Starting phenix.real_space_refine on Sun Mar 17 14:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ee7_28048/03_2024/8ee7_28048_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ee7_28048/03_2024/8ee7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ee7_28048/03_2024/8ee7_28048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ee7_28048/03_2024/8ee7_28048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ee7_28048/03_2024/8ee7_28048_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ee7_28048/03_2024/8ee7_28048_trim_updated.pdb" } 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 Residue "B ASP 392": "OD1" <-> "OD2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.72, per 1000 atoms: 0.43 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.36 Conformation dependent library (CDL) restraints added in 2.0 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... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 43.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 35 through 46 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.780A pdb=" N GLY A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 119 through 136 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 176 through 183 removed outlier: 3.599A pdb=" N SER A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 216 Processing helix chain 'A' and resid 218 through 250 removed outlier: 5.123A pdb=" N LEU A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU A 224 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLY A 225 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 226 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 228 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 229 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLN A 247 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN A 248 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 249 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A 250 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 301 removed outlier: 3.746A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 354 through 359 removed outlier: 4.113A pdb=" N THR A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 427 through 440 Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.833A pdb=" N GLY B 53 " --> pdb=" O PRO B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 119 through 135 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 176 through 183 removed outlier: 4.026A pdb=" N GLY B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 216 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 226 through 246 removed outlier: 3.601A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 303 through 312 removed outlier: 6.870A pdb=" N ASN B 307 " --> pdb=" O HIS B 304 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ALA B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS B 312 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.389A pdb=" N THR B 359 " --> pdb=" O GLN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 427 through 440 Processing helix chain 'B' and resid 445 through 456 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 25 through 49 removed outlier: 4.012A pdb=" N ARG C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ALA C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 42 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 116 through 120 removed outlier: 3.647A pdb=" N ASP C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 120' Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 173 through 196 Processing helix chain 'C' and resid 204 through 208 removed outlier: 4.012A pdb=" N LEU C 208 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 Processing helix chain 'C' and resid 228 through 237 removed outlier: 4.024A pdb=" N GLU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 376 through 379 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) removed outlier: 6.660A pdb=" N PHE A 347 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LEU A 28 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 349 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 148 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU A 318 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU A 150 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 258 Processing sheet with id= D, 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= E, first strand: chain 'B' and resid 376 through 379 removed outlier: 7.900A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N GLN B 370 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE B 347 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU B 28 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 349 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 148 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 318 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 150 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= F, 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= G, first strand: chain 'B' and resid 256 through 258 Processing sheet with id= H, first strand: chain 'C' and resid 68 through 72 Processing sheet with id= I, first strand: chain 'C' and resid 139 through 141 348 hydrogen bonds defined for protein. 