Starting phenix.real_space_refine on Mon Jun 16 03:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ee7_28048/06_2025/8ee7_28048_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ee7_28048/06_2025/8ee7_28048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ee7_28048/06_2025/8ee7_28048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ee7_28048/06_2025/8ee7_28048.map" model { file = "/net/cci-nas-00/data/ceres_data/8ee7_28048/06_2025/8ee7_28048_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ee7_28048/06_2025/8ee7_28048_trim.cif" } resolution = 2.72 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= 0.085 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 3 5.49 5 S 41 5.16 5 C 5780 2.51 5 N 1642 2.21 5 O 1722 1.98 5 H 8906 0.53 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-5710/modules/chem_data/mon_lib" Total number of atoms: 18094 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 7308 Classifications: {'peptide': 456} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 436} Chain breaks: 1 Chain: "B" Number of atoms: 7010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 7010 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 425} Chain breaks: 2 Chain: "C" Number of atoms: 3745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3745 Classifications: {'peptide': 234} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.07, per 1000 atoms: 0.50 Number of scatterers: 18094 At special positions: 0 Unit cell: (103.04, 104.16, 99.68, 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 41 16.00 P 3 15.00 O 1722 8.00 N 1642 7.00 C 5780 6.00 H 8906 1.00 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: 4.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 50.8% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 34 through 47 Processing helix chain 'A' and resid 47 through 53 removed outlier: 4.019A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 4.365A pdb=" N VAL A 60 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.707A pdb=" N LEU A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.729A pdb=" N LEU A 72 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 removed outlier: 3.505A pdb=" N THR A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 181 through 184 Processing helix chain 'A' and resid 192 through 217 removed outlier: 3.652A pdb=" N PHE A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 251 removed outlier: 5.026A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.746A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 359 through 360 No H-bonds generated for 'chain 'A' and resid 359 through 360' Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 408 through 421 removed outlier: 3.696A pdb=" N GLN A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 444 through 461 Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.656A pdb=" N ILE B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.513A pdb=" N LEU B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 66 " --> pdb=" O LYS B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 66' Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.519A pdb=" N LEU B 72 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.759A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 192 through 217 removed outlier: 3.657A pdb=" N GLN B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.601A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 303 through 307 removed outlier: 6.870A pdb=" N ASN B 307 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.626A pdb=" N LEU B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 360 No H-bonds generated for 'chain 'B' and resid 359 through 360' Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 389 through 397 Processing helix chain 'B' and resid 408 through 421 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 444 through 457 Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.942A pdb=" N VAL C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 111 through 114 removed outlier: 3.865A pdb=" N HIS C 114 " --> pdb=" O PHE C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 121 removed outlier: 3.647A pdb=" N ASP C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 156 through 168 Processing helix chain 'C' and resid 172 through 197 Processing helix chain 'C' and resid 203 through 209 removed outlier: 4.036A pdb=" N ASP C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 227 Processing helix chain 'C' and resid 227 through 238 removed outlier: 4.024A pdb=" N GLU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 6.877A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 removed outlier: 6.493A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR A 26 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 75 removed outlier: 4.332A pdb=" N ARG A 73 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 75 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 84 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 5.623A pdb=" N ASP A 254 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A 268 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.929A pdb=" N THR B 94 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 6 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 