Starting phenix.real_space_refine on Fri Mar 15 17:26:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pb9_17581/03_2024/8pb9_17581_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.025 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 10 5.49 5 S 55 5.16 5 C 7701 2.51 5 N 2220 2.21 5 O 2279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 370": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12265 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3097 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain: "A" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2003 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "B" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2003 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 12, 'TRANS': 252} Chain: "C" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1995 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 10, 'TRANS': 241} Chain: "E" Number of atoms: 3013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3013 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'C2E': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.55 Number of scatterers: 12265 At special positions: 0 Unit cell: (75.207, 99.33, 168.861, 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 55 16.00 P 10 15.00 O 2279 8.00 N 2220 7.00 C 7701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.73 Conformation dependent library (CDL) restraints added in 2.1 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 10 sheets defined 43.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 39 through 45 removed outlier: 3.874A pdb=" N GLY D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 111 through 128 Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.857A pdb=" N VAL D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.600A pdb=" N VAL D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 296 removed outlier: 4.465A pdb=" N GLU D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 307 Processing helix chain 'D' and resid 317 through 337 removed outlier: 4.048A pdb=" N VAL D 321 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D 322 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALA D 325 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 331 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 355 removed outlier: 3.591A pdb=" N ARG D 355 " --> pdb=" O MET D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 375 Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.963A pdb=" N SER A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.799A pdb=" N ARG A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.870A pdb=" N GLN A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 97 through 100 No H-bonds generated for 'chain 'B' and resid 97 through 100' Processing helix chain 'B' and resid 104 through 115 removed outlier: 3.725A pdb=" N ALA B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.777A pdb=" N ARG B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 208 through 215 removed outlier: 4.713A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 252 through 264 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 301 through 310 removed outlier: 5.763A pdb=" N PHE C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 321 through 338 removed outlier: 4.688A pdb=" N ALA C 325 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE C 332 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 338 " --> pdb=" O MET C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 361 through 375 Processing helix chain 'E' and resid 14 through 26 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 67 through 76 Processing helix chain 'E' and resid 95 through 98 No H-bonds generated for 'chain 'E' and resid 95 through 98' Processing helix chain 'E' and resid 111 through 128 Processing helix chain 'E' and resid 151 through 164 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 208 through 215 removed outlier: 4.624A pdb=" N GLU E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 252 through 263 Processing