Starting phenix.real_space_refine on Tue Jan 13 23:29:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f18_28787/01_2026/8f18_28787.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f18_28787/01_2026/8f18_28787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f18_28787/01_2026/8f18_28787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f18_28787/01_2026/8f18_28787.map" model { file = "/net/cci-nas-00/data/ceres_data/8f18_28787/01_2026/8f18_28787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f18_28787/01_2026/8f18_28787.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 6237 2.51 5 N 1687 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9889 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3446 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Chain: "K" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2944 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 6 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 9889 At special positions: 0 Unit cell: (110.564, 80.18, 114.784, 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 61 16.00 P 5 15.00 Mg 1 11.99 O 1898 8.00 N 1687 7.00 C 6237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 515.5 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 47.3% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.303A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.573A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.659A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.601A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.684A pdb=" N TYR A 282 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.878A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.219A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 434 removed outlier: 4.287A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.135A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.124A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.727A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.664A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.825A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 4.187A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.954A pdb=" N GLN B 280 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.530A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 removed outlier: 3.673A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.992A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 405 through 425 removed outlier: 3.705A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 80 removed outlier: 3.535A pdb=" N ARG K 80 " --> pdb=" O SER K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 139 removed outlier: 3.515A pdb=" N LEU K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 150 removed outlier: 4.091A pdb=" N MET K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 170 removed outlier: 3.636A pdb=" N GLN K 170 " --> pdb=" O THR K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 190 Processing helix chain 'K' and resid 212 through 229 Processing helix chain 'K' and resid 350 through 364 removed outlier: 3.550A pdb=" N ALA K 354 " --> pdb=" O ASP K 350 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS K 363 " --> pdb=" O LYS K 359 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN K 364 " --> pdb=" O VAL K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 423 through 446 Processing helix chain 'K' and resid 457 through 460 removed outlier: 3.523A pdb=" N ASP K 460 " --> pdb=" O PRO K 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 457 through 460' Processing helix chain 'K' and resid 461 through 467 Processing helix chain 'K' and resid 467 through 473 removed outlier: 3.528A pdb=" N PHE K 471 " --> pdb=" O PHE K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.314A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 65 removed outlier: 5.627A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 198 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'K' and resid 124 through 126 removed outlier: 3.599A pdb=" N GLN K 124 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR K 67 " --> pdb=" O VAL K 481 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL K 483 " --> pdb=" O TYR K 67 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG K 69 " --> pdb=" O VAL K 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 124 through 126 removed outlier: 3.599A pdb=" N GLN K 124 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TYR K 67 " --> pdb=" O VAL K 481 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N VAL K 483 " --> pdb=" O TYR K 67 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG K 69 " --> pdb=" O VAL K 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 87 through 89 removed outlier: 5.982A pdb=" N THR K 117 " --> pdb=" O VAL K 507 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA K 503 " --> pdb=" O THR K 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 200 through 204 removed outlier: 3.726A