92 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 8 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 90 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 152 removed outlier: 6.422A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR B 26 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR B 351 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU B 28 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.902A pdb=" N ARG B 73 " --> pdb=" O SER B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 253 through 258 removed outlier: 5.683A pdb=" N ASP B 254 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B 268 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 68 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 139 through 141 417 hydrogen bonds defined for protein. 1194 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: 5.85 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8894 1.03 - 1.23: 22 1.23 - 1.42: 3925 1.42 - 1.62: 5370 1.62 - 1.81: 70 Bond restraints: 18281 Sorted by residual: bond pdb=" CG PHE A 296 " pdb=" CD1 PHE A 296 " ideal model delta sigma weight residual 1.384 1.358 0.026 2.10e-02 2.27e+03 1.58e+00 bond pdb=" C GLY B 387 " pdb=" N GLU B 388 " ideal model delta sigma weight residual 1.335 1.310 0.025 3.04e-02 1.08e+03 6.61e-01 bond pdb=" C1' ATP B 501 " pdb=" C2' ATP B 501 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.20e-02 6.94e+03 6.54e-01 bond pdb=" C ILE A 242 " pdb=" O ILE A 242 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.19e-02 7.06e+03 6.21e-01 bond pdb=" C ALA A 234 " pdb=" O ALA A 234 " ideal model delta sigma weight residual 1.236 1.245 -0.009 1.15e-02 7.56e+03 5.95e-01 ... (remaining 18276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.29: 32909 7.29 - 14.57: 1 14.57 - 21.86: 0 21.86 - 29.15: 0 29.15 - 36.43: 12 Bond angle restraints: 32922 Sorted by residual: angle pdb=" C LEU C 105 " pdb=" CA LEU C 105 " pdb=" HA LEU C 105 " ideal model delta sigma weight residual 109.00 72.57 36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C ASP A 173 " pdb=" CA ASP A 173 " pdb=" HA ASP A 173 " ideal model delta sigma weight residual 109.00 73.66 35.34 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N GLN B 170 " pdb=" CA GLN B 170 " pdb=" HA GLN B 170 " ideal model delta sigma weight residual 110.00 74.79 35.21 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C GLN B 170 " pdb=" CA GLN B 170 " pdb=" HA GLN B 170 " ideal model delta sigma weight residual 109.00 73.83 35.17 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N LEU A 172 " pdb=" CA LEU A 172 " pdb=" HA LEU A 172 " ideal model delta sigma weight residual 110.00 74.88 35.12 3.00e+00 1.11e-01 1.37e+02 ... (remaining 32917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 7727 17.17 - 34.33: 617 34.33 - 51.50: 166 51.50 - 68.66: 62 68.66 - 85.83: 12 Dihedral angle restraints: 8584 sinusoidal: 4731 harmonic: 3853 Sorted by residual: dihedral pdb=" C LEU C 105 " pdb=" N LEU C 105 " pdb=" CA LEU C 105 " pdb=" CB LEU C 105 " ideal model delta harmonic sigma weight residual -122.60 -134.08 11.48 0 2.50e+00 1.60e-01 2.11e+01 dihedral pdb=" CA THR A 246 " pdb=" C THR A 246 " pdb=" N GLN A 247 " pdb=" CA GLN A 247 " ideal model delta harmonic sigma weight residual -180.00 -159.55 -20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C ASP A 173 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " pdb=" CB ASP A 173 " ideal model delta harmonic sigma weight residual -122.60 -132.09 9.49 0 2.50e+00 1.60e-01 1.44e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1320 0.092 - 0.184: 61 0.184 - 0.277: 1 0.277 - 0.369: 5 0.369 - 0.461: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA GLN B 170 " pdb=" N GLN B 170 " pdb=" C GLN B 170 " pdb=" CB GLN B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA LEU C 105 " pdb=" N LEU C 105 " pdb=" C LEU C 105 " pdb=" CB LEU C 105 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA ASP A 173 " pdb=" N ASP A 173 " pdb=" C ASP A 173 " pdb=" CB ASP A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 1385 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 48 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 49 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 48 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 49 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 275 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A 276 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.017 5.00e-02 4.00e+02 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 921 2.20 - 2.80: 35846 2.80 - 3.40: 46607 3.40 - 4.00: 63148 4.00 - 4.60: 99589 Nonbonded interactions: 246111 Sorted by model distance: nonbonded pdb=" HA LEU A 172 " pdb=" HB3 LEU A 172 " model vdw 1.599 1.952 nonbonded pdb=" HZ3 LYS B 119 " pdb=" OE1 GLN B 123 " model vdw 1.599 2.450 nonbonded pdb=" HZ2 LYS B 109 " pdb=" O GLN B 113 " model vdw 1.606 2.450 nonbonded pdb=" O ASN C 20 " pdb="HH12 ARG C 31 " model vdw 1.633 2.450 nonbonded pdb=" H GLY B 33 " pdb=" O1B ATP B 501 " model vdw 1.641 2.450 ... (remaining 246106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name SD or name CE )) or (resid 2 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 3 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 