R 180 " --> pdb=" O TYR R 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 193 " --> pdb=" O ALA R 189 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 194 " --> pdb=" O LEU R 190 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 246 removed outlier: 3.948A pdb=" N VAL R 220 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN R 229 " --> pdb=" O CYS R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 265 removed outlier: 3.603A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 280 removed outlier: 4.095A pdb=" N ALA R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 325 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 336 through 352 removed outlier: 4.617A pdb=" N ARG R 342 " --> pdb=" O LYS R 338 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU R 346 " --> pdb=" O ARG R 342 " (cutoff:3.500A) Proline residue: R 349 - end of helix Processing helix chain 'R' and resid 353 through 359 removed outlier: 3.977A pdb=" N PHE R 358 " --> pdb=" O TYR R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 368 removed outlier: 5.821A pdb=" N GLU R 367 " --> pdb=" O ASP R 364 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE R 368 " --> pdb=" O ALA R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 369 through 374 removed outlier: 3.569A pdb=" N GLU R 373 " --> pdb=" O GLN R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 390 Processing helix chain 'R' and resid 393 through 408 removed outlier: 3.514A pdb=" N GLU R 398 " --> pdb=" O GLU R 394 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 399 " --> pdb=" O VAL R 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS R 401 " --> pdb=" O LEU R 397 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS R 407 " --> pdb=" O TRP R 403 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.590A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.066A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.183A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.414A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.794A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.789A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.807A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 69 through 70 removed outlier: 3.677A pdb=" N MET R 69 " --> pdb=" O TRP R 76 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TRP R 76 " --> pdb=" O MET R 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 85 through 87 removed outlier: 4.269A pdb=" N LEU R 103 " --> pdb=" O VAL R 87 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2851 1.35 - 1.46: 2108 1.46 - 1.58: 3684 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8716 Sorted by residual: bond pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.37e-02 5.33e+03 1.81e+00 bond pdb=" CA ILE R 246 " pdb=" CB ILE R 246 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.19e-02 7.06e+03 9.69e-01 bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 9.13e-01 bond pdb=" CA ILE N 51 " pdb=" CB ILE N 51 " ideal model delta sigma weight residual 1.550 1.541 0.009 1.03e-02 9.43e+03 7.69e-01 bond pdb=" C GLU R 67 " pdb=" N GLY R 68 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 7.03e-01 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11468 1.31 - 2.61: 266 2.61 - 3.92: 51 3.92 - 5.22: 9 5.22 - 6.53: 3 Bond angle restraints: 11797 Sorted by residual: angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 114.56 109.65 4.91 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N ILE R 73 " pdb=" CA ILE R 73 " pdb=" C ILE R 73 " ideal model delta sigma weight residual 111.62 108.73 2.89 7.90e-01 1.60e+00 1.34e+01 angle pdb=" N ILE G 9 " pdb=" CA ILE G 9 " pdb=" C ILE G 9 " ideal model delta sigma weight residual 112.12 109.09 3.03 8.40e-01 1.42e+00 