933 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: 6.19 Time building geometry restraints manager: 14.00 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: 72.57 - 86.01: 12 86.01 - 99.45: 0 99.45 - 112.89: 21289 112.89 - 126.33: 11377 126.33 - 139.77: 244 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: 951 2.20 - 2.80: 35904 2.80 - 3.40: 46662 3.40 - 4.00: 63219 4.00 - 4.60: 99721 Nonbonded interactions: 246457 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 1.850 nonbonded pdb=" HZ2 LYS B 109 " pdb=" O GLN B 113 " model vdw 1.606 1.850 nonbonded pdb=" O ASN C 20 " pdb="HH12 ARG C 31 " model vdw 1.633 1.850 nonbonded pdb=" H GLY B 33 " pdb=" O1B ATP B 501 " model vdw 1.641 1.850 ... (remaining 246452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' 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: 1.310 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: 0.250 Extract box with map and model: 4.560 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 57.490 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.210 ------------------------------------------------------------------------------- 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= 0.177 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.428 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: 3.0579 time to fit residues: 504.7254 Evaluate side-chains 125 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 4.9990 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: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN C 34 ASN C 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9375 Z= 0.207 Angle : 0.508 10.558 12687 Z= 0.272 Chirality : 0.043 0.457 1388 Planarity : 0.004 0.045 1647 Dihedral : 6.711 55.463 1262 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.11 % Allowed : 6.35 % Favored : 92.54 % 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: 0.59 (0.25), residues: 1121 helix: 1.48 (0.24), residues: 469 sheet: -0.32 (0.35), residues: 195 loop : -0.34 (0.30), residues: 457 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 0.008 0.001 TYR C 68 ARG 0.002 0.000 ARG B 110 *********************** 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 131 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 4 ASP cc_start: 0.9106 (m-30) cc_final: 0.8870 (m-30) REVERT: A 233 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: A 333 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: B 101 LYS cc_start: 0.7849 (tptp) cc_final: 0.7583 (tptm) REVERT: B 123 GLN cc_start: 0.7822 (mt0) cc_final: 0.7534 (mm110) REVERT: B 271 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6911 (mp-120) REVERT: C 36 ARG cc_start: 0.7055 (ptp-110) cc_final: 0.6818 (ptm160) REVERT: C 48 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7761 (t0) REVERT: C 233 GLN cc_start: 0.7185 (tp-100) cc_final: 0.6393 (mm110) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 2.8859 time to fit residues: 389.7191 Evaluate side-chains 127 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 333 GLN 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 Chi-restraints excluded: chain C residue 48 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9375 Z= 0.249 Angle : 0.530 10.515 12687 Z= 0.284 Chirality : 0.044 0.457 1388 Planarity : 0.005 0.047 1647 Dihedral : 6.494 59.951 1262 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.61 % Allowed : 7.46 % Favored : 90.93 % 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: 0.50 (0.25), residues: 1121 helix: 1.41 (0.25), residues: 468 sheet: -0.34 (0.35), residues: 195 loop : -0.39 (0.30), residues: 458 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 0.008 0.001 PHE C 220 TYR 0.009 0.001 TYR C 68 ARG 0.005 0.000 ARG A 126 *********************** 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 135 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 1.422 Fit side-chains revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: A 245 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8508 (mp) REVERT: A 333 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: B 1 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8383 (tpp) REVERT: B 101 LYS cc_start: 0.7854 (tptp) cc_final: 0.7581 (tptm) REVERT: B 271 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6926 (mp-120) REVERT: C 36 ARG cc_start: 0.7095 (ptp-110) cc_final: 0.6857 (ptm160) REVERT: C 48 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7817 (t0) REVERT: C 233 GLN cc_start: 0.7296 (tp-100) cc_final: 0.6668 (tp40) outliers start: 16 outliers final: 6 residues processed: 126 average time/residue: 2.9744 time to fit residues: 399.1106 Evaluate side-chains 129 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 245 LEU 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 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 Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 370 GLN C 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9375 Z= 0.270 Angle : 0.545 10.597 12687 Z= 0.291 Chirality : 0.044 0.459 1388 Planarity : 0.005 0.048 1647 Dihedral : 6.411 63.660 1262 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.02 % Allowed : 8.67 % Favored : 89.31 % 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: 0.38 (0.25), residues: 1121 helix: 1.28 (0.24), residues: 473 sheet: -0.34 (0.35), residues: 195 loop : -0.48 (0.30), residues: 453 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 0.008 0.001 PHE A 177 TYR 0.009 0.001 TYR C 68 ARG 0.003 0.000 ARG A 156 *********************** 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 fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: B 1 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8391 (tpp) REVERT: B 101 LYS cc_start: 0.7852 (tptp) cc_final: 0.7580 (tptm) REVERT: B 271 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6929 (mp-120) REVERT: C 36 ARG cc_start: 0.7098 (ptp-110) cc_final: 0.6896 (ptm160) REVERT: C 