Starting phenix.real_space_refine on Thu Nov 14 17:05:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh7_40480/11_2024/8sh7_40480.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh7_40480/11_2024/8sh7_40480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh7_40480/11_2024/8sh7_40480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh7_40480/11_2024/8sh7_40480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh7_40480/11_2024/8sh7_40480.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh7_40480/11_2024/8sh7_40480.cif" } resolution = 2.8 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= 0.001 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 4283 2.51 5 N 1164 2.21 5 O 1318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6819 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3410 Classifications: {'peptide': 436} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3348 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.37, per 1000 atoms: 0.93 Number of scatterers: 6819 At special positions: 0 Unit cell: (71.24, 71.24, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 5 15.00 Mg 1 11.99 O 1318 8.00 N 1164 7.00 C 4283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1590 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 54.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.771A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 removed outlier: 4.114A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 79 removed outlier: 4.811A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.954A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 3.991A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.525A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.571A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.551A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.515A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.547A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.526A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.591A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.836A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.112A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.080A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.623A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.701A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.689A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 4.366A pdb=" N GLN B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.699A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.907A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.561A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 removed outlier: 3.540A pdb=" N ASP B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.941A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.656A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.871A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.538A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.716A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.081A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 424 removed outlier: 3.521A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.926A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N SER A 140 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N VAL A 9 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.613A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.357A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS B 6 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.539A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 879 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: 2.08 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1435 1.33 - 1.45: 1626 1.45 - 1.57: 3829 