1.30e+01 angle pdb=" C GLU R 52 " pdb=" N GLN R 53 " pdb=" CA GLN R 53 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N VAL N 64 " pdb=" CA VAL N 64 " pdb=" C VAL N 64 " ideal model delta sigma weight residual 113.20 110.06 3.14 9.60e-01 1.09e+00 1.07e+01 ... (remaining 11792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4768 17.83 - 35.67: 347 35.67 - 53.50: 39 53.50 - 71.34: 6 71.34 - 89.17: 15 Dihedral angle restraints: 5175 sinusoidal: 1970 harmonic: 3205 Sorted by residual: dihedral pdb=" CB CYS R 215 " pdb=" SG CYS R 215 " pdb=" SG CYS R 285 " pdb=" CB CYS R 285 " ideal model delta sinusoidal sigma weight residual 93.00 42.54 50.46 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS R 45 " pdb=" SG CYS R 45 " pdb=" SG CYS R 75 " pdb=" CB CYS R 75 " ideal model delta sinusoidal sigma weight residual 93.00 128.25 -35.25 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CB GLU R 373 " pdb=" CG GLU R 373 " pdb=" CD GLU R 373 " pdb=" OE1 GLU R 373 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 940 0.035 - 0.071: 282 0.071 - 0.106: 87 0.106 - 0.142: 12 0.142 - 0.177: 2 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CB ILE R 246 " pdb=" CA ILE R 246 " pdb=" CG1 ILE R 246 " pdb=" CG2 ILE R 246 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CB THR B 128 " pdb=" CA THR B 128 " pdb=" OG1 THR B 128 " pdb=" CG2 THR B 128 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CA ILE R 288 " pdb=" N ILE R 288 " pdb=" C ILE R 288 " pdb=" CB ILE R 288 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1320 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 321 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 300 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 301 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.017 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1049 2.75 - 3.29: 8547 3.29 - 3.83: 13270 3.83 - 4.36: 15713 4.36 - 4.90: 26736 Nonbonded interactions: 65315 Sorted by model distance: nonbonded pdb=" NH1 ARG B 42 " pdb=" O ILE B 43 " model vdw 2.214 3.120 nonbonded pdb=" O ASP B 76 " pdb=" OG SER B 98 " model vdw 2.236 3.040 nonbonded pdb=" O ARG R 339 " pdb=" OG SER R 343 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN R 291 " pdb=" OG SER R 293 " model vdw 2.312 3.040 nonbonded pdb=" O GLY B 182 " pdb=" NZ LYS B 209 " model vdw 2.317 3.120 ... (remaining 65310 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.002 0.020 8716 Z= 0.110 Angle : 0.502 6.528 11797 Z= 0.312 Chirality : 0.038 0.177 1323 Planarity : 0.002 0.033 1516 Dihedral : 12.848 89.170 3086 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.21), residues: 1086 helix: -2.77 (0.18), residues: 377 sheet: -1.64 (0.32), residues: 208 loop : -2.50 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.001 0.000 HIS R 241 PHE 0.013 0.001 PHE A 315 TYR 0.004 0.001 TYR B 124 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 VAL cc_start: 0.8933 (t) cc_final: 0.8615 (t) REVERT: A 374 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7522 (ttt180) REVERT: B 16 ASN cc_start: 0.9351 (m110) cc_final: 0.8821 (m110) REVERT: B 45 MET cc_start: 0.7078 (mmm) cc_final: 0.6780 (tpp) REVERT: B 78 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8541 (mmmt) REVERT: B 145 TYR cc_start: 0.8584 (p90) cc_final: 0.8363 (p90) REVERT: B 165 THR cc_start: 0.7995 (p) cc_final: 0.7711 (t) REVERT: B 188 MET cc_start: 0.7775 (tpt) cc_final: 0.7508 (mmm) REVERT: B 339 TRP cc_start: 0.8630 (m100) cc_final: 0.8350 (m100) REVERT: G 41 CYS cc_start: 0.8871 (m) cc_final: 0.8592 (m) REVERT: G 59 ASN cc_start: 0.7332 (t0) cc_final: 0.6484 (p0) REVERT: N 61 THR cc_start: 0.8397 (p) cc_final: 0.8140 (t) REVERT: N 83 MET cc_start: 0.8048 (pmm) cc_final: 0.7716 (pmm) REVERT: P 3 ASP cc_start: 