Starting phenix.real_space_refine on Wed Sep 17 13:03:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fv8_50792/09_2025/9fv8_50792.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fv8_50792/09_2025/9fv8_50792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fv8_50792/09_2025/9fv8_50792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fv8_50792/09_2025/9fv8_50792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fv8_50792/09_2025/9fv8_50792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fv8_50792/09_2025/9fv8_50792.map" } resolution = 3.4 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= 0.015 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5590 2.51 5 N 1536 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8822 At special positions: 0 Unit cell: (120.36, 106.08, 138.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1642 8.00 N 1536 7.00 C 5590 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: 0.78 Conformation dependent library (CDL) restraints added in 241.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 54.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.613A pdb=" N ILE A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 62 through 91 removed outlier: 3.858A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix removed outlier: 3.755A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS A 88 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.606A pdb=" N ARG A 102 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 147 through 163 removed outlier: 5.311A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 209 removed outlier: 3.793A pdb=" N ILE A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.761A pdb=" N ARG A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.655A pdb=" N ILE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.856A pdb=" N ILE A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.517A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.562A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 313 through 323 removed outlier: 4.253A pdb=" N PHE A 319 " --> pdb=" O CYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.013A pdb=" N LEU A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 465 removed outlier: 3.597A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 removed outlier: 3.646A pdb=" N ARG A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 538 through 545 removed outlier: 3.682A pdb=" N ILE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.923A pdb=" N TRP B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Proline residue: B 68 - end of helix removed outlier: 3.710A pdb=" N ILE B 72 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.536A pdb=" N THR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.511A pdb=" N LYS B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 4.042A pdb=" N LYS B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.828A pdb=" N THR B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 4.244A pdb=" N MET B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 212 removed outlier: 3.744A pdb=" N ILE B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Proline residue: B 176 - end of helix removed outlier: 3.719A pdb=" N ARG B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.757A pdb=" N ILE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 250 through 272 removed outlier: 3.857A pdb=" N ILE B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 293 removed outlier: 3.604A pdb=" N MET B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.785A pdb=" N SER B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 381 through 390 removed outlier: 4.074A pdb=" N ILE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 removed outlier: 3.837A pdb=" N ASN B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.569A pdb=" N ILE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 538 through 544 removed outlier: 3.769A pdb=" N ILE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 570 through 580 Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 366 removed outlier: 3.876A pdb=" N VAL A 342 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 399 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.774A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 547 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 548 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 560 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.893A pdb=" N ASN B 361 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 347 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLU B 399 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.727A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 372 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU B 547 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 375 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL B 549 " --> pdb=" O VAL B 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 311 hydrogen bonds defined for protein. 