pdb=" N LEU K 203 " --> pdb=" O GLU K 207 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU K 207 " --> pdb=" O LEU K 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 329 through 332 removed outlier: 4.174A pdb=" N ARG K 329 " --> pdb=" O LYS K 341 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1389 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: 1.63 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1739 1.32 - 1.44: 2641 1.44 - 1.57: 5619 1.57 - 1.69: 12 1.69 - 1.81: 94 Bond restraints: 10105 Sorted by residual: bond pdb=" C GLU B 69 " pdb=" N PRO B 70 " ideal model delta sigma weight residual 1.333 1.368 -0.035 1.44e-02 4.82e+03 5.75e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.45e+00 bond pdb=" CB GLU A 220 " pdb=" CG GLU A 220 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 10100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 13381 2.08 - 4.16: 281 4.16 - 6.24: 47 6.24 - 8.32: 5 8.32 - 10.40: 2 Bond angle restraints: 13716 Sorted by residual: angle pdb=" C VAL A 275 " pdb=" N ILE A 276 " pdb=" CA ILE A 276 " ideal model delta sigma weight residual 121.97 128.73 -6.76 1.80e+00 3.09e-01 1.41e+01 angle pdb=" C VAL K 507 " pdb=" N HIS K 508 " pdb=" CA HIS K 508 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" O GLY A 144 " pdb=" C GLY A 144 " pdb=" N THR A 145 " ideal model delta sigma weight residual 121.85 123.76 -1.91 5.60e-01 3.19e+00 1.17e+01 angle pdb=" CA CYS A 129 " pdb=" CB CYS A 129 " pdb=" SG CYS A 129 " ideal model delta sigma weight residual 114.40 106.60 7.80 2.30e+00 1.89e-01 1.15e+01 angle pdb=" N PRO K 510 " pdb=" CA PRO K 510 " pdb=" C PRO K 510 " ideal model delta sigma weight residual 110.70 114.76 -4.06 1.22e+00 6.72e-01 1.11e+01 ... (remaining 13711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.98: 5924 27.98 - 55.96: 155 55.96 - 83.95: 21 83.95 - 111.93: 8 111.93 - 139.91: 1 Dihedral angle restraints: 6109 sinusoidal: 2528 harmonic: 3581 Sorted by residual: dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -35.32 139.91 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" O2B GDP B 501 " pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sinusoidal sigma weight residual 180.00 72.53 107.47 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5' GTP A 502 " pdb=" O5' GTP A 502 " pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " ideal model delta sinusoidal sigma weight residual 69.27 167.32 -98.05 1 2.00e+01 2.50e-03 2.74e+01 ... (remaining 6106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 956 0.037 - 0.075: 416 0.075 - 0.112: 96 0.112 - 0.150: 48 0.150 - 0.187: 2 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CB VAL A 182 " pdb=" CA VAL A 182 " pdb=" CG1 VAL A 182 " pdb=" CG2 VAL A 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA ILE B 345 " pdb=" N ILE B 345 " pdb=" C ILE B 345 " pdb=" CB ILE B 345 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE K 456 " pdb=" N ILE K 456 " pdb=" C ILE K 456 " pdb=" CB ILE K 456 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 1515 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS K 508 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.86e+01 pdb=" C HIS K 508 " -0.075 2.00e-02 2.50e+03 pdb=" O HIS K 508 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA K 509 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO K 510 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO K 511 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO K 511 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 511 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 429 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C ILE K 429 " 0.044 2.00e-02 2.50e+03 pdb=" O ILE K 429 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN K 430 " -0.015 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 43 2.52 - 3.11: 7590 3.11 - 3.71: 15000 3.71 - 4.30: 21803 4.30 - 4.90: 36829 Nonbonded interactions: 81265 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O1G GTP A 502 " model vdw 1.919 2.170 nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 501 " model vdw 2.085 2.170 nonbonded pdb=" O06 TA1 B 502 " pdb=" O07 TA1 B 502 " model vdw 2.137 3.040 nonbonded pdb=" N THR B 143 " pdb=" O1B GDP B 501 " model vdw 2.238 3.120 nonbonded pdb=" NZ LYS B 174 " pdb=" OE2 GLU B 205 " model vdw 2.261 3.120 ... (remaining 81260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.005 0.046 10105 Z= 0.232 Angle : 0.772 10.399 13716 Z= 0.424 Chirality : 0.046 0.187 1518 Planarity : 0.007 0.067 1774 Dihedral : 13.387 139.909 3803 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1225 helix: 0.59 (0.23), residues: 478 sheet: -0.33 (0.34), residues: 217 loop : -0.20 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 79 TYR 0.015 0.002 TYR K 156 PHE 0.028 0.002 PHE B 167 TRP 0.012 0.002 TRP A 388 HIS 0.008 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00512 (10105) covalent geometry : angle 0.77198 (13716) hydrogen bonds : bond 