0.8242 (t0) cc_final: 0.7914 (t0) REVERT: R 132 ASN cc_start: 0.8938 (p0) cc_final: 0.8731 (p0) REVERT: R 175 ASN cc_start: 0.9107 (m-40) cc_final: 0.8702 (m-40) REVERT: R 179 MET cc_start: 0.8074 (mmm) cc_final: 0.7814 (tpp) REVERT: R 230 TYR cc_start: 0.8606 (m-80) cc_final: 0.8047 (m-10) REVERT: R 256 GLN cc_start: 0.7622 (mt0) cc_final: 0.6522 (tm-30) REVERT: R 261 PHE cc_start: 0.9038 (t80) cc_final: 0.8828 (t80) REVERT: R 282 ASP cc_start: 0.7871 (t0) cc_final: 0.7609 (t0) REVERT: R 321 MET cc_start: 0.8108 (mtt) cc_final: 0.7812 (mmm) REVERT: R 354 HIS cc_start: 0.9050 (p-80) cc_final: 0.8655 (p-80) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2310 time to fit residues: 97.8359 Evaluate side-chains 211 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 218 ASN B 17 GLN B 91 HIS B 220 GLN N 3 GLN R 180 HIS R 223 GLN R 229 ASN R 354 HIS R 392 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8716 Z= 0.222 Angle : 0.593 6.039 11797 Z= 0.319 Chirality : 0.043 0.227 1323 Planarity : 0.004 0.038 1516 Dihedral : 3.868 16.952 1203 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.24), residues: 1086 helix: -0.52 (0.25), residues: 375 sheet: -1.15 (0.34), residues: 203 loop : -2.07 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 295 HIS 0.007 0.001 HIS R 241 PHE 0.025 0.002 PHE R 358 TYR 0.017 0.002 TYR R 138 ARG 0.007 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7946 (t80) cc_final: 0.7224 (t80) REVERT: A 374 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7456 (ttt180) REVERT: B 9 GLN cc_start: 0.8868 (tp40) cc_final: 0.8647 (mm110) REVERT: B 78 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8468 (mmmt) REVERT: B 188 MET cc_start: 0.8206 (tpt) cc_final: 0.7825 (mmm) REVERT: B 217 MET cc_start: 0.8685 (ppp) cc_final: 0.8148 (ppp) REVERT: B 339 TRP cc_start: 0.8855 (m100) cc_final: 0.8595 (m100) REVERT: G 59 ASN cc_start: 0.7267 (t0) cc_final: 0.6955 (t0) REVERT: N 68 PHE cc_start: 0.8193 (m-10) cc_final: 0.7751 (m-10) REVERT: R 175 ASN cc_start: 0.9135 (m-40) cc_final: 0.8730 (m-40) REVERT: R 179 MET cc_start: 0.8046 (mmm) cc_final: 0.7775 (mmm) REVERT: R 230 TYR cc_start: 0.8711 (m-80) cc_final: 0.8434 (m-10) REVERT: R 251 GLU cc_start: 0.7582 (pm20) cc_final: 0.7226 (pm20) REVERT: R 321 MET cc_start: 0.8120 (mtt) cc_final: 0.7850 (mmm) REVERT: R 342 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7911 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2111 time to fit residues: 75.2702 Evaluate side-chains 205 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 40.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN N 53 GLN R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8716 Z= 0.238 Angle : 0.596 6.125 11797 Z= 0.316 Chirality : 0.043 0.216 1323 Planarity : 0.004 0.038 1516 Dihedral : 4.164 15.856 1203 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1086 helix: 0.03 (0.26), residues: 379 sheet: -0.84 (0.35), residues: 203 loop : -1.79 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 281 HIS 0.008 0.001 HIS R 241 PHE 0.014 0.002 PHE A 315 TYR 0.018 0.002 TYR R 138 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 TRP cc_start: 0.8589 (m100) cc_final: 0.8206 (m100) REVERT: A 374 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7374 (mtt180) REVERT: B 78 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8326 (mmmt) REVERT: B 188 MET cc_start: 0.8251 (tpt) cc_final: 0.7975 (mmm) REVERT: B 217 MET cc_start: 0.8625 (ppp) cc_final: 0.8179 (ppp) REVERT: B 312 ASP cc_start: 0.7704 (p0) cc_final: 0.7176 (p0) REVERT: B 339 TRP cc_start: 0.8987 (m100) cc_final: 0.8621 (m100) REVERT: G 14 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8175 (mtmm) REVERT: G 41 CYS cc_start: 0.8780 (m) cc_final: 0.8433 (m) REVERT: G 