4 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name OD2)) or resid 5 through 54 \ or (resid 55 and (name N or name CA or name C or name O or name CB or name CG or \ name OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 56 through 7 \ 7 or (resid 78 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 or name HG \ 2 or name HG3 or name HE21 or name HE22)) or resid 79 through 159 or (resid 160 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or n \ ame OE1 or name NE2 or name HA )) or resid 171 through 218 or resid 224 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ )) or (resid 233 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or re \ sid 234 through 235 or (resid 236 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name OE1 or name NE2)) or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB or name CG or name C \ D )) or (resid 304 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 305 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) o \ r (resid 306 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name NE2)) or (resid 307 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 308 and (n \ ame N or name CA or name C or name O or name CB or name CG or name OD1 or name O \ D2)) or (resid 309 through 310 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 311 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2)) or resid 312 through 460)) selection = (chain 'B' and (resid 1 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid \ 25 through 115 or (resid 116 and (name N or name CA or name C or name O or name \ CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name \ HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 117 through 138 o \ r (resid 139 and (name N or name CA or name C or name O or name CB or name CG or \ name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 o \ r name HB3 or name HD2 or name HE1)) or resid 140 through 170 or (resid 171 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2)) or (resid 172 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name HA or nam \ e HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 \ or name HD22 or name HD23)) or resid 173 through 175 or (resid 176 and (name N \ or name CA or name C or name O or name CB )) or resid 177 through 209 or (resid \ 210 and (name N or name CA or name C or name O or name CB or name CG or name ND1 \ or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB \ 3 or name HD2 or name HE1)) or resid 211 through 252 or (resid 253 and (name N o \ r name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or n \ ame CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or \ name HE1)) or resid 254 through 260 or (resid 261 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or res \ id 262 through 326 or (resid 327 and (name N or name CA or name C or name O or n \ ame CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or n \ ame HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 328 through 35 \ 1 or (resid 352 and (name N or name CA or name C or name O or name CB or name CG \ or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB \ 2 or name HB3 or name HD2 or name HE1)) or resid 353 through 460)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.290 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 38.970 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9375 Z= 0.121 Angle : 0.517 10.661 12687 Z= 0.283 Chirality : 0.045 0.461 1388 Planarity : 0.004 0.046 1647 Dihedral : 14.760 85.829 3552 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.65 % 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: 0.68 (0.26), residues: 1121 helix: 1.58 (0.25), residues: 469 sheet: -0.32 (0.35), residues: 195 loop : -0.29 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 199 HIS 0.005 0.001 HIS B 352 PHE 0.012 0.001 PHE A 296 TYR 0.009 0.001 TYR C 68 ARG 0.002 0.000 ARG A 227 Details of bonding type rmsd hydrogen bonds : bond 0.14863 ( 417) hydrogen bonds : angle 6.00669 ( 1194) covalent geometry : bond 0.00271 ( 9375) covalent geometry : angle 0.51706 (12687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 4 ASP cc_start: 0.9134 (m-30) cc_final: 0.8877 (m-30) REVERT: A 372 GLU cc_start: 0.7562 (pm20) cc_final: 0.7334 (pm20) REVERT: B 101 LYS cc_start: 0.7837 (tptp) cc_final: 0.7577 (tptm) REVERT: B 123 GLN cc_start: 0.7825 (mt0) cc_final: 0.7536 (mm110) REVERT: B 227 ARG cc_start: 0.7109 (ttt-90) cc_final: 0.6897 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 3.3781 time to fit residues: 559.0118 Evaluate side-chains 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 430 GLN B 174 ASN C 34 ASN C 201 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.154852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117850 restraints weight = 26753.167| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.62 r_work: 0.3099 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9375 Z= 0.144 Angle : 0.534 10.554 12687 Z= 0.290 Chirality : 0.044 0.458 1388 Planarity : 0.004 0.045 1647 Dihedral : 6.896 55.620 1262 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.11 % Allowed : 6.75 % Favored : 92.14 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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: 