helix chain 'E' and resid 290 through 296 Processing helix chain 'E' and resid 301 through 307 Processing helix chain 'E' and resid 317 through 337 removed outlier: 3.904A pdb=" N VAL E 321 " --> pdb=" O ARG E 318 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLU E 322 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA E 325 " --> pdb=" O GLU E 322 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN E 329 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS E 337 " --> pdb=" O ARG E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 354 Processing helix chain 'E' and resid 361 through 375 removed outlier: 3.875A pdb=" N LEU E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.638A pdb=" N LEU D 32 " --> pdb=" O LEU D 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 311 through 313 removed outlier: 6.674A pdb=" N LEU D 171 " --> pdb=" O ILE D 312 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 266 through 268 Processing sheet with id= D, first strand: chain 'D' and resid 82 through 85 removed outlier: 7.675A pdb=" N LEU D 84 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER D 104 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.556A pdb=" N GLU A 145 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR A 16 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 147 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ARG A 175 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N LEU A 148 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 177 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 150 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 179 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA A 207 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 178 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN A 209 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA A 180 " --> pdb=" O GLN A 209 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N VAL A 211 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 207 through 214 removed outlier: 7.019A pdb=" N ALA B 180 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL B 213 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL B 146 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 311 through 313 removed outlier: 6.961A pdb=" N LEU C 171 " --> pdb=" O ILE C 312 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.777A pdb=" N LEU E 7 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N CYS E 34 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU E 9 " --> pdb=" O CYS E 34 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU E 8 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL E 55 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE E 10 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU E 57 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU E 57 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU E 83 " --> pdb=" O LEU E 57 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 311 through 313 removed outlier: 6.511A pdb=" N LEU E 171 " --> pdb=" O ILE E 312 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 266 through 268 440 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4177 1.34 - 1.46: 2307 1.46 - 1.58: 5885 1.58 - 1.70: 14 1.70 - 1.82: 100 Bond restraints: 12483 Sorted by residual: bond pdb=" C3A C2E D 401 " pdb=" C4A C2E D 401 " ideal model delta sigma weight residual 1.223 1.522 -0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C3A C2E D 402 " pdb=" C4A C2E D 402 " ideal model delta sigma weight residual 1.223 1.518 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C1A C2E D 402 " pdb=" C2A C2E D 402 " ideal model delta sigma weight residual 1.258 1.529 -0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C1A C2E D 401 " pdb=" C2A C2E D 401 " ideal model delta sigma weight residual 1.258 1.526 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C1' C2E D 401 " pdb=" C2' C2E D 401 " ideal model delta sigma weight residual 1.297 1.528 -0.231 2.00e-02 2.50e+03 1.33e+02 ... (remaining 12478 not shown) Histogram