59 ASN cc_start: 0.7350 (t0) cc_final: 0.6998 (t0) REVERT: N 19 ARG cc_start: 0.8224 (ttp80) cc_final: 0.8005 (ttt90) REVERT: N 64 VAL cc_start: 0.8017 (m) cc_final: 0.7581 (m) REVERT: N 72 ARG cc_start: 0.6561 (ptm-80) cc_final: 0.6159 (ptt90) REVERT: R 175 ASN cc_start: 0.9125 (m-40) cc_final: 0.8749 (m-40) REVERT: R 179 MET cc_start: 0.8006 (mmm) cc_final: 0.7675 (tpp) REVERT: R 251 GLU cc_start: 0.7400 (pm20) cc_final: 0.6438 (pp20) REVERT: R 321 MET cc_start: 0.8163 (mtt) cc_final: 0.7849 (mmm) REVERT: R 342 ARG cc_start: 0.8319 (mtm180) cc_final: 0.7903 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2373 time to fit residues: 79.8045 Evaluate side-chains 203 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 40.0000 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN N 53 GLN R 229 ASN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8716 Z= 0.176 Angle : 0.553 6.511 11797 Z= 0.294 Chirality : 0.042 0.158 1323 Planarity : 0.004 0.040 1516 Dihedral : 4.081 16.811 1203 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1086 helix: 0.37 (0.26), residues: 381 sheet: -0.49 (0.36), residues: 201 loop : -1.53 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS B 225 PHE 0.027 0.002 PHE A 340 TYR 0.017 0.002 TYR R 138 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7325 (mtt180) REVERT: B 15 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8320 (mtpt) REVERT: B 16 ASN cc_start: 0.9346 (m110) cc_final: 0.9096 (m110) REVERT: B 188 MET cc_start: 0.8352 (tpt) cc_final: 0.7953 (tpp) REVERT: B 217 MET cc_start: 0.8587 (ppp) cc_final: 0.8189 (ppp) REVERT: B 222 PHE cc_start: 0.8502 (m-80) cc_final: 0.8238 (m-10) REVERT: B 339 TRP cc_start: 0.8953 (m100) cc_final: 0.8632 (m100) REVERT: G 41 CYS cc_start: 0.8685 (m) cc_final: 0.8430 (m) REVERT: G 59 ASN cc_start: 0.7302 (t0) cc_final: 0.6965 (t0) REVERT: N 64 VAL cc_start: 0.8002 (m) cc_final: 0.7665 (m) REVERT: N 72 ARG cc_start: 0.6541 (ptm-80) cc_final: 0.6054 (ptt90) REVERT: N 73 ASP cc_start: 0.7771 (t70) cc_final: 0.7571 (t70) REVERT: N 76 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8472 (mtmm) REVERT: N 83 MET cc_start: 0.7820 (tmm) cc_final: 0.7612 (tmm) REVERT: N 84 ASN cc_start: 0.8935 (p0) cc_final: 0.8576 (p0) REVERT: N 95 TYR cc_start: 0.8587 (m-80) cc_final: 0.8156 (m-80) REVERT: N 104 THR cc_start: 0.8470 (p) cc_final: 0.8226 (p) REVERT: R 147 THR cc_start: 0.8858 (m) cc_final: 0.8598 (m) REVERT: R 175 ASN cc_start: 0.9006 (m-40) cc_final: 0.8616 (m-40) REVERT: R 179 MET cc_start: 0.7922 (mmm) cc_final: 0.7545 (tpp) REVERT: R 251 GLU cc_start: 0.7222 (pm20) cc_final: 0.6403 (pp20) REVERT: R 282 ASP cc_start: 0.8321 (t70) cc_final: 0.8120 (t0) REVERT: R 321 MET cc_start: 0.8091 (mtt) cc_final: 0.7757 (mmm) REVERT: R 342 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7830 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2184 time to fit residues: 72.7328 Evaluate side-chains 194 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 53 GLN R 229 ASN ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8716 Z= 0.228 Angle : 0.582 7.636 11797 Z= 0.308 Chirality : 0.042 0.239 1323 Planarity : 0.004 0.046 1516 Dihedral : 4.248 17.748 1203 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.26), residues: 1086 helix: 0.41 (0.27), residues: 389 sheet: -0.33 (0.36), residues: 199 loop : -1.49 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS R 241 PHE 0.023 0.002 PHE A 340 TYR 0.024 0.002 TYR N 80 ARG 0.003 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 TYR cc_start: 0.7635 (t80) cc_final: 0.7429 (t80) REVERT: A 360 TYR cc_start: 0.8911 (m-80) cc_final: 0.8515 (m-80) REVERT: A 374 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7350 (mtt180) REVERT: B 188 MET cc_start: 0.8392 (tpt) cc_final: 