894 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: 1.25 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1357 1.46 - 1.58: 4645 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 8950 Sorted by residual: bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 bond pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.84e+00 bond pdb=" N ILE B 389 " pdb=" CA ILE B 389 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.37e+00 bond pdb=" N ILE B 170 " pdb=" CA ILE B 170 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N VAL B 433 " pdb=" CA VAL B 433 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.90e+00 ... (remaining 8945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 11205 1.64 - 3.27: 745 3.27 - 4.91: 107 4.91 - 6.54: 33 6.54 - 8.18: 2 Bond angle restraints: 12092 Sorted by residual: angle pdb=" N PHE A 43 " pdb=" CA PHE A 43 " pdb=" C PHE A 43 " ideal model delta sigma weight residual 113.72 105.54 8.18 1.30e+00 5.92e-01 3.96e+01 angle pdb=" N VAL A 245 " pdb=" CA VAL A 245 " pdb=" C VAL A 245 " ideal model delta sigma weight residual 112.96 107.92 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N VAL B 97 " pdb=" CA VAL B 97 " pdb=" C VAL B 97 " ideal model delta sigma weight residual 111.81 107.48 4.33 8.60e-01 1.35e+00 2.53e+01 angle pdb=" N ARG A 127 " pdb=" CA ARG A 127 " pdb=" C ARG A 127 " ideal model delta sigma weight residual 113.88 108.28 5.60 1.23e+00 6.61e-01 2.07e+01 angle pdb=" N VAL A 571 " pdb=" CA VAL A 571 " pdb=" C VAL A 571 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 4616 16.87 - 33.74: 621 33.74 - 50.62: 173 50.62 - 67.49: 36 67.49 - 84.36: 8 Dihedral angle restraints: 5454 sinusoidal: 2164 harmonic: 3290 Sorted by residual: dihedral pdb=" CA ASN A 529 " pdb=" C ASN A 529 " pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA MET B 75 " pdb=" C MET B 75 " pdb=" N ILE B 76 " pdb=" CA ILE B 76 " ideal model delta harmonic sigma weight residual 180.00 151.34 28.66 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ARG B 14 " pdb=" C ARG B 14 " pdb=" N ARG B 15 " pdb=" CA ARG B 15 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1238 0.064 - 0.128: 170 0.128 - 0.192: 30 0.192 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CB VAL B 433 " pdb=" CA VAL B 433 " pdb=" CG1 VAL B 433 " pdb=" CG2 VAL B 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHE A 13 " pdb=" N PHE A 13 " pdb=" C PHE A 13 " pdb=" CB PHE A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA LEU B 322 " pdb=" N LEU B 322 " pdb=" C LEU B 322 " pdb=" CB LEU B 322 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 1437 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 127 " -0.216 9.50e-02 1.11e+02 9.71e-02 6.35e+00 pdb=" NE ARG B 127 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 127 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 127 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 127 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 42 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C THR A 42 " -0.034 2.00e-02 2.50e+03 pdb=" O THR A 42 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 43 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 67 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 68 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.025 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2130 2.80 - 3.32: 8369 3.32 - 3.85: 13668 3.85 - 4.37: 16516 4.37 - 4.90: 27844 Nonbonded interactions: 68527 Sorted by model distance: nonbonded pdb=" O THR B 317 " pdb=" OG1 THR B 320 " model vdw 2.273 3.040 nonbonded pdb=" OD1 ASN B 435 " pdb=" OG1 THR B 442 " model vdw 2.308 3.040 nonbonded pdb=" O PRO A 357 " pdb=" NH1 ARG A 360 " model vdw 2.318 3.120 nonbonded pdb=" OD1 ASP A 431 " pdb=" N THR A 432 " model vdw 2.329 3.120 nonbonded pdb=" O MET A 402 " pdb=" OH TYR A 410 " model vdw 2.331 3.040 ... (remaining 68522 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.100 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 0.042 8950 Z= 0.291 Angle : 0.912 8.180 12092 Z= 0.541 Chirality : 0.049 0.319 1440 Planarity : 0.005 0.097 1532 Dihedral : 16.943 84.360 3326 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.03 % Rotamer: Outliers : 0.31 % Allowed : 21.49 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.46 (0.23), residues: 1134 helix: -2.34 (0.18), residues: 674 sheet: -2.12 (0.71), residues: 46 loop : -1.90 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 127 TYR 0.010 0.001 TYR B 572 PHE 0.030 0.002 PHE A 115 TRP 0.017 0.002 TRP B 66 HIS 0.008 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8950) covalent geometry : angle 0.91189 (12092) hydrogen bonds : bond 0.21635 ( 311) hydrogen bonds : angle 7.93639 ( 894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.357 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.1045 time to fit residues: 17.6504 Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 436 ASN B 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.189556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156281 restraints weight = 10784.735| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.65 r_work: 0.3549 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8950 Z= 0.166 Angle : 0.644 8.411 12092 Z= 0.341 Chirality : 0.044 0.143 1440 Planarity : 0.004 0.037 1532 Dihedral : 5.809 26.703 1238 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.20 % Allowed : 23.66 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.06 (0.24), residues: 1134 helix: -2.07 (0.18), residues: 710 sheet: -1.29 (0.64), residues: 64 loop : -1.62 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 530 TYR 0.016 0.001 TYR B 410 PHE 0.018 0.001 PHE B 115 TRP 0.014 0.002 TRP B 17 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8950) covalent geometry : angle 0.64448 (12092) hydrogen bonds : bond 0.04087 ( 311) hydrogen bonds : angle 4.97850 ( 894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.238 Fit side-chains REVERT: A 23 PHE cc_start: 0.7339 (m-80) cc_final: 0.7126 (m-10) REVERT: A 267 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8289 (mp) REVERT: B 48 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8007 (mp) REVERT: B 115 PHE cc_start: 0.7814 (t80) cc_final: 0.7347 (t80) REVERT: B 462 PHE cc_start: 0.6540 (m-10) cc_final: 0.5992 (m-10) REVERT: B 466 MET cc_start: 0.6059 (mtt) cc_final: 0.5610 (mmm) REVERT: B 488 ARG cc_start: 0.7159 (ttm170) cc_final: 0.6841 (ttp-170) outliers start: 31 outliers final: 20 residues processed: 140 average time/residue: 0.1048 time to fit residues: 19.7386 Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.0010 chunk 39 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 96 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 overall best weight: 0.