of bond angle deviations from ideal: 98.55 - 107.09: 412 107.09 - 115.64: 7830 115.64 - 124.19: 8352 124.19 - 132.73: 316 132.73 - 141.28: 12 Bond angle restraints: 16922 Sorted by residual: angle pdb=" C1' C2E D 402 " pdb=" N9 C2E D 402 " pdb=" C8 C2E D 402 " ideal model delta sigma weight residual 98.76 126.70 -27.94 3.00e+00 1.11e-01 8.67e+01 angle pdb=" C1' C2E D 401 " pdb=" N9 C2E D 401 " pdb=" C8 C2E D 401 " ideal model delta sigma weight residual 98.76 126.65 -27.89 3.00e+00 1.11e-01 8.64e+01 angle pdb=" C1' C2E D 402 " pdb=" N9 C2E D 402 " pdb=" C4 C2E D 402 " ideal model delta sigma weight residual 152.55 127.17 25.38 3.00e+00 1.11e-01 7.16e+01 angle pdb=" C1' C2E D 401 " pdb=" N9 C2E D 401 " pdb=" C4 C2E D 401 " ideal model delta sigma weight residual 152.55 127.25 25.30 3.00e+00 1.11e-01 7.11e+01 angle pdb=" PA ACP A 301 " pdb=" O3A ACP A 301 " pdb=" PB ACP A 301 " ideal model delta sigma weight residual 125.06 141.28 -16.22 3.00e+00 1.11e-01 2.92e+01 ... (remaining 16917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 7253 27.84 - 55.67: 314 55.67 - 83.51: 44 83.51 - 111.35: 10 111.35 - 139.18: 9 Dihedral angle restraints: 7630 sinusoidal: 3178 harmonic: 4452 Sorted by residual: dihedral pdb=" CA MET E 107 " pdb=" C MET E 107 " pdb=" N PRO E 108 " pdb=" CA PRO E 108 " ideal model delta harmonic sigma weight residual -180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLU B 71 " pdb=" C GLU B 71 " pdb=" N GLY B 72 " pdb=" CA GLY B 72 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY C 360 " pdb=" C GLY C 360 " pdb=" N ASN C 361 " pdb=" CA ASN C 361 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 7627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1741 0.067 - 0.135: 179 0.135 - 0.202: 6 0.202 - 0.270: 4 0.270 - 0.337: 4 Chirality restraints: 1934 Sorted by residual: chirality pdb=" C2' C2E D 402 " pdb=" C1' C2E D 402 " pdb=" C3' C2E D 402 " pdb=" O2' C2E D 402 " both_signs ideal model delta sigma weight residual False -2.39 -2.73 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C2' C2E D 401 " pdb=" C1' C2E D 401 " pdb=" C3' C2E D 401 " pdb=" O2' C2E D 401 " both_signs ideal model delta sigma weight residual False -2.39 -2.72 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C2A C2E D 402 " pdb=" C1A C2E D 402 " pdb=" C3A C2E D 402 " pdb=" O2A C2E D 402 " both_signs ideal model delta sigma weight residual False -2.44 -2.73 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1931 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 196 " -0.063 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO E 197 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO E 197 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO E 197 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 253 " 0.038 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A 254 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 250 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO D 251 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " -0.029 5.00e-02 4.00e+02 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2282 2.77 - 3.30: 12512 3.30 - 3.84: 20620 3.84 - 4.37: 24211 4.37 - 4.90: 40060 Nonbonded interactions: 99685 Sorted by model distance: nonbonded pdb=" O LYS B 249 " pdb=" OG SER B 252 " model vdw 2.240 2.440 nonbonded pdb=" O GLU C 330 " pdb=" OG SER C 333 " model vdw 2.251 2.440 nonbonded pdb=" OD2 ASP A 170 " pdb=" NE2 GLN B 97 " model vdw 2.257 2.520 nonbonded pdb=" O PHE B 234 " pdb=" OG SER B 240 " model vdw 2.260 2.440 nonbonded pdb=" OG SER D 342 " pdb=" NH1 ARG D 344 " model vdw 2.266 2.520 ... (remaining 99680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 4 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 393)) selection = (chain 'E' and resid 4 through 393) } 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 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: 4.420 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: 2.790 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.880 Find NCS groups from input model: 0.650 