0.7992 (tpp) REVERT: B 217 MET cc_start: 0.8596 (ppp) cc_final: 0.8186 (ppp) REVERT: B 339 TRP cc_start: 0.9010 (m100) cc_final: 0.8619 (m100) REVERT: G 59 ASN cc_start: 0.7336 (t0) cc_final: 0.6958 (t0) REVERT: N 64 VAL cc_start: 0.8007 (m) cc_final: 0.7709 (m) REVERT: N 72 ARG cc_start: 0.6427 (ptm-80) cc_final: 0.6017 (ptt90) REVERT: N 76 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8624 (mtmm) REVERT: R 147 THR cc_start: 0.8825 (m) cc_final: 0.8551 (m) REVERT: R 175 ASN cc_start: 0.8994 (m-40) cc_final: 0.8626 (m-40) REVERT: R 282 ASP cc_start: 0.8381 (t70) cc_final: 0.8074 (t0) REVERT: R 321 MET cc_start: 0.8115 (mtt) cc_final: 0.7781 (mmm) REVERT: R 342 ARG cc_start: 0.8331 (mtm180) cc_final: 0.7866 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2041 time to fit residues: 67.5151 Evaluate side-chains 201 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 chunk 99 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 259 GLN N 53 GLN R 229 ASN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8716 Z= 0.149 Angle : 0.573 8.913 11797 Z= 0.296 Chirality : 0.041 0.197 1323 Planarity : 0.003 0.041 1516 Dihedral : 4.107 15.936 1203 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1086 helix: 0.52 (0.27), residues: 387 sheet: -0.28 (0.37), residues: 199 loop : -1.39 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 281 HIS 0.004 0.001 HIS B 225 PHE 0.024 0.002 PHE A 340 TYR 0.021 0.002 TYR G 40 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8837 (tp40) cc_final: 0.8407 (mp10) REVERT: B 45 MET cc_start: 0.6992 (mmp) cc_final: 0.6676 (tpp) REVERT: B 78 LYS cc_start: 0.8806 (mmpt) cc_final: 0.8397 (mmmt) REVERT: B 138 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6924 (tm-30) REVERT: B 188 MET cc_start: 0.8408 (tpt) cc_final: 0.7818 (tpt) REVERT: B 217 MET cc_start: 0.8517 (ppp) cc_final: 0.8123 (ppp) REVERT: B 222 PHE cc_start: 0.8487 (m-80) cc_final: 0.8234 (m-10) REVERT: B 275 SER cc_start: 0.8862 (t) cc_final: 0.8597 (p) REVERT: B 339 TRP cc_start: 0.8939 (m100) cc_final: 0.8573 (m100) REVERT: G 21 MET cc_start: 0.8029 (mmm) cc_final: 0.7822 (mmt) REVERT: G 59 ASN cc_start: 0.7274 (t0) cc_final: 0.7001 (t0) REVERT: N 39 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7810 (tm-30) REVERT: N 72 ARG cc_start: 0.6480 (ptm-80) cc_final: 0.6052 (ptt90) REVERT: N 73 ASP cc_start: 0.7772 (t70) cc_final: 0.7554 (t70) REVERT: N 76 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8533 (mtmm) REVERT: N 117 TYR cc_start: 0.8215 (m-80) cc_final: 0.7956 (m-80) REVERT: R 147 THR cc_start: 0.8752 (m) cc_final: 0.8492 (m) REVERT: R 175 ASN cc_start: 0.8820 (m-40) cc_final: 0.8485 (m-40) REVERT: R 342 ARG cc_start: 0.8218 (mtm180) cc_final: 0.7769 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1999 time to fit residues: 73.0600 Evaluate side-chains 203 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN R 229 ASN ** R 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8716 Z= 0.158 Angle : 0.574 9.924 11797 Z= 0.297 Chirality : 0.042 0.181 1323 Planarity : 0.003 0.041 1516 Dihedral : 4.089 17.519 1203 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1086 helix: 0.73 (0.27), residues: 387 sheet: -0.11 (0.37), residues: 199 loop : -1.44 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.006 0.001 HIS B 225 PHE 0.026 0.002 PHE N 68 TYR 0.015 0.001 TYR A 318 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.9038 (m-80) cc_final: 0.8659 (m-80) REVERT: A 374 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7469 (mtt180) REVERT: B 45 MET cc_start: 0.7021 (mmp) cc_final: 0.6707 (tpp) REVERT: B 78 LYS cc_start: 0.8754 (mmpt) cc_final: 0.8406 (mmmt) REVERT: B 188 MET cc_start: 0.8402 (tpt) cc_final: 0.7904 (tpt) REVERT: B 217 MET cc_start: 