0.16146 ( 456) hydrogen bonds : angle 6.96190 ( 1389) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0880 time to fit residues: 11.3949 Evaluate side-chains 62 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 50 ASN K 335 ASN K 445 GLN K 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.123865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079854 restraints weight = 19558.143| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.76 r_work: 0.3104 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10105 Z= 0.150 Angle : 0.575 6.881 13716 Z= 0.294 Chirality : 0.044 0.196 1518 Planarity : 0.005 0.062 1774 Dihedral : 8.626 134.992 1468 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 0.93 % Allowed : 3.63 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1225 helix: 1.31 (0.23), residues: 510 sheet: -0.17 (0.34), residues: 221 loop : -0.15 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 309 TYR 0.013 0.001 TYR B 310 PHE 0.014 0.001 PHE K 135 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00342 (10105) covalent geometry : angle 0.57466 (13716) hydrogen bonds : bond 0.04443 ( 456) hydrogen bonds : angle 4.87393 ( 1389) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8901 (t0) cc_final: 0.8689 (t0) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 0.0938 time to fit residues: 11.3649 Evaluate side-chains 68 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 105 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 113 optimal weight: 40.0000 chunk 79 optimal weight: 0.0020 chunk 28 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 overall best weight: 3.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.118899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075638 restraints weight = 19691.669| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.56 r_work: 0.3022 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10105 Z= 0.166 Angle : 0.573 7.189 13716 Z= 0.289 Chirality : 0.044 0.182 1518 Planarity : 0.004 0.063 1774 Dihedral : 8.129 131.273 1468 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.74 % Allowed : 6.42 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1225 helix: 1.42 (0.23), residues: 505 sheet: -0.02 (0.34), residues: 221 loop : -0.16 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.013 0.001 TYR K 156 PHE 0.014 0.002 PHE A 67 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00383 (10105) covalent geometry : angle 0.57268 (13716) hydrogen bonds : bond 0.04147 ( 456) hydrogen bonds : angle 4.64765 ( 1389) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.9048 (t0) cc_final: 0.8802 (t0) REVERT: B 203 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7998 (m-30) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.0823 time to fit residues: 9.6798 Evaluate side-chains 67 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 30.0000 chunk 59 optimal weight: 0.4980 chunk 109 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.124932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081483 restraints weight = 19764.157| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.67 r_work: 0.3142 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10105 Z= 0.104 Angle : 0.512 7.378 13716 Z= 0.256 Chirality : 0.042 0.168 1518 Planarity : 0.004 0.063 1774 Dihedral : 7.382 126.601 1468 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 0.74 % Allowed : 7.26 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1225 helix: 1.63 (0.24), residues: 507 sheet: 0.13 (0.35), residues: 214 loop : -0.17 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 309 TYR 0.011 0.001 TYR B 310 PHE 0.011 0.001 PHE K 135 TRP 0.011 0.001 TRP A 21 HIS 0.002 0.000 HIS K 380 Details of bonding type rmsd covalent geometry : bond 0.00225 (10105) covalent geometry : angle 0.51234 (13716) hydrogen bonds : bond 0.03441 ( 456) hydrogen bonds : angle 4.39209 ( 1389) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.468 Fit side-chains REVERT: A 203 MET cc_start: 0.9263 (mtt) cc_final: 0.9042 (mmm) REVERT: A 218 ASP cc_start: 0.9025 (t0) cc_final: 0.8803 (t0) REVERT: A 425 MET cc_start: 0.7669 (tpp) cc_final: 0.7351 (mmm) REVERT: B 1 MET cc_start: 0.6221 (tpp) cc_final: 0.5902 (tpp) REVERT: B 203 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: B 239 CYS cc_start: 0.8632 (m) cc_final: 0.8325 (t) outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 0.0814 time to fit residues: 10.0719 Evaluate side-chains 72 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 113 optimal weight: 50.0000 chunk 56 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 90 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.124353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.081344 restraints weight = 19648.171| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.61 r_work: 0.3156 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10105 Z= 0.117 Angle : 0.515 6.795 13716 Z= 0.257 Chirality : 0.042 0.173 1518 Planarity : 0.004 0.063 1774 Dihedral : 7.002 120.433 1468 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.74 % Allowed : 7.54 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1225 helix: 1.75 (0.24), residues: 505 sheet: 0.25 (0.34), residues: 220 loop : -0.17 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 391 TYR 0.011 0.001 TYR B 310 PHE 0.012 0.001 PHE K 135 TRP 0.010 0.001 TRP B 344 HIS 0.003 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00262 (10105) covalent geometry : angle 0.51506 (13716) hydrogen bonds : bond 0.03525 ( 456) hydrogen bonds : angle 4.31932 ( 1389) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 203 MET cc_start: 0.9292 (mtt) cc_final: 0.9058 (mmm) REVERT: A 218 ASP cc_start: 0.9065 (t0) cc_final: 0.8846 (t0) REVERT: A 425 MET cc_start: 0.7704 (tpp) cc_final: 0.7382 (mmm) REVERT: B 203 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7827 (m-30) REVERT: B 239 CYS cc_start: 0.8630 (m) cc_final: 0.8331 (t) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.0860 time to fit residues: 9.8279 Evaluate side-chains 69 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.122321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079139 restraints weight = 19767.272| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.60 r_work: 0.3096 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10105 Z= 0.180 Angle : 0.577 9.772 13716 Z= 0.288 Chirality : 0.044 0.169 1518 Planarity : 0.004 0.062 1774 Dihedral : 7.104 119.324 1468 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.76 % Rotamer: Outliers : 0.84 % Allowed : 7.82 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1225 helix: 1.71 (0.24), residues: 502 sheet: 0.20 (0.34), residues: 216 loop : -0.20 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.012 0.001 TYR B 51 PHE 0.013 0.001 PHE A 67 TRP 0.009 0.001 TRP B 344 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00421 (10105) covalent geometry : angle 0.57696 (13716) hydrogen bonds : bond 0.03933 ( 456) hydrogen bonds : angle 4.43145 ( 1389) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.9092 (t0) cc_final: 0.8846 (t0) REVERT: A 425 MET cc_start: 0.7756 (tpp) cc_final: 0.7454 (mmm) REVERT: B 203 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: B 388 MET cc_start: 0.7942 (mtp) cc_final: 0.7500 (ttm) REVERT: K 313 TYR cc_start: 0.8350 (m-80) cc_final: 0.7674 (m-80) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.0786 time to fit residues: 8.7505 Evaluate side-chains 68 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.120589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077276 restraints weight = 20292.707| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.63 r_work: 0.3082 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10105 Z= 0.190 Angle : 0.583 9.072 13716 Z= 0.291 Chirality : 0.044 0.165 1518 Planarity : 0.004 0.063 1774 Dihedral : 7.097 119.107 1468 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 1.12 % Allowed : 8.29 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.25), residues: 1225 helix: 1.66 (0.23), residues: 503 sheet: 0.15 (0.34), residues: 216 loop : -0.25 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.012 0.001 TYR B 51 PHE 0.013 0.002 PHE K 135 TRP 0.009 0.001 TRP B 344 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00445 (10105) covalent geometry : angle 0.58273 (13716) hydrogen bonds : bond 0.03936 ( 456) hydrogen bonds : angle 4.46501 ( 1389) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 276 ILE cc_start: 0.8655 (tp) cc_final: 0.8338 (tt) REVERT: A 326 LYS cc_start: 0.4170 (mttt) cc_final: 0.3949 (mttp) REVERT: A 425 MET cc_start: 0.7718 (tpp) cc_final: 0.7438 (mmm) REVERT: B 203 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: B 388 MET cc_start: 0.7931 (mtp) cc_final: 0.7481 (ttm) REVERT: K 313 TYR cc_start: 0.8332 (m-80) cc_final: 0.7662 (m-80) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.0809 time to fit residues: 8.9228 Evaluate side-chains 69 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 7 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.077886 restraints weight = 19807.796| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.55 r_work: 0.3078 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10105 Z= 0.203 Angle : 0.606 8.729 13716 Z= 0.301 Chirality : 0.045 0.216 1518 Planarity : 0.004 0.063 1774 Dihedral : 7.174 119.317 1468 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 1.02 % Allowed : 8.47 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1225 helix: 1.62 (0.23), residues: 503 sheet: 0.10 (0.35), residues: 216 loop : -0.33 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.015 0.001 TYR B 51 PHE 0.014 0.002 PHE A 67 TRP 0.009 0.001 TRP B 344 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00478 (10105) covalent geometry : angle 0.60584 (13716) hydrogen bonds : bond 0.04025 ( 456) hydrogen bonds : angle 4.52841 ( 1389) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 