1.57 - 1.69: 8 1.69 - 1.81: 76 Bond restraints: 6974 Sorted by residual: bond pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.02e+00 bond pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 8.91e+00 bond pdb=" N CYS B 354 " pdb=" CA CYS B 354 " ideal model delta sigma weight residual 1.454 1.488 -0.035 1.18e-02 7.18e+03 8.58e+00 bond pdb=" N VAL B 353 " pdb=" CA VAL B 353 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.24e-02 6.50e+03 7.57e+00 bond pdb=" N ASP A 98 " pdb=" CA ASP A 98 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.34e-02 5.57e+03 7.50e+00 ... (remaining 6969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 9207 2.36 - 4.72: 239 4.72 - 7.09: 13 7.09 - 9.45: 7 9.45 - 11.81: 5 Bond angle restraints: 9471 Sorted by residual: angle pdb=" CA GLY B 319 " pdb=" C GLY B 319 " pdb=" O GLY B 319 " ideal model delta sigma weight residual 121.66 118.05 3.61 8.80e-01 1.29e+00 1.68e+01 angle pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sigma weight residual 120.50 132.31 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C1' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " ideal model delta sigma weight residual 111.00 99.71 11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" PB GTP A 501 " pdb=" O3B GTP A 501 " pdb=" PG GTP A 501 " ideal model delta sigma weight residual 120.50 131.68 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" N ALA A 99 " pdb=" CA ALA A 99 " pdb=" C ALA A 99 " ideal model delta sigma weight residual 112.87 108.73 4.14 1.20e+00 6.94e-01 1.19e+01 ... (remaining 9466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.73: 4002 28.73 - 57.46: 117 57.46 - 86.19: 18 86.19 - 114.93: 3 114.93 - 143.66: 3 Dihedral angle restraints: 4143 sinusoidal: 1660 harmonic: 2483 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -39.06 143.66 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -157.71 -133.02 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 172.67 118.41 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 4140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 588 0.045 - 0.091: 311 0.091 - 0.136: 105 0.136 - 0.182: 27 0.182 - 0.227: 3 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA ILE A 93 " pdb=" N ILE A 93 " pdb=" C ILE A 93 " pdb=" CB ILE A 93 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C3' GTP A 501 " pdb=" C2' GTP A 501 " pdb=" C4' GTP A 501 " pdb=" O3' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ARG B 241 " pdb=" N ARG B 241 " pdb=" C ARG B 241 " pdb=" CB ARG B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 1031 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 320 " 0.280 9.50e-02 1.11e+02 1.25e-01 9.68e+00 pdb=" NE ARG B 320 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 320 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 320 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 320 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 215 " -0.275 9.50e-02 1.11e+02 1.23e-01 9.33e+00 pdb=" NE ARG A 215 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 215 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 215 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 215 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 241 " -0.234 9.50e-02 1.11e+02 1.05e-01 7.60e+00 pdb=" NE ARG B 241 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 241 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 241 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 241 " -0.003 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 19 2.53 - 3.12: 5264 3.12 - 3.72: 9792 3.72 - 4.31: 14981 4.31 - 4.90: 25284 Nonbonded interactions: 55340 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG B 501 " model vdw 1.939 2.170 nonbonded pdb=" NZ LYS B 174 " pdb=" OE2 GLU