48 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7796 (t0) REVERT: C 233 GLN cc_start: 0.7274 (tp-100) cc_final: 0.6645 (tp40) outliers start: 20 outliers final: 10 residues processed: 127 average time/residue: 2.8403 time to fit residues: 383.9080 Evaluate side-chains 131 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 245 LEU 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 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 Chi-restraints excluded: chain C residue 193 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9375 Z= 0.203 Angle : 0.507 10.619 12687 Z= 0.272 Chirality : 0.043 0.459 1388 Planarity : 0.004 0.047 1647 Dihedral : 6.243 69.202 1262 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.81 % Allowed : 9.58 % Favored : 88.61 % 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: 0.57 (0.26), residues: 1121 helix: 1.47 (0.25), residues: 468 sheet: -0.31 (0.35), residues: 195 loop : -0.36 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 199 HIS 0.004 0.001 HIS A 352 PHE 0.007 0.001 PHE A 296 TYR 0.008 0.001 TYR C 68 ARG 0.006 0.000 ARG A 126 *********************** 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 134 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 126 ARG cc_start: 0.8108 (mmp80) cc_final: 0.7724 (mtm-85) REVERT: A 245 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 1 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8436 (tpp) REVERT: B 101 LYS cc_start: 0.7840 (tptp) cc_final: 0.7561 (tptm) REVERT: B 271 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6890 (mp-120) REVERT: C 36 ARG cc_start: 0.7032 (ptp-110) cc_final: 0.6805 (ptm160) REVERT: C 48 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7803 (t0) REVERT: C 233 GLN cc_start: 0.7302 (tp-100) cc_final: 0.6655 (tp40) outliers start: 18 outliers final: 7 residues processed: 124 average time/residue: 2.8863 time to fit residues: 380.4404 Evaluate side-chains 127 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain B residue 1 MET 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 Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 A 333 GLN C 34 ASN C 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9375 Z= 0.276 Angle : 0.547 10.573 12687 Z= 0.292 Chirality : 0.044 0.459 1388 Planarity : 0.005 0.048 1647 Dihedral : 6.339 67.940 1262 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.12 % Allowed : 9.58 % Favored : 88.31 % 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: 0.36 (0.25), residues: 1121 helix: 1.26 (0.24), residues: 474 sheet: -0.33 (0.35), residues: 195 loop : -0.49 (0.29), residues: 452 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 0.008 0.001 PHE A 177 TYR 0.009 0.001 TYR C 68 ARG 0.003 0.000 ARG A 156 *********************** 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 139 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 245 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8556 (mp) REVERT: B 1 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8433 (tpp) REVERT: B 101 LYS cc_start: 0.7855 (tptp) cc_final: 0.7581 (tptm) REVERT: B 271 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6887 (mp-120) REVERT: B 369 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: C 36 ARG cc_start: 0.7059 (ptp-110) cc_final: 0.6836 (ptm160) REVERT: C 48 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7807 (t0) REVERT: C 233 GLN cc_start: 0.7281 (tp-100) cc_final: 0.6656 (tp40) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 2.8404 time to fit residues: 390.1466 Evaluate side-chains 132 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 171 ARG Chi-restraints excluded: chain A residue 245 LEU 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 106 MET Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.0070 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0832 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= 0.182 Angle : 0.496 10.620 12687 Z= 0.265 Chirality : 0.043 0.459 1388 Planarity : 0.004 0.047 1647 Dihedral : 6.074 73.676 1262 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.59 (0.25), residues: 1121 helix: 1.46 (0.25), residues: 475 sheet: -0.26 (0.35), residues: 195 loop : -0.37 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.004 0.001 HIS A 352 PHE 0.007 0.001 PHE A 196 TYR 0.008 0.001 TYR C 68 ARG 0.005 0.000 ARG A 126 *********************** 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 132 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 126 ARG cc_start: 0.8105 (mmp80) cc_final: 0.7724 (mtm-85) REVERT: A 245 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8520 (mp) REVERT: A 380 MET cc_start: 0.8823 (mtt) cc_final: 0.8559 (mtt) REVERT: B 1 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: B 84 GLU cc_start: 0.7749 (tt0) cc_final: 0.7387 (tt0) REVERT: B 101 LYS cc_start: 0.7838 (tptp) cc_final: 0.7562 (tptm) REVERT: B 271 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6875 (mp-120) REVERT: B 369 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7946 (pm20) REVERT: C 36 ARG cc_start: 0.7031 (ptp-110) cc_final: 0.6807 (ptm160) REVERT: C 48 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7776 (t0) REVERT: C 233 GLN cc_start: 0.7331 (tp-100) cc_final: 0.6694 (tp40) outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 2.8494 time to fit residues: 376.3928 Evaluate side-chains 128 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 245 LEU 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 369 GLU Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 C 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0897 