276 ILE cc_start: 0.8688 (tp) cc_final: 0.8359 (tt) REVERT: A 377 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6919 (tpp) REVERT: B 203 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: B 388 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7474 (ttm) REVERT: K 313 TYR cc_start: 0.8399 (m-80) cc_final: 0.7728 (m-80) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.0912 time to fit residues: 9.6666 Evaluate side-chains 72 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.124740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.081282 restraints weight = 19751.285| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.63 r_work: 0.3147 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10105 Z= 0.107 Angle : 0.540 8.638 13716 Z= 0.266 Chirality : 0.043 0.182 1518 Planarity : 0.004 0.064 1774 Dihedral : 6.740 115.518 1468 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.56 % Allowed : 9.12 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1225 helix: 1.82 (0.24), residues: 505 sheet: 0.14 (0.35), residues: 214 loop : -0.31 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 77 TYR 0.013 0.001 TYR K 156 PHE 0.009 0.001 PHE A 141 TRP 0.012 0.001 TRP A 21 HIS 0.002 0.000 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00236 (10105) covalent geometry : angle 0.54039 (13716) hydrogen bonds : bond 0.03271 ( 456) hydrogen bonds : angle 4.27940 ( 1389) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.466 Fit side-chains REVERT: A 163 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8509 (pttm) REVERT: A 276 ILE cc_start: 0.8709 (tp) cc_final: 0.8369 (tt) REVERT: B 203 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7849 (m-30) REVERT: B 312 THR cc_start: 0.8785 (m) cc_final: 0.8469 (p) REVERT: B 388 MET cc_start: 0.7850 (mtp) cc_final: 0.7567 (ttm) REVERT: K 313 TYR cc_start: 0.8442 (m-80) cc_final: 0.7754 (m-80) outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 0.0879 time to fit residues: 9.8907 Evaluate side-chains 70 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 78 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.122859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.079649 restraints weight = 19699.313| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.54 r_work: 0.3124 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10105 Z= 0.140 Angle : 0.583 8.551 13716 Z= 0.287 Chirality : 0.044 0.185 1518 Planarity : 0.004 0.063 1774 Dihedral : 6.804 115.168 1468 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 0.47 % Allowed : 9.78 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1225 helix: 1.80 (0.24), residues: 505 sheet: 0.19 (0.35), residues: 221 loop : -0.27 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.017 0.001 TYR B 200 PHE 0.032 0.001 PHE B 167 TRP 0.010 0.001 TRP A 21 HIS 0.003 0.000 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00323 (10105) covalent geometry : angle 0.58276 (13716) hydrogen bonds : bond 0.03513 ( 456) hydrogen bonds : angle 4.29725 ( 1389) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.368 Fit side-chains REVERT: A 163 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8544 (pttm) REVERT: A 276 ILE cc_start: 0.8633 (tp) cc_final: 0.8300 (tt) REVERT: B 41 ASP cc_start: 0.8045 (p0) cc_final: 0.7605 (t70) REVERT: B 203 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: B 388 MET cc_start: 0.7892 (mtp) cc_final: 0.7502 (ttm) REVERT: K 143 MET cc_start: 0.8780 (tpp) cc_final: 0.8494 (tpp) REVERT: K 313 TYR cc_start: 0.8456 (m-80) cc_final: 0.7771 (m-80) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.0825 time to fit residues: 9.1210 Evaluate side-chains 68 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain K residue 331 CYS Chi-restraints excluded: chain K residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 6.9990 chunk 112 optimal weight: 40.0000 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.124522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081021 restraints weight = 19793.752| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.57 r_work: 0.3148 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10105 Z= 0.117 Angle : 0.585 14.230 13716 Z= 0.287 Chirality : 0.043 0.280 1518 Planarity : 0.004 0.063 1774 Dihedral : 6.672 114.002 1468 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.47 % Allowed : 9.87 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.25), residues: 1225 helix: 1.84 (0.24), residues: 505 sheet: 0.26 (0.36), residues: 212 loop : -0.32 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.011 0.001 TYR K 490 PHE 0.018 0.001 PHE B 167 TRP 0.011 0.001 TRP A 21 HIS 0.002 0.000 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00262 (10105) covalent geometry : angle 0.58451 (13716) hydrogen bonds : bond 0.03274 ( 456) hydrogen bonds : angle 4.23080 ( 1389) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2364.45 seconds wall clock time: 41 minutes 19.17 seconds (2479.17 seconds total)