B 205 " model vdw 2.300 3.120 nonbonded pdb=" NH1 ARG B 282 " pdb=" OE2 GLU B 288 " model vdw 2.310 3.120 nonbonded pdb=" NZ LYS A 311 " pdb=" O GLY A 436 " model vdw 2.400 3.120 nonbonded pdb=" N GLY B 142 " pdb=" O1B GDP B 502 " model vdw 2.453 3.120 ... (remaining 55335 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.380 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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 : 0.008 0.061 6974 Z= 0.530 Angle : 0.923 11.812 9471 Z= 0.544 Chirality : 0.060 0.227 1034 Planarity : 0.010 0.125 1234 Dihedral : 14.910 143.657 2553 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.35 (0.25), residues: 856 helix: -1.38 (0.22), residues: 365 sheet: 0.55 (0.41), residues: 145 loop : -0.77 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 101 HIS 0.008 0.002 HIS A 8 PHE 0.017 0.003 PHE A 53 TYR 0.025 0.004 TYR A 319 ARG 0.021 0.003 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.690 Fit side-chains REVERT: A 254 GLU cc_start: 0.8708 (tt0) cc_final: 0.8099 (tp30) REVERT: A 302 MET cc_start: 0.8632 (mtt) cc_final: 0.7950 (mtt) REVERT: A 423 GLU cc_start: 0.8354 (tp30) cc_final: 0.7776 (tm-30) REVERT: B 26 ASP cc_start: 0.8404 (t0) cc_final: 0.8078 (t0) REVERT: B 31 ASP cc_start: 0.8289 (m-30) cc_final: 0.7603 (m-30) REVERT: B 37 HIS cc_start: 0.8695 (m-70) cc_final: 0.7585 (m-70) REVERT: B 114 ASP cc_start: 0.8332 (m-30) cc_final: 0.7783 (m-30) REVERT: B 122 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8586 (tptt) REVERT: B 145 SER cc_start: 0.8765 (t) cc_final: 0.8541 (p) REVERT: B 213 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8701 (ttm170) REVERT: B 299 MET cc_start: 0.9437 (mmp) cc_final: 0.9033 (mmp) REVERT: B 324 LYS cc_start: 0.8726 (tttp) cc_final: 0.8345 (tttt) REVERT: B 388 MET cc_start: 0.8318 (mtp) cc_final: 0.8113 (mtp) REVERT: B 390 ARG cc_start: 0.8087 (ptm-80) cc_final: 0.7524 (tpt170) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 1.7450 time to fit residues: 255.3387 Evaluate side-chains 97 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 139 HIS A 293 ASN A 356 ASN A 406 HIS B 43 GLN B 137 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6974 Z= 0.292 Angle : 0.623 7.728 9471 Z= 0.331 Chirality : 0.046 0.159 1034 Planarity : 0.005 0.039 1234 Dihedral : 11.076 151.903 961 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.50 % Allowed : 10.37 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.00 (0.27), residues: 856 helix: 0.41 (0.26), residues: 381 sheet: 0.62 (0.42), residues: 145 loop : -0.65 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 21 HIS 0.004 0.001 HIS B 28 PHE 0.018 0.002 PHE A 255 TYR 0.011 0.001 TYR A 103 ARG 0.005 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.791 Fit side-chains REVERT: A 24 TYR cc_start: 0.8831 (m-10) cc_final: 0.8561 (m-10) REVERT: A 26 LEU cc_start: 0.8972 (tp) cc_final: 0.8719 (mt) REVERT: A 176 GLN cc_start: 0.8170 (mt0) cc_final: 0.7945 (mm-40) REVERT: A 254 GLU cc_start: 0.8073 (tt0) cc_final: 0.7509 (tp30) REVERT: A 290 GLU cc_start: 0.8661 (tt0) cc_final: 0.8420 (mt-10) REVERT: A 302 MET cc_start: 0.8523 (mtt) cc_final: 0.7805 (mtt) REVERT: A 377 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7911 (tmm) REVERT: A 393 HIS cc_start: 0.8876 (t70) cc_final: 0.8652 (t70) REVERT: B 26 ASP cc_start: 0.8564 (t0) cc_final: 0.8287 (t0) REVERT: B 31 ASP cc_start: 0.8292 (m-30) cc_final: 0.7595 (m-30) REVERT: B 37 HIS cc_start: 0.8711 (m-70) cc_final: 0.7747 (m-70) REVERT: B 114 ASP cc_start: 0.7919 (m-30) cc_final: 0.7534 (m-30) REVERT: B 122 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8614 (tptt) REVERT: B 157 GLU cc_start: 0.8367 (mp0) cc_final: 0.8067 (mp0) REVERT: B 299 MET cc_start: 0.9349 (mmp) cc_final: 0.8994 (mmp) REVERT: B 324 LYS cc_start: 0.8834 (tttp) cc_final: 0.8406 (tttm) REVERT: B 374 ILE cc_start: 0.9083 (tp) cc_final: 0.8837 (tt) REVERT: B 388 MET cc_start: 0.8419 (mtp) cc_final: 0.8209 (mtp) REVERT: B 390 ARG cc_start: 0.8052 (ptm-80) cc_final: 0.7441 (tpt170) REVERT: B 421 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8048 (mt-10) outliers start: 11 outliers final: 2 residues processed: 122 average time/residue: 1.6128 time to fit residues: 205.1420 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 77 optimal weight: 0.0470 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6974 Z= 0.167 Angle : 0.516 6.492 9471 Z= 0.268 Chirality : 0.042 0.135 1034 Planarity : 0.004 0.041 1234 Dihedral : 10.294 160.229 961 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.18 % Allowed : 11.60 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.53 (0.28), residues: 856 helix: 1.07 (0.28), residues: 371 sheet: 0.61 (0.42), residues: 149 loop : -0.49 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.002 0.000 HIS A 406 PHE 0.019 0.001 PHE A 255 TYR 0.008 0.001 TYR B 310 ARG 0.005 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.805 Fit side-chains REVERT: A 15 GLN cc_start: 0.9066 (mt0) cc_final: 0.8794 (mt0) REVERT: A 24 TYR cc_start: 0.8890 (m-10) cc_final: 0.8597 (m-10) REVERT: A 26 LEU cc_start: 0.8970 (tp) cc_final: 0.8684 (mt) REVERT: A 176 GLN cc_start: 0.8144 (mt0) cc_final: 0.7938 (mm-40) REVERT: A 254 GLU cc_start: 0.7870 (tt0) cc_final: 0.7458 (tp30) REVERT: A 302 MET cc_start: 0.8149 (mtt) cc_final: 0.7578 (mtt) REVERT: A 414 GLU cc_start: 0.8295 (pt0) cc_final: 0.7905 (pm20) REVERT: A 434 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7798 (tp30) REVERT: B 26 ASP cc_start: 0.8565 (t0) cc_final: 0.8347 (t0) REVERT: B 31 ASP cc_start: 0.8309 (m-30) cc_final: 0.7615 (m-30) REVERT: B 37 HIS cc_start: 0.8715 (m-70) cc_final: 0.7727 (m-70) REVERT: B 114 ASP cc_start: 0.7919 (m-30) cc_final: 0.7596 (m-30) REVERT: B 157 GLU cc_start: 0.8361 (mp0) cc_final: 0.8086 (mp0) REVERT: B 197 ASP cc_start: 0.8534 (m-30) cc_final: 0.8256 (m-30) REVERT: B 203 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8307 (m-30) REVERT: B 299 MET cc_start: 0.9330 (mmp) cc_final: 0.8967 (mmp) REVERT: B 324 LYS cc_start: 0.8821 (tttp) cc_final: 0.8399 (tttm) REVERT: B 332 ASN cc_start: 0.8767 (t0) cc_final: 0.8482 (t0) REVERT: B 388 MET cc_start: 0.8364 (mtp) cc_final: 0.7909 (mtm) REVERT: B 390 ARG cc_start: 0.7984 (ptm-80) cc_final: 0.7507 (tpt170) REVERT: B 421 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8029 (mt-10) outliers start: 16 outliers final: 4 residues processed: 127 average time/residue: 1.4434 time to fit residues: 191.4924 Evaluate side-chains 110 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain B residue 22 GLU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 256 GLN B 6 HIS B 8 GLN B 48 ASN B 280 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6974 Z= 0.308 Angle : 0.570 7.611 9471 Z= 0.294 Chirality : 0.044 0.133 1034 Planarity : 0.004 0.042 1234 Dihedral : 10.385 162.418 961 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 12.82 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.33 (0.28), residues: 856 helix: 0.97 (0.27), residues: 374 sheet: 0.62 (0.42), residues: 148 loop : -0.76 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.005 0.001 HIS B 264 PHE 0.019 0.002 PHE A 255 TYR 0.012 0.001 TYR A 103 ARG 0.004 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.772 Fit side-chains REVERT: A 24 TYR cc_start: 0.8898 (m-10) cc_final: 0.8595 (m-10) REVERT: A 26 LEU cc_start: 0.8966 (tp) cc_final: 0.8636 (mt) REVERT: A 176 GLN cc_start: 0.8181 (mt0) cc_final: 0.7955 (mm-40) REVERT: A 254 GLU cc_start: 0.8058 (tt0) cc_final: 0.7496 (tp30) REVERT: A 302 MET cc_start: 0.8278 (mtt) cc_final: 0.7859 (mtt) REVERT: A 377 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7964 (tmm) REVERT: A 413 MET cc_start: 0.8467 (ttp) cc_final: 0.8223 (ttp) REVERT: A 434 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7713 (tp30) REVERT: B 26 ASP cc_start: 0.8587 (t0) cc_final: 0.8376 (t0) REVERT: B 31 ASP cc_start: 0.8099 (m-30) cc_final: 0.7444 (m-30) REVERT: B 37 HIS cc_start: 0.8748 (m-70) cc_final: 0.7697 (m-70) REVERT: B 114 ASP cc_start: 0.7931 (m-30) cc_final: 0.7667 (m-30) REVERT: B 157 GLU cc_start: 0.8362 (mp0) cc_final: 0.8092 (mp0) REVERT: B 203 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: B 288 GLU cc_start: 0.8010 (pt0) cc_final: 0.7719 (pt0) REVERT: B 324 LYS cc_start: 0.8880 (tttp) cc_final: 0.8490 (tttm) REVERT: B 388 MET cc_start: 0.8395 (mtp) cc_final: 0.7953 (mtm) REVERT: B 390 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7402 (tpt170) REVERT: B 421 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8090 (mt-10) outliers start: 17 outliers final: 5 residues processed: 115 average time/residue: 1.4318 time to fit residues: 171.6264 Evaluate side-chains 107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 70 optimal weight: 0.0470 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 6 HIS B 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6974 Z= 0.201 Angle : 0.519 6.804 9471 Z= 0.267 Chirality : 0.042 0.135 1034 Planarity : 0.004 0.041 1234 Dihedral : 10.192 165.546 961 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 13.92 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.48 (0.28), residues: 856 helix: 1.06 (0.27), residues: 379 sheet: 0.82 (0.42), residues: 148 loop : -0.72 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.002 0.001 HIS B 28 PHE 0.019 0.001 PHE A 255 TYR 0.009 0.001 TYR A 103 ARG 0.003 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.775 Fit side-chains REVERT: A 24 TYR cc_start: 0.8876 (m-10) cc_final: 0.8565 (m-10) REVERT: A 176 GLN cc_start: 0.8161 (mt0) cc_final: 0.7948 (mm-40) REVERT: A 254 GLU cc_start: 0.7946 (tt0) cc_final: 0.7496 (tp30) REVERT: A 302 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7784 (mtt) REVERT: A 377 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7993 (tmm) REVERT: A 413 MET cc_start: 0.8498 (ttp) cc_final: 0.8254 (ttp) REVERT: A 423 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7141 (mt-10) REVERT: A 434 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7744 (tp30) REVERT: B 26 ASP cc_start: 0.8595 (t0) cc_final: 0.8372 (t0) REVERT: B 31 ASP cc_start: 0.8068 (m-30) cc_final: 0.7381 (m-30) REVERT: B 37 HIS cc_start: 0.8748 (m-70) cc_final: 0.7653 (m-70) REVERT: B 114 ASP cc_start: 0.7929 (m-30) cc_final: 0.7605 (m-30) REVERT: B 157 GLU cc_start: 0.8334 (mp0) cc_final: 0.8035 (mp0) REVERT: B 197 ASP cc_start: 0.8625 (m-30) cc_final: 0.8345 (m-30) REVERT: B 203 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: B 288 GLU cc_start: 0.7986 (pt0) cc_final: 0.7702 (pt0) REVERT: B 324 LYS cc_start: 0.8747 (tttp) cc_final: 0.8389 (tttm) REVERT: B 388 MET cc_start: 0.8385 (mtp) cc_final: 0.7995 (mtm) REVERT: B 390 ARG cc_start: 0.7990 (ptm-80) cc_final: 0.7397 (tpt170) REVERT: B 421 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8092 (mt-10) outliers start: 13 outliers final: 5 residues processed: 113 average time/residue: 1.4740 time to fit residues: 174.0196 Evaluate side-chains 110 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6974 Z= 0.200 Angle : 0.514 6.727 9471 Z= 0.262 Chirality : 0.042 0.134 1034 Planarity : 0.004 0.039 1234 Dihedral : 10.109 167.302 961 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 14.60 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.58 (0.28), residues: 856 helix: 1.13 (0.28), residues: 379 sheet: 0.95 (0.42), residues: 148 loop : -0.70 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.003 0.001 HIS B 264 PHE 0.019 0.001 PHE A 255 TYR 0.008 0.001 TYR A 103 ARG 0.003 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.734 Fit side-chains REVERT: A 24 TYR cc_start: 0.8888 (m-10) cc_final: 0.8570 (m-10) REVERT: A 176 GLN cc_start: 0.8160 (mt0) cc_final: 0.7950 (mm-40) REVERT: A 254 GLU cc_start: 0.7784 (tt0) cc_final: 0.7393 (tp30) REVERT: A 302 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7828 (mtt) REVERT: A 377 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7972 (tmm) REVERT: A 413 MET cc_start: 0.8519 (ttp) cc_final: 0.8284 (ttp) REVERT: A 414 GLU cc_start: 0.8318 (pt0) cc_final: 0.7671 (pm20) REVERT: A 423 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7142 (mt-10) REVERT: A 434 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7744 (tp30) REVERT: B 26 ASP cc_start: 0.8596 (t0) cc_final: 0.8368 (t0) REVERT: B 31 ASP cc_start: 0.8084 (m-30) cc_final: 0.7395 (m-30) REVERT: B 37 HIS cc_start: 0.8775 (m-70) cc_final: 0.7657 (m-70) REVERT: B 41 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8129 (p0) REVERT: B 114 ASP cc_start: 0.7952 (m-30) cc_final: 0.7578 (m-30) REVERT: B 157 GLU cc_start: 0.8324 (mp0) cc_final: 0.8035 (mp0) REVERT: B 197 ASP cc_start: 0.8631 (m-30) cc_final: 0.8365 (m-30) REVERT: B 203 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8420 (m-30) REVERT: B 324 LYS cc_start: 0.8730 (tttp) cc_final: 0.8380 (tttm) REVERT: B 388 MET cc_start: 0.8387 (mtp) cc_final: 0.7930 (mtm) REVERT: B 390 ARG cc_start: 0.7993 (ptm-80) cc_final: 0.7446 (tpt170) REVERT: B 421 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8087 (mt-10) outliers start: 13 outliers final: 4 residues processed: 115 average time/residue: 1.5657 time to fit residues: 187.8353 Evaluate side-chains 114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6974 Z= 0.254 Angle : 0.536 6.908 9471 Z= 0.275 Chirality : 0.043 0.132 1034 Planarity : 0.004 0.039 1234 Dihedral : 10.192 168.239 961 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.91 % Allowed : 14.73 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.28), residues: 856 helix: 1.11 (0.28), residues: 377 sheet: 0.97 (0.41), residues: 148 loop : -0.72 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 88 PHE 0.020 0.001 PHE A 255 TYR 0.010 0.001 TYR A 103 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.785 Fit side-chains REVERT: A 24 TYR cc_start: 0.8892 (m-10) cc_final: 0.8574 (m-10) REVERT: A 176 GLN cc_start: 0.8065 (mt0) cc_final: 0.7825 (mm-40) REVERT: A 254 GLU cc_start: 0.7939 (tt0) cc_final: 0.7478 (tp30) REVERT: A 302 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7800 (mtt) REVERT: A 377 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: A 413 MET cc_start: 0.8557 (ttp) cc_final: 0.8322 (ttp) REVERT: A 414 GLU cc_start: 0.8297 (pt0) cc_final: 0.7737 (pm20) REVERT: A 423 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 434 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7722 (tp30) REVERT: B 26 ASP cc_start: 0.8596 (t0) cc_final: 0.8369 (t0) REVERT: B 31 ASP cc_start: 0.8098 (m-30) cc_final: 0.7326 (m-30) REVERT: B 37 HIS cc_start: 0.8782 (m-70) cc_final: 0.7854 (m170) REVERT: B 41 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8154 (p0) REVERT: B 114 ASP cc_start: 0.7946 (m-30) cc_final: 0.7586 (m-30) REVERT: B 157 GLU cc_start: 0.8305 (mp0) cc_final: 0.7962 (mp0) REVERT: B 203 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: B 324 LYS cc_start: 0.8837 (tttp) cc_final: 0.8463 (tttm) REVERT: B 388 MET cc_start: 0.8391 (mtp) cc_final: 0.7970 (mtm) REVERT: B 390 ARG cc_start: 0.8002 (ptm-80) cc_final: 0.7395 (tpt170) REVERT: B 421 