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 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 : 0.010 0.299 12483 Z= 0.723 Angle : 0.903 27.939 16922 Z= 0.382 Chirality : 0.044 0.337 1934 Planarity : 0.005 0.095 2185 Dihedral : 16.347 139.185 4752 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.84 (0.21), residues: 1540 helix: 0.24 (0.20), residues: 703 sheet: -0.86 (0.38), residues: 175 loop : -1.26 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 93 HIS 0.004 0.001 HIS B 171 PHE 0.016 0.001 PHE E 26 TYR 0.029 0.001 TYR D 111 ARG 0.009 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 1.375 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: symmetry clash REVERT: D 151 ARG cc_start: 0.5914 (tpt170) cc_final: 0.5664 (tpt90) REVERT: D 181 GLU cc_start: 0.7235 (tp30) cc_final: 0.7003 (tp30) REVERT: D 246 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 68 ASP cc_start: 0.7212 (m-30) cc_final: 0.6767 (m-30) REVERT: C 157 ARG cc_start: 0.5506 (mtm-85) cc_final: 0.5248 (mtm-85) REVERT: C 214 GLU cc_start: 0.5266 (mm-30) cc_final: 0.4813 (mm-30) REVERT: E 173 LEU cc_start: 0.8238 (mt) cc_final: 0.7981 (mt) REVERT: E 212 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6422 (tp30) REVERT: E 238 ASN cc_start: 0.7395 (t0) cc_final: 0.7099 (t0) REVERT: E 255 GLN cc_start: 0.6082 (tt0) cc_final: 0.5866 (tt0) outliers start: 1 outliers final: 1 residues processed: 289 average time/residue: 0.2753 time to fit residues: 108.6959 Evaluate side-chains 257 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 122 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.0670 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN E 155 GLN E 158 GLN ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12483 Z= 0.254 Angle : 0.579 6.959 16922 Z= 0.287 Chirality : 0.041 0.215 1934 Planarity : 0.004 0.071 2185 Dihedral : 13.455 172.023 1800 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.23 % Allowed : 10.67 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.78 (0.21), residues: 1540 helix: 0.32 (0.20), residues: 687 sheet: -0.92 (0.37), residues: 187 loop : -1.22 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 358 HIS 0.006 0.001 HIS E 376 PHE 0.024 0.002 PHE D 267 TYR 0.017 0.002 TYR C 189 ARG 0.005 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 1.276 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: D 102 LEU cc_start: 0.7924 (tp) cc_final: 0.7710 (tp) REVERT: D 327 LEU cc_start: 0.8555 (mp) cc_final: 0.8339 (mp) REVERT: D 329 ASN cc_start: 0.8235 (t0) cc_final: 0.8010 (t0) REVERT: D 370 GLU cc_start: 0.6976 (tt0) cc_final: 0.6556 (tt0) REVERT: A 68 ASP cc_start: 0.7117 (m-30) cc_final: 0.6823 (m-30) REVERT: B 112 GLN cc_start: 0.8035 (mp10) cc_final: 0.7266 (mp10) REVERT: C 293 MET cc_start: 0.7208 (tpt) cc_final: 0.7004 (tpt) REVERT: C 356 HIS cc_start: 0.5862 (t-90) cc_final: 0.5648 (t-90) REVERT: E 202 ASN cc_start: 0.7819 (t0) cc_final: 0.7590 (t0) REVERT: E 250 MET cc_start: 0.6998 (tpp) cc_final: 0.6713 (tpp) REVERT: E 254 MET cc_start: 0.5796 (tpt) cc_final: 0.5525 (tpt) outliers start: 16 outliers final: 14 residues processed: 283 average time/residue: 0.2871 time to fit residues: 110.4349 Evaluate side-chains 278 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 264 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 276 GLN Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 140 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 287 HIS D 361 ASN ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN E 158 GLN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12483 Z= 0.201 Angle : 0.537 6.822 16922 Z= 0.266 Chirality : 0.040 0.160 1934 Planarity : 0.004 0.061 2185 Dihedral : 13.035 165.016 1797 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.53 % Allowed : 13.28 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.72 (0.21), residues: 1540 helix: 0.39 (0.20), residues: 689 sheet: -0.89 (0.37), residues: 185 loop : -1.21 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 93 HIS 0.008 0.001 HIS E 376 PHE 0.018 