0.8486 (ppp) cc_final: 0.8197 (ppp) REVERT: B 222 PHE cc_start: 0.8418 (m-80) cc_final: 0.8127 (m-10) REVERT: B 339 TRP cc_start: 0.8956 (m100) cc_final: 0.8567 (m100) REVERT: G 21 MET cc_start: 0.8031 (mmm) cc_final: 0.6876 (mmm) REVERT: G 59 ASN cc_start: 0.7289 (t0) cc_final: 0.6958 (t0) REVERT: N 39 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7894 (tm-30) REVERT: N 72 ARG cc_start: 0.6443 (ptm-80) cc_final: 0.5963 (ptt90) REVERT: N 73 ASP cc_start: 0.7700 (t70) cc_final: 0.7473 (t70) REVERT: N 76 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8516 (mtmm) REVERT: R 147 THR cc_start: 0.8787 (m) cc_final: 0.8553 (m) REVERT: R 321 MET cc_start: 0.8148 (mmm) cc_final: 0.7632 (mmm) REVERT: R 342 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7766 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2000 time to fit residues: 68.4414 Evaluate side-chains 196 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 53 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN R 354 HIS R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8716 Z= 0.179 Angle : 0.603 11.729 11797 Z= 0.309 Chirality : 0.042 0.168 1323 Planarity : 0.004 0.042 1516 Dihedral : 4.161 18.327 1203 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1086 helix: 0.79 (0.27), residues: 390 sheet: -0.17 (0.37), residues: 204 loop : -1.42 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.026 0.002 PHE N 68 TYR 0.015 0.001 TYR A 318 ARG 0.004 0.000 ARG R 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.9011 (m-80) cc_final: 0.8629 (m-80) REVERT: A 374 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7553 (mtt180) REVERT: B 15 LYS cc_start: 0.9166 (mtpt) cc_final: 0.8313 (mtpt) REVERT: B 16 ASN cc_start: 0.9296 (m110) cc_final: 0.9088 (m110) REVERT: B 78 LYS cc_start: 0.8725 (mmpt) cc_final: 0.8490 (mmmt) REVERT: B 188 MET cc_start: 0.8388 (tpt) cc_final: 0.7865 (tpt) REVERT: B 217 MET cc_start: 0.8488 (ppp) cc_final: 0.8219 (ppp) REVERT: B 222 PHE cc_start: 0.8455 (m-80) cc_final: 0.8236 (m-10) REVERT: B 339 TRP cc_start: 0.8968 (m100) cc_final: 0.8597 (m100) REVERT: G 59 ASN cc_start: 0.7304 (t0) cc_final: 0.6913 (t0) REVERT: N 39 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7893 (tm-30) REVERT: N 76 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8495 (mtmm) REVERT: R 147 THR cc_start: 0.8769 (m) cc_final: 0.8494 (m) REVERT: R 150 TYR cc_start: 0.7876 (m-10) cc_final: 0.7593 (m-80) REVERT: R 175 ASN cc_start: 0.8344 (m-40) cc_final: 0.8031 (m-40) REVERT: R 282 ASP cc_start: 0.8256 (t0) cc_final: 0.7919 (t0) REVERT: R 321 MET cc_start: 0.8186 (mmm) cc_final: 0.7665 (mmm) REVERT: R 342 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7762 (tmt-80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1948 time to fit residues: 65.1716 Evaluate side-chains 190 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS N 53 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN R 392 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8716 Z= 0.184 Angle : 0.620 12.181 11797 Z= 0.317 Chirality : 0.042 0.236 1323 Planarity : 0.004 0.055 1516 Dihedral : 4.219 18.529 1203 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.26), residues: 1086 helix: 0.68 (0.26), residues: 390 sheet: -0.19 (0.37), residues: 204 loop : -1.39 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 241 PHE 0.033 0.001 PHE N 68 TYR 0.025 0.001 TYR A 318 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.9016 (m-80) cc_final: 0.8662 (m-80) REVERT: B 78 LYS cc_start: 0.8768 (mmpt) cc_final: 0.8402 (mmmt) REVERT: B 188 MET cc_start: 0.8364 (tpt) cc_final: 0.7849 (tpt) REVERT: B 209 LYS cc_start: 0.8939 (mttt) cc_final: 0.8349 (mttt) REVERT: B 217 MET cc_start: 0.8569 (ppp) cc_final: 0.8331 (ppp) REVERT: B 222 PHE