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS A 436 ASN B 468 ASN B 576 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.195620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163599 restraints weight = 10599.421| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.62 r_work: 0.3625 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8950 Z= 0.100 Angle : 0.557 7.583 12092 Z= 0.296 Chirality : 0.041 0.147 1440 Planarity : 0.003 0.035 1532 Dihedral : 5.219 26.304 1238 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.89 % Allowed : 25.72 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.48 (0.25), residues: 1134 helix: -1.55 (0.19), residues: 722 sheet: -1.07 (0.65), residues: 66 loop : -1.53 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 530 TYR 0.021 0.001 TYR B 87 PHE 0.010 0.001 PHE A 105 TRP 0.012 0.001 TRP B 66 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8950) covalent geometry : angle 0.55676 (12092) hydrogen bonds : bond 0.03108 ( 311) hydrogen bonds : angle 4.40398 ( 894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8142 (tt0) cc_final: 0.7823 (tp40) REVERT: A 267 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8053 (mp) REVERT: A 431 ASP cc_start: 0.7191 (t0) cc_final: 0.6422 (m-30) REVERT: B 98 MET cc_start: 0.8159 (ttp) cc_final: 0.7930 (ttp) REVERT: B 115 PHE cc_start: 0.7745 (t80) cc_final: 0.7312 (t80) REVERT: B 196 MET cc_start: 0.7828 (tpp) cc_final: 0.7486 (mmt) REVERT: B 360 ARG cc_start: 0.7937 (mmt180) cc_final: 0.7725 (mmt180) REVERT: B 388 LEU cc_start: 0.8469 (mp) cc_final: 0.8237 (tp) REVERT: B 488 ARG cc_start: 0.6994 (ttm170) cc_final: 0.6668 (ttm170) outliers start: 28 outliers final: 21 residues processed: 133 average time/residue: 0.1081 time to fit residues: 19.1825 Evaluate side-chains 127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 405 HIS A 576 HIS B 520 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.190871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.158304 restraints weight = 10750.071| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.67 r_work: 0.3547 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8950 Z= 0.144 Angle : 0.589 9.329 12092 Z= 0.308 Chirality : 0.043 0.142 1440 Planarity : 0.003 0.034 1532 Dihedral : 5.280 26.375 1238 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.93 % Allowed : 25.83 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.37 (0.25), residues: 1134 helix: -1.47 (0.19), residues: 724 sheet: -0.95 (0.68), residues: 66 loop : -1.49 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 530 TYR 0.008 0.001 TYR B 410 PHE 0.009 0.001 PHE B 189 TRP 0.012 0.001 TRP B 17 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8950) covalent geometry : angle 0.58896 (12092) hydrogen bonds : bond 0.03464 ( 311) hydrogen bonds : angle 4.24447 ( 894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 288 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: A 431 ASP cc_start: 0.7564 (t0) cc_final: 0.7010 (m-30) REVERT: B 115 PHE cc_start: 0.8118 (t80) cc_final: 0.7868 (t80) REVERT: B 388 LEU cc_start: 0.8494 (mp) cc_final: 0.8261 (tp) REVERT: B 462 PHE cc_start: 0.6345 (m-10) cc_final: 0.5747 (m-10) REVERT: B 466 MET cc_start: 0.5546 (mtt) cc_final: 0.5138 (mmm) REVERT: B 488 ARG cc_start: 0.7078 (ttm170) cc_final: 0.6634 (ttm170) REVERT: B 520 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7660 (mm110) outliers start: 38 outliers final: 26 residues processed: 138 average time/residue: 0.1066 time to fit residues: 19.7295 Evaluate side-chains 138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS B 520 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.192516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160352 restraints weight = 10721.951| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.68 r_work: 0.3572 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8950 Z= 0.114 Angle : 0.543 6.509 12092 Z= 0.287 Chirality : 0.041 0.144 1440 Planarity : 0.003 0.033 1532 Dihedral : 5.094 25.826 1238 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.17 % Allowed : 25.21 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.10 (0.25), residues: 1134 helix: -1.24 (0.20), residues: 722 sheet: -0.81 (0.69), residues: 66 loop : -1.44 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 530 TYR 0.006 0.001 TYR B 410 PHE 0.009 0.001 PHE A 23 TRP 0.011 0.001 TRP B 17 HIS 0.002 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8950) covalent geometry : angle 0.54280 (12092) hydrogen bonds : bond 0.03094 ( 311) hydrogen bonds : angle 4.08357 ( 894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.313 Fit side-chains REVERT: A 267 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 431 ASP cc_start: 0.7649 (t0) cc_final: 0.7221 (m-30) REVERT: B 127 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8257 (ttm-80) REVERT: B 196 MET cc_start: 0.7830 (tpp) cc_final: 0.7432 (mmt) REVERT: B 388 LEU cc_start: 0.8511 (mp) cc_final: 0.8287 (tp) REVERT: B 466 MET cc_start: 0.5670 (mtt) cc_final: 0.5336 (mmm) REVERT: B 488 ARG cc_start: 0.7058 (ttm170) cc_final: 0.6649 (ttm170) REVERT: B 578 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6287 (mmp) outliers start: 50 outliers final: 33 residues processed: 149 average time/residue: 0.1075 