0.001 PHE E 26 TYR 0.015 0.001 TYR E 124 ARG 0.007 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 282 time to evaluate : 1.421 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: D 245 ASP cc_start: 0.6862 (t0) cc_final: 0.6610 (t0) REVERT: D 330 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6847 (tm-30) REVERT: A 68 ASP cc_start: 0.7111 (m-30) cc_final: 0.6790 (m-30) REVERT: A 190 ARG cc_start: 0.6543 (mtm110) cc_final: 0.6336 (mtm110) REVERT: B 112 GLN cc_start: 0.7949 (mp10) cc_final: 0.7167 (mp10) REVERT: C 356 HIS cc_start: 0.5811 (t-90) cc_final: 0.5597 (t-90) REVERT: E 202 ASN cc_start: 0.7801 (t0) cc_final: 0.7567 (t0) REVERT: E 254 MET cc_start: 0.5758 (tpt) cc_final: 0.5229 (tpt) REVERT: E 344 ARG cc_start: 0.6844 (ttm110) cc_final: 0.6615 (ttp-110) outliers start: 33 outliers final: 26 residues processed: 291 average time/residue: 0.2917 time to fit residues: 114.6497 Evaluate side-chains 303 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 277 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 186 ASN D 287 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12483 Z= 0.199 Angle : 0.537 8.022 16922 Z= 0.266 Chirality : 0.040 0.150 1934 Planarity : 0.004 0.054 2185 Dihedral : 12.887 165.468 1797 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.69 % Allowed : 15.12 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.67 (0.21), residues: 1540 helix: 0.44 (0.20), residues: 689 sheet: -0.87 (0.37), residues: 185 loop : -1.18 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 93 HIS 0.016 0.001 HIS C 376 PHE 0.023 0.001 PHE E 26 TYR 0.016 0.001 TYR E 124 ARG 0.007 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 1.349 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: D 102 LEU cc_start: 0.7783 (tp) cc_final: 0.7528 (tp) REVERT: D 245 ASP cc_start: 0.6858 (t0) cc_final: 0.6624 (t0) REVERT: D 330 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6759 (tm-30) REVERT: A 41 ARG cc_start: 0.6279 (ptt-90) cc_final: 0.5845 (ptt180) REVERT: A 68 ASP cc_start: 0.7106 (m-30) cc_final: 0.6798 (m-30) REVERT: B 112 GLN cc_start: 0.7906 (mt0) cc_final: 0.7441 (mp10) REVERT: B 205 ASP cc_start: 0.8013 (p0) cc_final: 0.7796 (p0) REVERT: B 243 PHE cc_start: 0.7288 (t80) cc_final: 0.7083 (t80) REVERT: C 293 MET cc_start: 0.7303 (tpt) cc_final: 0.6843 (tpt) REVERT: C 356 HIS cc_start: 0.5707 (t-90) cc_final: 0.5493 (t-90) REVERT: E 202 ASN cc_start: 0.7794 (t0) cc_final: 0.7560 (t0) REVERT: E 254 MET cc_start: 0.5747 (tpt) cc_final: 0.5241 (tpt) REVERT: E 314 MET cc_start: 0.7660 (tpp) cc_final: 0.6728 (tpp) REVERT: E 344 ARG cc_start: 0.6839 (ttm110) cc_final: 0.6607 (ttp-110) outliers start: 35 outliers final: 25 residues processed: 292 average time/residue: 0.2948 time to fit residues: 116.7264 Evaluate side-chains 295 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 270 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 0.0970 chunk 133 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12483 Z= 0.189 Angle : 0.524 7.063 16922 Z= 0.261 Chirality : 0.039 0.146 1934 Planarity : 0.004 0.051 2185 Dihedral : 12.734 165.395 1797 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.15 % Allowed : 15.81 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 (0.21), residues: 1540 helix: 0.50 (0.20), residues: 690 sheet: -0.89 (0.37), residues: 185 loop : -1.16 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.016 0.001 HIS C 376 PHE 0.026 0.001 PHE E 26 TYR 0.014 0.001 TYR E 124 ARG 0.008 0.000 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 276 time to evaluate : 1.374 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: symmetry clash REVERT: D 102 LEU cc_start: 0.7763 (tp) cc_final: 0.7529 (tp) REVERT: D 124 TYR cc_start: 0.7814 (m-80) cc_final: 0.7591 (m-80) REVERT: D 230 ARG cc_start: 0.6478 (ttt90) cc_final: 0.5807 (ttt90) REVERT: D 245 ASP cc_start: 0.6841 (t0) cc_final: 0.6592 (t0) REVERT: D 330 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6731 (tm-30) REVERT: D 361 ASN cc_start: 0.7405 (m110) cc_final: 0.7154 (m-40) REVERT: A 68 ASP cc_start: 0.7067 (m-30) cc_final: 0.6822 (m-30) REVERT: A 170 ASP cc_start: 0.6128 (m-30) cc_final: 0.5920 (m-30) REVERT: B 112 GLN cc_start: 0.7927 (mt0) cc_final: 0.7533 (mt0) REVERT: B 123 VAL cc_start: 0.8567 (p) cc_final: 0.8185 (m) REVERT: C 293 MET cc_start: 0.7361 (tpt) cc_final: 0.7107 (tpt) REVERT: E 202 ASN cc_start: 0.7811 (t0) cc_final: 0.7568 (t0) REVERT: E 314 MET cc_start: 0.7592 (tpp) cc_final: 0.6684 (tpp) REVERT: E 344 ARG cc_start: 0.6825 (ttm110) cc_final: 0.6596 (ttp-110) outliers start: 41 outliers final: 31 residues processed: 292 average time/residue: 0.2649 time to fit residues: 105.4170 Evaluate side-chains 299 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 87 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 149 optimal weight: 0.1980 chunk 123 optimal weight: 0.0270 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 HIS ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12483 Z= 0.156 Angle : 0.526 9.497 16922 Z= 0.260 Chirality : 0.039 0.138 1934 Planarity : 0.004 0.047 2185 Dihedral : 12.440 160.363 1797 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.53 % Allowed : 17.34 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.54 (0.21), residues: 1540 helix: 0.58 (0.20), residues: 691 sheet: -0.94 (0.37), residues: 187 loop : -1.13 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 39 HIS 0.014 0.001 HIS C 376 PHE 0.017 0.001 PHE E 26 TYR 0.021 0.001 TYR E 124 ARG 0.011 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 273 time to evaluate : 1.505 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: symmetry clash REVERT: D 102 LEU cc_start: 0.7736 (tp) cc_final: 0.7512 (tt) REVERT: D 230 ARG cc_start: 0.6426 (ttt90) cc_final: 0.5825 (ttt90) REVERT: D 245 ASP cc_start: 0.6775 (t0) cc_final: 0.6521 (t0) REVERT: D 274 LYS cc_start: 0.7559 (mmmm) cc_final: 0.7139 (tttm) REVERT: D 330 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 41 ARG cc_start: 0.6359 (ptt-90) cc_final: 0.6032 (ptt180) REVERT: B 112 GLN cc_start: 0.7970 (mt0) cc_final: 0.7618 (mt0) REVERT: B 123 VAL cc_start: 0.8527 (p) cc_final: 0.8174 (m) REVERT: B 152 ASP cc_start: 0.5819 (t0) cc_final: 0.5357 (t70) REVERT: B 205 ASP cc_start: 0.7990 (p0) cc_final: 0.7698 (p0) REVERT: C 157 ARG cc_start: 0.5482 (mtm-85) cc_final: 0.5270 (mtt90) REVERT: C 293 MET cc_start: 0.7345 (tpt) cc_final: 0.7035 (tpt) REVERT: C 375 MET cc_start: 0.5132 (ppp) cc_final: 0.4102 (ppp) REVERT: E 9 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3607 (tt) REVERT: E 202 ASN cc_start: 0.7857 (t0) cc_final: 0.7574 (t0) REVERT: E 313 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7088 (mm-30) REVERT: E 314 MET cc_start: 0.7308 (tpp) cc_final: 0.6486 (tpp) outliers start: 33 outliers final: 26 residues processed: 292 average time/residue: 0.2809 time to fit residues: 111.4850 Evaluate side-chains 294 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 chunk 125 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 287 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12483 Z= 0.180 Angle : 0.537 9.349 16922 Z= 0.264 Chirality : 0.039 0.140 1934 Planarity : 0.004 0.045 2185 Dihedral : 12.217 165.484 1797 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.30 % Allowed : 17.34 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.53 (0.21), residues: 1540 helix: 0.60 (0.20), residues: 691 sheet: -0.88 (0.37), residues: 187 loop : -1.15 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 39 HIS 0.014 0.001 HIS C 376 PHE 0.017 0.001 PHE E 26 TYR 0.020 0.001 TYR D 111 ARG 0.010 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 1.332 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: symmetry clash REVERT: D 102 LEU cc_start: 0.7773 (tp) cc_final: 0.7562 (tt) REVERT: D 230 ARG cc_start: 0.6458 (ttt90) cc_final: 0.5860 (ttt90) REVERT: D 245 ASP cc_start: 0.6814 (t0) cc_final: 0.6554 (t0) REVERT: D 274 LYS cc_start: 0.7535 (mmmm) cc_final: 0.7135 (tttm) REVERT: D 330 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6760 (tm-30) REVERT: A 41 ARG cc_start: 