0.66 (0.25), residues: 1121 helix: 1.63 (0.24), residues: 484 sheet: -0.40 (0.35), residues: 195 loop : -0.42 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.005 0.001 HIS A 352 PHE 0.007 0.001 PHE A 196 TYR 0.009 0.001 TYR B 193 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.06173 ( 417) hydrogen bonds : angle 4.80640 ( 1194) covalent geometry : bond 0.00331 ( 9375) covalent geometry : angle 0.53448 (12687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 1.420 Fit side-chains REVERT: A 4 ASP cc_start: 0.9006 (m-30) cc_final: 0.8768 (m-30) REVERT: A 372 GLU cc_start: 0.7700 (pm20) cc_final: 0.7393 (pm20) REVERT: B 101 LYS cc_start: 0.7784 (tptp) cc_final: 0.7524 (tptm) REVERT: B 123 GLN cc_start: 0.7889 (mt0) cc_final: 0.7591 (mm110) REVERT: B 271 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.6949 (mp-120) REVERT: C 36 ARG cc_start: 0.6999 (ptp-110) cc_final: 0.6760 (ptm160) outliers start: 11 outliers final: 4 residues processed: 126 average time/residue: 2.8865 time to fit residues: 387.1305 Evaluate side-chains 123 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN A 370 GLN B 174 ASN B 192 ASN C 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115052 restraints weight = 26673.329| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.62 r_work: 0.3118 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9375 Z= 0.181 Angle : 0.560 10.549 12687 Z= 0.302 Chirality : 0.045 0.457 1388 Planarity : 0.005 0.046 1647 Dihedral : 6.962 72.849 1262 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.31 % Allowed : 7.26 % Favored : 91.43 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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 (0.25), residues: 1121 helix: 1.56 (0.24), residues: 485 sheet: -0.48 (0.34), residues: 195 loop : -0.49 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 199 HIS 0.006 0.001 HIS A 352 PHE 0.009 0.002 PHE C 226 TYR 0.010 0.001 TYR C 68 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.06573 ( 417) hydrogen bonds : angle 4.69252 ( 1194) covalent geometry : bond 0.00433 ( 9375) covalent geometry : angle 0.56025 (12687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 1.340 Fit side-chains REVERT: A 372 GLU cc_start: 0.7669 (pm20) cc_final: 0.7335 (pm20) REVERT: B 1 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8482 (tpp) REVERT: B 101 LYS cc_start: 0.7670 (tptp) cc_final: 0.7390 (tptm) REVERT: B 271 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6922 (mp-120) REVERT: C 36 ARG cc_start: 0.6944 (ptp-110) cc_final: 0.6695 (ptm160) outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 2.9839 time to fit residues: 396.4311 Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 333 GLN B 130 GLN B 174 ASN C 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.117182 restraints weight = 26767.129| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.55 r_work: 0.3168 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9375 Z= 0.193 Angle : 0.577 10.545 12687 Z= 0.310 Chirality : 0.045 0.457 1388 Planarity : 0.005 0.046 1647 Dihedral : 6.738 84.986 1262 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.92 % Allowed : 8.47 % Favored : 89.62 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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: 0.44 (0.25), residues: 1121 helix: 1.47 (0.24), residues: 485 sheet: -0.44 (0.35), residues: 192 loop : -0.62 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 199 HIS 0.005 0.001 HIS A 352 PHE 0.010 0.002 PHE B 196 TYR 0.010 0.001 TYR C 68 ARG 0.004 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.06629 ( 417) hydrogen bonds : angle 4.66132 ( 1194) covalent geometry : bond 0.00466 ( 9375) covalent geometry : angle 0.57713 (12687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.423 Fit side-chains REVERT: A 233 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: B 101 LYS cc_start: 0.7719 (tptp) cc_final: 0.7440 (tptm) REVERT: B 271 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6944 (mp-120) REVERT: C 36 ARG cc_start: 0.6975 (ptp-110) cc_final: 0.6766 (ptm160) REVERT: C 48 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7597 (t0) outliers start: 19 outliers final: 8 residues processed: 129 average time/residue: 3.1043 time to fit residues: 424.1295 Evaluate side-chains 128 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN A 373 ASN B 174 ASN C 34 ASN C 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117815 restraints weight = 26881.557| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.59 r_work: 0.3102 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9375 Z= 0.119 Angle : 0.509 10.592 12687 Z= 0.274 Chirality : 0.043 0.458 1388 Planarity : 0.004 0.044 1647 Dihedral : 6.288 87.753 1262 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.31 % Allowed : 9.58 % Favored : 89.11 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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 (0.25), residues: 1121 helix: 1.76 (0.24), residues: 485 sheet: -0.42 (0.34), residues: 195 loop : -0.49 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.006 0.001 HIS C 193 PHE 0.007 0.001 PHE A 196 TYR 0.008 0.001 TYR C 68 ARG 0.002 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 