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 14 outliers final: 4 residues processed: 116 average time/residue: 1.5277 time to fit residues: 184.9438 Evaluate side-chains 111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6974 Z= 0.191 Angle : 0.510 6.603 9471 Z= 0.260 Chirality : 0.042 0.136 1034 Planarity : 0.004 0.039 1234 Dihedral : 10.093 169.418 961 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.36 % Allowed : 15.69 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.28), residues: 856 helix: 1.20 (0.28), residues: 373 sheet: 1.08 (0.42), residues: 148 loop : -0.61 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.002 0.001 HIS A 28 PHE 0.020 0.001 PHE A 255 TYR 0.007 0.001 TYR A 103 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.757 Fit side-chains REVERT: A 24 TYR cc_start: 0.8878 (m-10) cc_final: 0.8587 (m-10) REVERT: A 176 GLN cc_start: 0.8030 (mt0) cc_final: 0.7789 (mm-40) REVERT: A 254 GLU cc_start: 0.7783 (tt0) cc_final: 0.7394 (tp30) REVERT: A 302 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7798 (mtt) REVERT: A 414 GLU cc_start: 0.8302 (pt0) cc_final: 0.7828 (pm20) REVERT: A 423 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7142 (mt-10) REVERT: A 434 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7673 (tp30) REVERT: B 26 ASP cc_start: 0.8589 (t0) cc_final: 0.8357 (t0) REVERT: B 31 ASP cc_start: 0.8102 (m-30) cc_final: 0.7336 (m-30) REVERT: B 37 HIS cc_start: 0.8751 (m-70) cc_final: 0.7804 (m170) REVERT: B 41 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8154 (p0) REVERT: B 114 ASP cc_start: 0.7917 (m-30) cc_final: 0.7578 (m-30) REVERT: B 157 GLU cc_start: 0.8233 (mp0) cc_final: 0.8023 (mp0) REVERT: B 197 ASP cc_start: 0.8642 (m-30) cc_final: 0.8374 (m-30) REVERT: B 203 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: B 324 LYS cc_start: 0.8782 (tttp) cc_final: 0.8439 (tttm) REVERT: B 388 MET cc_start: 0.8364 (mtp) cc_final: 0.7932 (mtm) REVERT: B 390 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7477 (tpt170) REVERT: B 421 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8096 (mt-10) outliers start: 10 outliers final: 4 residues processed: 114 average time/residue: 1.5387 time to fit residues: 183.6259 Evaluate side-chains 113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6974 Z= 0.244 Angle : 0.535 6.795 9471 Z= 0.274 Chirality : 0.043 0.132 1034 Planarity : 0.004 0.039 1234 Dihedral : 10.167 169.529 961 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.36 % Allowed : 15.69 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.28), residues: 856 helix: 1.18 (0.27), residues: 377 sheet: 1.03 (0.42), residues: 148 loop : -0.73 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 88 PHE 0.020 0.001 PHE A 255 TYR 0.009 0.001 TYR A 103 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.783 Fit side-chains REVERT: A 24 TYR cc_start: 0.8891 (m-10) cc_final: 0.8570 (m-10) REVERT: A 176 GLN cc_start: 0.8046 (mt0) cc_final: 0.7798 (mm-40) REVERT: A 254 GLU cc_start: 0.7955 (tt0) cc_final: 0.7592 (tp30) REVERT: A 302 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7857 (mtt) REVERT: A 414 GLU cc_start: 0.8314 (pt0) cc_final: 0.7793 (pm20) REVERT: A 423 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 434 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7663 (tp30) REVERT: B 26 ASP cc_start: 0.8594 (t0) cc_final: 0.8361 (t0) REVERT: B 37 HIS cc_start: 0.8753 (m-70) cc_final: 0.8487 (m170) REVERT: B 41 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8155 (p0) REVERT: B 114 ASP cc_start: 0.7920 (m-30) cc_final: 0.7617 (m-30) REVERT: B 157 GLU cc_start: 0.8238 (mp0) cc_final: 0.7998 (mp0) REVERT: B 197 ASP cc_start: 0.8677 (m-30) cc_final: 0.8393 (m-30) REVERT: B 203 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: B 324 LYS cc_start: 0.8811 (tttp) cc_final: 0.8446 (tttm) REVERT: B 388 MET cc_start: 0.8384 (mtp) cc_final: 0.7945 (mtm) REVERT: B 390 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7417 (tpt170) REVERT: B 421 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8097 (mt-10) outliers start: 10 outliers final: 5 residues processed: 112 average time/residue: 1.5478 time to fit residues: 180.6886 Evaluate side-chains 116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 257 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6974 Z= 0.218 Angle : 0.525 6.662 9471 Z= 0.269 Chirality : 0.042 0.134 1034 Planarity : 0.004 0.039 1234 Dihedral : 10.135 169.698 961 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.09 % Allowed : 16.10 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.71 (0.28), residues: 856 helix: 1.26 (0.28), residues: 371 sheet: 1.07 (0.42), residues: 148 loop : -0.66 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.002 0.001 HIS A 28 PHE 0.020 0.001 PHE A 255 TYR 0.008 0.001 TYR A 103 ARG 0.003 0.000 ARG A 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.839 Fit side-chains REVERT: A 24 TYR cc_start: 0.8884 (m-10) cc_final: 0.8563 (m-10) REVERT: A 176 GLN cc_start: 0.8039 (mt0) cc_final: 0.7799 (mm-40) REVERT: A 254 GLU cc_start: 0.7941 (tt0) cc_final: 0.7583 (tp30) REVERT: A 302 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7833 (mtt) REVERT: A 390 ARG cc_start: 0.8135 (ttp-170) cc_final: 0.7880 (mtm-85) REVERT: A 413 MET cc_start: 0.8490 (ttp) cc_final: 0.8265 (ttt) REVERT: A 414 GLU cc_start: 0.8316 (pt0) cc_final: 0.7811 (pm20) REVERT: A 423 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7142 (mt-10) REVERT: A 434 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7632 (tp30) REVERT: B 26 ASP cc_start: 0.8590 (t0) cc_final: 0.8356 (t0) REVERT: B 37 HIS cc_start: 0.8724 (m-70) cc_final: 0.8441 (m170) REVERT: B 41 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8156 (p0) REVERT: B 114 ASP cc_start: 0.7868 (m-30) cc_final: 0.7579 (m-30) REVERT: B 157 GLU cc_start: 0.8228 (mp0) cc_final: 0.8000 (mp0) REVERT: B 164 MET cc_start: 0.8841 (tpp) cc_final: 0.8355 (tpp) REVERT: B 197 ASP cc_start: 0.8665 (m-30) cc_final: 0.8387 (m-30) REVERT: B 203 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: B 324 LYS cc_start: 0.8792 (tttp) cc_final: 0.8438 (tttm) REVERT: B 388 MET cc_start: 0.8378 (mtp) cc_final: 0.7942 (mtm) REVERT: B 390 ARG cc_start: 0.7992 (ptm-80) cc_final: 0.7462 (tpt170) REVERT: B 421 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8100 (mt-10) outliers start: 8 outliers final: 5 residues processed: 112 average time/residue: 1.5706 time to fit residues: 183.6496 Evaluate side-chains 114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 203 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.0050 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.094469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.082386 restraints weight = 9847.657| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.13 r_work: 0.2848 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6974 Z= 0.208 Angle : 0.521 6.617 9471 Z= 0.266 Chirality : 0.042 0.134 1034 Planarity : 0.004 0.039 1234 Dihedral : 10.120 169.608 961 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.50 % Allowed : 15.69 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.69 (0.28), residues: 856 helix: 1.25 (0.28), residues: 373 sheet: 1.04 (0.42), residues: 148 loop : -0.67 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.002 0.001 HIS A 28 PHE 0.020 0.001 PHE A 255 TYR 0.008 0.001 TYR A 103 ARG 0.003 0.000 ARG A 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3677.49 seconds wall clock time: 71 minutes 49.69 seconds (4309.69 seconds total)