0.6324 (ptt-90) cc_final: 0.5499 (ptt180) REVERT: B 112 GLN cc_start: 0.8021 (mt0) cc_final: 0.7696 (mt0) REVERT: B 123 VAL cc_start: 0.8571 (p) cc_final: 0.8187 (m) REVERT: B 152 ASP cc_start: 0.5831 (t0) cc_final: 0.5346 (t0) REVERT: C 293 MET cc_start: 0.7246 (tpt) cc_final: 0.6893 (tpt) REVERT: C 375 MET cc_start: 0.5240 (ppp) cc_final: 0.4207 (ppp) REVERT: E 9 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.3699 (tt) REVERT: E 202 ASN cc_start: 0.7869 (t0) cc_final: 0.7586 (t0) REVERT: E 313 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7096 (mm-30) outliers start: 43 outliers final: 35 residues processed: 287 average time/residue: 0.2723 time to fit residues: 106.9165 Evaluate side-chains 297 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 162 GLN Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 369 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 44 optimal weight: 0.0020 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12483 Z= 0.187 Angle : 0.549 8.600 16922 Z= 0.271 Chirality : 0.040 0.141 1934 Planarity : 0.004 0.044 2185 Dihedral : 12.060 176.121 1797 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.84 % Allowed : 18.34 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 (0.21), residues: 1540 helix: 0.58 (0.20), residues: 690 sheet: -0.95 (0.37), residues: 190 loop : -1.15 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.013 0.001 HIS C 376 PHE 0.029 0.001 PHE E 26 TYR 0.020 0.001 TYR D 111 ARG 0.010 0.000 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 1.290 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: symmetry clash REVERT: D 230 ARG cc_start: 0.6450 (ttt90) cc_final: 0.5863 (ttt90) REVERT: D 245 ASP cc_start: 0.6818 (t0) cc_final: 0.6573 (t0) REVERT: D 274 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7136 (tttm) REVERT: D 330 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6734 (tm-30) REVERT: D 351 MET cc_start: 0.7755 (mmt) cc_final: 0.7493 (mmt) REVERT: A 41 ARG cc_start: 0.6300 (ptt-90) cc_final: 0.5438 (ptt180) REVERT: B 71 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: B 112 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: B 123 VAL cc_start: 0.8579 (p) cc_final: 0.8197 (m) REVERT: B 152 ASP cc_start: 0.5736 (t0) cc_final: 0.5284 (t70) REVERT: B 205 ASP cc_start: 0.7905 (p0) cc_final: 0.7699 (p0) REVERT: C 293 MET cc_start: 0.7265 (tpt) cc_final: 0.6887 (tpt) REVERT: E 9 LEU cc_start: 0.4003 (OUTLIER) cc_final: 0.3667 (tt) REVERT: E 202 ASN cc_start: 0.7897 (t0) cc_final: 0.7625 (t0) REVERT: E 313 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7089 (tm-30) outliers start: 37 outliers final: 31 residues processed: 284 average time/residue: 0.2894 time to fit residues: 112.3674 Evaluate side-chains 295 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 261 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 287 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12483 Z= 0.335 Angle : 0.653 8.882 16922 Z= 0.325 Chirality : 0.044 0.198 1934 Planarity : 0.005 0.059 2185 Dihedral : 12.272 166.643 1797 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.92 % Allowed : 18.65 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.94 (0.21), residues: 1540 helix: 0.21 (0.20), residues: 690 sheet: -1.15 (0.38), residues: 177 loop : -1.29 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 358 HIS 0.011 0.001 HIS C 376 PHE 0.035 0.002 PHE E 26 TYR 0.026 0.002 TYR C 189 ARG 0.013 0.001 ARG C 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 277 time to evaluate : 1.424 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: symmetry clash REVERT: D 115 LEU cc_start: 0.7868 (mp) cc_final: 0.7560 (mp) REVERT: D 181 GLU cc_start: 0.7087 (tp30) cc_final: 0.6860 (tp30) REVERT: D 230 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6079 (ttt180) REVERT: D 245 ASP cc_start: 0.7181 (t0) cc_final: 0.6896 (t0) REVERT: D 274 LYS cc_start: 0.7634 (mmmm) cc_final: 0.7270 (tttm) REVERT: D 313 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6451 (pm20) REVERT: D 330 