417) hydrogen bonds : angle 4.51592 ( 1194) covalent geometry : bond 0.00270 ( 9375) covalent geometry : angle 0.50853 (12687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.386 Fit side-chains REVERT: A 126 ARG cc_start: 0.7995 (mmp80) cc_final: 0.7559 (mtm-85) REVERT: A 372 GLU cc_start: 0.7678 (pm20) cc_final: 0.7359 (pm20) REVERT: B 84 GLU cc_start: 0.7905 (tt0) cc_final: 0.7486 (tt0) REVERT: B 101 LYS cc_start: 0.7775 (tptp) cc_final: 0.7505 (tptm) REVERT: B 271 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6923 (mp-120) REVERT: C 36 ARG cc_start: 0.7004 (ptp-110) cc_final: 0.6786 (ptm160) outliers start: 13 outliers final: 3 residues processed: 129 average time/residue: 3.2083 time to fit residues: 440.4678 Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 214 GLN B 174 ASN C 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117597 restraints weight = 26769.687| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.58 r_work: 0.3136 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9375 Z= 0.138 Angle : 0.524 10.566 12687 Z= 0.281 Chirality : 0.044 0.459 1388 Planarity : 0.004 0.043 1647 Dihedral : 6.303 88.094 1262 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.31 % Allowed : 10.48 % Favored : 88.21 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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 (0.25), residues: 1121 helix: 1.78 (0.24), residues: 485 sheet: -0.44 (0.34), residues: 195 loop : -0.51 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.006 0.001 HIS C 193 PHE 0.007 0.001 PHE C 220 TYR 0.009 0.001 TYR C 68 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.05559 ( 417) hydrogen bonds : angle 4.48645 ( 1194) covalent geometry : bond 0.00325 ( 9375) covalent geometry : angle 0.52358 (12687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.321 Fit side-chains REVERT: B 84 GLU cc_start: 0.7920 (tt0) cc_final: 0.7514 (tt0) REVERT: B 101 LYS cc_start: 0.7808 (tptp) cc_final: 0.7549 (tptm) REVERT: B 271 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6929 (mp-120) REVERT: B 372 GLU cc_start: 0.7288 (pm20) cc_final: 0.7077 (pm20) REVERT: C 36 ARG cc_start: 0.6993 (ptp-110) cc_final: 0.6753 (ptm160) outliers start: 13 outliers final: 6 residues processed: 122 average time/residue: 3.1113 time to fit residues: 402.1202 Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117174 restraints weight = 26684.183| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.54 r_work: 0.3149 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9375 Z= 0.132 Angle : 0.515 10.575 12687 Z= 0.277 Chirality : 0.043 0.459 1388 Planarity : 0.004 0.043 1647 Dihedral : 6.226 87.066 1262 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.61 % Allowed : 10.48 % Favored : 87.90 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1121 helix: 1.82 (0.24), residues: 485 sheet: -0.39 (0.34), residues: 192 loop : -0.52 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.007 0.001 HIS C 193 PHE 0.007 0.001 PHE C 220 TYR 0.008 0.001 TYR C 68 ARG 0.002 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.05423 ( 417) hydrogen bonds : angle 4.45431 ( 1194) covalent geometry : bond 0.00308 ( 9375) covalent geometry : angle 0.51481 (12687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.326 Fit side-chains REVERT: A 333 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7975 (mt0) REVERT: B 68 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7666 (mtm110) REVERT: B 84 GLU cc_start: 0.7865 (tt0) cc_final: 0.7439 (tt0) REVERT: B 101 LYS cc_start: 0.7733 (tptp) cc_final: 0.7470 (tptm) REVERT: B 149 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.7605 (mmt) REVERT: B 271 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6892 (mp-120) REVERT: C 36 ARG cc_start: 0.6967 (ptp-110) cc_final: 0.6718 (ptm160) outliers start: 16 outliers final: 8 residues processed: 126 average time/residue: 3.0712 time to fit residues: 410.4793 Evaluate side-chains 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 174 ASN C 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116644 restraints weight = 26821.760| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.58 r_work: 0.3138 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9375 Z= 0.167 Angle : 0.552 10.553 12687 Z= 0.296 Chirality : 0.044 0.459 1388 Planarity : 0.004 0.043 1647 Dihedral : 6.451 88.634 1262 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.92 % Allowed : 10.48 % Favored : 87.60 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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: 0.63 (0.25), residues: 1121 helix: 1.70 (0.24), residues: 485 sheet: -0.40 (0.35), residues: 190 loop : -0.59 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 199 HIS 0.007 0.001 HIS C 193 PHE 0.009 0.001 PHE B 196 TYR 0.010 0.001 TYR C 68 ARG 0.003 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.06028 ( 417) hydrogen bonds : angle 4.50509 ( 1194) covalent geometry : bond 0.00402 ( 9375) covalent geometry : angle 0.55165 (12687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.526 Fit side-chains REVERT: A 333 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: B 68 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7771 (mtm110) REVERT: B 84 GLU cc_start: 