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= 0.276 Angle : 0.541 10.580 12687 Z= 0.289 Chirality : 0.044 0.459 1388 Planarity : 0.005 0.047 1647 Dihedral : 6.278 69.607 1262 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.32 % Allowed : 10.58 % Favored : 87.10 % 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: 0.37 (0.25), residues: 1121 helix: 1.27 (0.24), residues: 474 sheet: -0.32 (0.35), residues: 195 loop : -0.49 (0.29), residues: 452 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 0.015 0.002 PHE A 296 TYR 0.009 0.001 TYR C 68 ARG 0.004 0.000 ARG A 126 *********************** 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 139 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 245 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8538 (mp) REVERT: B 1 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8430 (tpp) REVERT: B 101 LYS cc_start: 0.7851 (tptp) cc_final: 0.7578 (tptm) REVERT: B 271 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6876 (mp-120) REVERT: B 369 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: C 36 ARG cc_start: 0.7055 (ptp-110) cc_final: 0.6834 (ptm160) REVERT: C 48 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7776 (t0) REVERT: C 233 GLN cc_start: 0.7286 (tp-100) cc_final: 0.6647 (tp40) outliers start: 23 outliers final: 10 residues processed: 128 average time/residue: 2.8183 time to fit residues: 384.2997 Evaluate side-chains 132 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 245 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 106 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 369 GLU Chi-restraints excluded: chain B residue 457 GLN Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 130 GLN C 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9375 Z= 0.352 Angle : 0.595 10.599 12687 Z= 0.319 Chirality : 0.046 0.460 1388 Planarity : 0.005 0.048 1647 Dihedral : 6.495 66.346 1262 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.02 % Allowed : 10.89 % Favored : 87.10 % 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: 0.11 (0.25), residues: 1121 helix: 0.99 (0.24), residues: 474 sheet: -0.38 (0.35), residues: 195 loop : -0.60 (0.29), residues: 452 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 0.015 0.002 PHE A 296 TYR 0.011 0.002 TYR C 68 ARG 0.005 0.001 ARG A 156 *********************** 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 138 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 101 LYS cc_start: 0.7815 (tptp) cc_final: 0.7552 (tptm) REVERT: B 271 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6885 (mp-120) REVERT: C 36 ARG cc_start: 0.7077 (ptp-110) cc_final: 0.6857 (ptm160) REVERT: C 48 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7781 (t0) REVERT: C 193 HIS cc_start: 0.7157 (OUTLIER) cc_final: 0.6641 (p-80) REVERT: C 233 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6669 (tp40) outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 2.8405 time to fit residues: 387.3748 Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU 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 245 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 106 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 Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9375 Z= 0.248 Angle : 0.541 10.661 12687 Z= 0.290 Chirality : 0.044 0.460 1388 Planarity : 0.005 0.049 1647 Dihedral : 6.387 67.764 1262 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.61 % Allowed : 11.59 % Favored : 86.79 % 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: 0.25 (0.25), residues: 1121 helix: 1.14 (0.24), residues: 474 sheet: -0.34 (0.35), residues: 195 loop : -0.55 (0.29), residues: 452 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 0.008 0.001 PHE B 196 TYR 0.008 0.001 TYR B 183 ARG 0.004 0.000 ARG A 126 ********************** 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 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: B 101 LYS cc_start: 0.7813 (tptp) cc_final: 0.7549 (tptm) REVERT: B 271 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6864 (mp-120) REVERT: C 36 ARG cc_start: 0.7058 (ptp-110) cc_final: 0.6836 (ptm160) REVERT: C 48 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7783 (t0) REVERT: C 233 GLN cc_start: 0.7297 (tp-100) cc_final: 0.6650 (tp40) outliers start: 16 outliers final: 12 residues processed: 124 average time/residue: 2.8177 time to fit residues: 372.1517 Evaluate side-chains 132 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 106 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 Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 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 = 0.3703 r_free = 0.3703 target = 0.154642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119783 restraints weight = 26735.231| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.58 r_work: 0.3188 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9375 Z= 0.147 Angle : 0.476 10.552 12687 Z= 0.255 Chirality : 0.042 0.458 1388 Planarity : 0.004 0.048 1647 Dihedral : 5.987 74.036 1262 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.11 % Allowed : 12.10 % Favored : 86.79 % 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: 0.70 (0.26), residues: 1121 helix: 1.61 (0.25), residues: 469 sheet: -0.20 (0.35), residues: 195 loop : -0.36 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 199 HIS 0.004 0.001 HIS A 352 PHE 0.009 0.001 PHE A 196 TYR 0.008 0.001 TYR B 183 ARG 0.005 0.000 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7247.08 seconds wall clock time: 126 minutes 43.35 seconds (7603.35 seconds total)