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6760 (tm-30) REVERT: A 41 ARG cc_start: 0.6625 (ptt-90) cc_final: 0.5316 (ptt180) REVERT: B 112 GLN cc_start: 0.8101 (mt0) cc_final: 0.7735 (mt0) REVERT: B 152 ASP cc_start: 0.5809 (t0) cc_final: 0.5170 (t0) REVERT: B 225 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: C 293 MET cc_start: 0.7504 (tpt) cc_final: 0.7143 (tpt) REVERT: E 9 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.3978 (tt) REVERT: E 202 ASN cc_start: 0.7909 (t0) cc_final: 0.7633 (t0) REVERT: E 212 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6513 (tm-30) REVERT: E 313 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7223 (tm-30) outliers start: 38 outliers final: 31 residues processed: 294 average time/residue: 0.2854 time to fit residues: 114.2124 Evaluate side-chains 306 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 272 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 12 optimal weight: 0.0980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 287 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12483 Z= 0.174 Angle : 0.586 8.485 16922 Z= 0.291 Chirality : 0.040 0.168 1934 Planarity : 0.004 0.054 2185 Dihedral : 11.788 162.947 1797 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.46 % Allowed : 20.34 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.72 (0.21), residues: 1540 helix: 0.43 (0.20), residues: 692 sheet: -1.04 (0.38), residues: 176 loop : -1.23 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 39 HIS 0.012 0.001 HIS C 376 PHE 0.021 0.001 PHE E 26 TYR 0.023 0.001 TYR D 111 ARG 0.015 0.000 ARG C 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 278 time to evaluate : 1.463 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: symmetry clash REVERT: D 115 LEU cc_start: 0.7731 (mp) cc_final: 0.7455 (mp) REVERT: D 230 ARG cc_start: 0.6481 (ttt90) cc_final: 0.5901 (ttt90) REVERT: D 245 ASP cc_start: 0.6899 (t0) cc_final: 0.6668 (t0) REVERT: D 274 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7206 (tttm) REVERT: D 330 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6717 (tm-30) REVERT: D 390 PHE cc_start: 0.7413 (m-80) cc_final: 0.6970 (m-80) REVERT: B 112 GLN cc_start: 0.8042 (mt0) cc_final: 0.7671 (mt0) REVERT: B 152 ASP cc_start: 0.5646 (t0) cc_final: 0.5171 (t0) REVERT: C 293 MET cc_start: 0.7277 (tpt) cc_final: 0.6874 (tpt) REVERT: E 9 LEU cc_start: 0.4070 (OUTLIER) cc_final: 0.3730 (tt) REVERT: E 115 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7199 (mp) REVERT: E 202 ASN cc_start: 0.7981 (t0) cc_final: 0.7698 (t0) outliers start: 32 outliers final: 29 residues processed: 289 average time/residue: 0.2927 time to fit residues: 115.3346 Evaluate side-chains 307 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 276 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 287 HIS Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 122 GLN Chi-restraints excluded: chain E residue 160 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 0.0030 chunk 125 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 287 HIS ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN E 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.180471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.159380 restraints weight = 17644.175| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.36 r_work: 0.3934 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12483 Z= 0.216 Angle : 0.610 9.920 16922 Z= 0.303 Chirality : 0.041 0.176 1934 Planarity : 0.004 0.045 2185 Dihedral : 11.723 162.960 1797 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.69 % Allowed : 19.95 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.76 (0.21), residues: 1540 helix: 0.41 (0.20), residues: 690 sheet: -1.02 (0.38), residues: 176 loop : -1.27 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 39 HIS 0.015 0.001 HIS D 287 PHE 0.025 0.001 PHE E 26 TYR 0.020 0.001 TYR D 111 ARG 0.018 0.000 ARG C 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3138.90 seconds wall clock time: 57 minutes 14.88 seconds (3434.88 seconds total)