0.7890 (tt0) cc_final: 0.7454 (tt0) REVERT: B 101 LYS cc_start: 0.7749 (tptp) cc_final: 0.7486 (tptm) REVERT: B 149 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.7798 (mmt) REVERT: B 271 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6902 (mp-120) REVERT: C 36 ARG cc_start: 0.6999 (ptp-110) cc_final: 0.6753 (ptm160) outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 3.0884 time to fit residues: 402.8659 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.0370 chunk 55 optimal weight: 0.9980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.155495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118861 restraints weight = 26814.767| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.58 r_work: 0.3146 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9375 Z= 0.109 Angle : 0.496 10.573 12687 Z= 0.266 Chirality : 0.043 0.458 1388 Planarity : 0.004 0.043 1647 Dihedral : 6.040 84.738 1262 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.01 % Allowed : 11.29 % Favored : 87.70 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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: 0.88 (0.26), residues: 1121 helix: 1.96 (0.24), residues: 485 sheet: -0.36 (0.34), residues: 192 loop : -0.48 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 199 HIS 0.005 0.001 HIS C 193 PHE 0.007 0.001 PHE A 196 TYR 0.007 0.001 TYR C 68 ARG 0.002 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 417) hydrogen bonds : angle 4.38060 ( 1194) covalent geometry : bond 0.00243 ( 9375) covalent geometry : angle 0.49602 (12687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.331 Fit side-chains REVERT: B 1 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8210 (tpp) REVERT: B 68 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7788 (mtm110) REVERT: B 84 GLU cc_start: 0.7897 (tt0) cc_final: 0.7483 (tt0) REVERT: B 101 LYS cc_start: 0.7678 (tptp) cc_final: 0.7419 (tptm) REVERT: B 271 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6812 (mp-120) REVERT: C 36 ARG cc_start: 0.7025 (ptp-110) cc_final: 0.6782 (ptm160) outliers start: 10 outliers final: 5 residues processed: 120 average time/residue: 3.1003 time to fit residues: 394.2662 Evaluate side-chains 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.155323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118635 restraints weight = 26775.223| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.58 r_work: 0.3169 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9375 Z= 0.118 Angle : 0.501 10.562 12687 Z= 0.269 Chirality : 0.043 0.459 1388 Planarity : 0.004 0.043 1647 Dihedral : 6.018 84.494 1262 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.91 % Allowed : 11.39 % Favored : 87.70 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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: 0.91 (0.26), residues: 1121 helix: 2.00 (0.24), residues: 485 sheet: -0.38 (0.34), residues: 193 loop : -0.46 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.005 0.001 HIS C 193 PHE 0.007 0.001 PHE C 220 TYR 0.008 0.001 TYR C 68 ARG 0.002 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 417) hydrogen bonds : angle 4.36705 ( 1194) covalent geometry : bond 0.00269 ( 9375) covalent geometry : angle 0.50133 (12687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.439 Fit side-chains REVERT: A 380 MET cc_start: 0.8754 (mtt) cc_final: 0.8474 (mtt) REVERT: B 1 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8176 (tpp) REVERT: B 68 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7733 (mtm110) REVERT: B 84 GLU cc_start: 0.7867 (tt0) cc_final: 0.7441 (tt0) REVERT: B 101 LYS cc_start: 0.7639 (tptp) cc_final: 0.7375 (tptm) REVERT: B 271 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6842 (mp-120) REVERT: C 36 ARG cc_start: 0.6947 (ptp-110) cc_final: 0.6688 (ptm160) outliers start: 9 outliers final: 6 residues processed: 122 average time/residue: 3.1051 time to fit residues: 403.4513 Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 171 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 457 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 90 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118813 restraints weight = 26620.737| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.55 r_work: 0.3147 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9375 Z= 0.102 Angle : 0.484 10.521 12687 Z= 0.259 Chirality : 0.043 0.458 1388 Planarity : 0.004 0.043 1647 Dihedral : 5.795 81.317 1262 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.21 % Allowed : 11.09 % Favored : 87.70 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 4.65 % 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: 1.03 (0.26), residues: 1121 helix: 2.14 (0.25), residues: 485 sheet: -0.45 (0.34), residues: 201 loop : -0.38 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.005 0.001 HIS C 193 PHE 0.008 0.001 PHE A 196 TYR 0.008 0.001 TYR C 68 ARG 0.002 0.000 ARG C 180 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 417) hydrogen bonds : angle 4.30544 ( 1194) covalent geometry : bond 0.00226 ( 9375) covalent geometry : angle 0.48396 (12687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14017.78 seconds wall clock time: 237 minutes 56.76 seconds (14276.76 seconds total)