cc_start: 0.8436 (m-80) cc_final: 0.8166 (m-10) REVERT: B 339 TRP cc_start: 0.8956 (m100) cc_final: 0.8608 (m100) REVERT: G 59 ASN cc_start: 0.7262 (t0) cc_final: 0.6893 (t0) REVERT: N 39 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7837 (tm-30) REVERT: N 76 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8466 (mtmm) REVERT: N 81 LEU cc_start: 0.7503 (tt) cc_final: 0.7173 (tp) REVERT: N 82 GLN cc_start: 0.7744 (mm110) cc_final: 0.7525 (mm-40) REVERT: R 147 THR cc_start: 0.8768 (m) cc_final: 0.8500 (m) REVERT: R 150 TYR cc_start: 0.7845 (m-10) cc_final: 0.7605 (m-80) REVERT: R 175 ASN cc_start: 0.8435 (m-40) cc_final: 0.8208 (m-40) REVERT: R 342 ARG cc_start: 0.8334 (mtm180) cc_final: 0.7755 (tmt-80) REVERT: R 387 LEU cc_start: 0.8297 (tt) cc_final: 0.8031 (tt) REVERT: R 406 TRP cc_start: 0.7631 (t60) cc_final: 0.6331 (m100) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.1830 time to fit residues: 60.4495 Evaluate side-chains 190 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8716 Z= 0.176 Angle : 0.627 12.280 11797 Z= 0.319 Chirality : 0.042 0.155 1323 Planarity : 0.004 0.045 1516 Dihedral : 4.217 20.029 1203 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1086 helix: 0.67 (0.26), residues: 388 sheet: -0.12 (0.37), residues: 204 loop : -1.37 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS B 225 PHE 0.031 0.002 PHE N 68 TYR 0.021 0.001 TYR A 318 ARG 0.006 0.000 ARG B 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 TYR cc_start: 0.9046 (m-80) cc_final: 0.8693 (m-80) REVERT: B 78 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8384 (mmmt) REVERT: B 188 MET cc_start: 0.8314 (tpt) cc_final: 0.7775 (tpt) REVERT: B 217 MET cc_start: 0.8547 (ppp) cc_final: 0.8233 (ppp) REVERT: B 222 PHE cc_start: 0.8404 (m-80) cc_final: 0.8194 (m-10) REVERT: B 339 TRP cc_start: 0.8940 (m100) cc_final: 0.8588 (m100) REVERT: G 59 ASN cc_start: 0.7278 (t0) cc_final: 0.6944 (t0) REVERT: N 39 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7915 (tm-30) REVERT: N 64 VAL cc_start: 0.7748 (m) cc_final: 0.7131 (m) REVERT: N 76 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8440 (mtmm) REVERT: R 147 THR cc_start: 0.8711 (m) cc_final: 0.8461 (m) REVERT: R 175 ASN cc_start: 0.8327 (m-40) cc_final: 0.8025 (m-40) REVERT: R 221 LEU cc_start: 0.9362 (tp) cc_final: 0.9112 (pp) REVERT: R 342 ARG cc_start: 0.8179 (mtm180) cc_final: 0.7668 (tmt-80) REVERT: R 406 TRP cc_start: 0.7649 (t60) cc_final: 0.6322 (m100) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2081 time to fit residues: 69.5673 Evaluate side-chains 192 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.0010 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 chunk 4 optimal weight: 5.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 13 GLN B 91 HIS N 53 GLN ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 ASN ** R 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.108216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085931 restraints weight = 23421.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088449 restraints weight = 13888.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090217 restraints weight = 9652.132| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8716 Z= 0.206 Angle : 0.636 12.707 11797 Z= 0.326 Chirality : 0.043 0.157 1323 Planarity : 0.004 0.048 1516 Dihedral : 4.274 18.451 1203 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1086 helix: 0.57 (0.26), residues: 393 sheet: -0.26 (0.37), residues: 206 loop : -1.40 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS R 241 PHE 0.019 0.001 PHE A 315 TYR 0.020 0.001 TYR A 318 ARG 0.007 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.92 seconds wall clock time: 39 minutes 27.28 seconds (2367.28 seconds total)