time to fit residues: 21.3809 Evaluate side-chains 142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 576 HIS ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157055 restraints weight = 10650.146| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.59 r_work: 0.3537 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8950 Z= 0.156 Angle : 0.605 11.649 12092 Z= 0.312 Chirality : 0.043 0.139 1440 Planarity : 0.003 0.033 1532 Dihedral : 5.258 30.137 1238 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 5.27 % Allowed : 25.41 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -2.17 (0.25), residues: 1134 helix: -1.31 (0.19), residues: 722 sheet: -1.41 (0.69), residues: 62 loop : -1.29 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 530 TYR 0.006 0.001 TYR B 393 PHE 0.023 0.001 PHE B 115 TRP 0.012 0.001 TRP B 17 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8950) covalent geometry : angle 0.60506 (12092) hydrogen bonds : bond 0.03472 ( 311) hydrogen bonds : angle 4.15542 ( 894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 0.282 Fit side-chains REVERT: A 267 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 288 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: A 431 ASP cc_start: 0.7813 (t0) cc_final: 0.7476 (m-30) REVERT: B 48 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7969 (mp) REVERT: B 127 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8331 (ttm-80) REVERT: B 288 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: B 388 LEU cc_start: 0.8484 (mp) cc_final: 0.8247 (tp) REVERT: B 488 ARG cc_start: 0.7114 (ttm170) cc_final: 0.6665 (ttm170) REVERT: B 578 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6263 (mmp) outliers start: 51 outliers final: 37 residues processed: 143 average time/residue: 0.1044 time to fit residues: 20.0866 Evaluate side-chains 144 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 288 PHE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 576 HIS B 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.190740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157934 restraints weight = 10691.171| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.57 r_work: 0.3558 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8950 Z= 0.128 Angle : 0.593 10.767 12092 Z= 0.302 Chirality : 0.042 0.141 1440 Planarity : 0.003 0.034 1532 Dihedral : 5.172 29.307 1238 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.35 % Favored : 93.56 % Rotamer: Outliers : 5.48 % Allowed : 26.34 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.06 (0.25), residues: 1134 helix: -1.21 (0.20), residues: 722 sheet: -1.11 (0.65), residues: 78 loop : -1.34 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 530 TYR 0.006 0.001 TYR A 572 PHE 0.024 0.001 PHE B 115 TRP 0.012 0.001 TRP B 17 HIS 0.002 0.001 HIS A 107 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8950) covalent geometry : angle 0.59301 (12092) hydrogen bonds : bond 0.03238 ( 311) hydrogen bonds : angle 4.09194 ( 894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 104 time to evaluate : 0.323 Fit side-chains REVERT: A 267 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 288 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: A 431 ASP cc_start: 0.7826 (t0) cc_final: 0.7523 (m-30) REVERT: B 48 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 127 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8315 (ttm-80) REVERT: B 288 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: B 322 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8317 (tt) REVERT: B 466 MET cc_start: 0.5186 (mtt) cc_final: 0.4976 (mmm) REVERT: B 488 ARG cc_start: 0.7072 (ttm170) cc_final: 0.6623 (ttm170) REVERT: B 578 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6202 (mmp) outliers start: 53 outliers final: 41 residues processed: 144 average time/residue: 0.1034 time to fit residues: 20.0387 Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 PHE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 HIS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.191529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158813 restraints weight = 10599.519| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.70 r_work: 0.3544 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8950 Z= 0.115 Angle : 0.567 9.890 12092 Z= 0.294 Chirality : 0.041 0.140 1440 Planarity : 0.003 0.034 1532 Dihedral : 5.037 29.404 1238 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer: Outliers : 5.48 % Allowed : 26.65 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.92 (0.26), residues: 1134 helix: -1.09 (0.20), residues: 722 sheet: -1.07 (0.65), residues: 78 loop : -1.30 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 530 TYR 0.006 0.001 TYR A 572 PHE 0.022 0.001 PHE B 115 TRP 0.012 0.001 TRP B 17 HIS 0.002 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8950) covalent geometry : angle 0.56701 (12092) hydrogen bonds : bond 0.03084 ( 311) hydrogen bonds : angle 4.01388 ( 894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 104 time to evaluate : 0.261 Fit side-chains REVERT: A 267 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 288 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: A 397 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6990 (tm-30) REVERT: A 431 ASP cc_start: 0.7836 (t0) cc_final: 0.7553 (m-30) REVERT: B 48 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 288 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: B 322 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8295 (tt) REVERT: B 397 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7320 (pm20) REVERT: B 466 MET cc_start: 0.5266 (mtt) cc_final: 0.5034 (mmm) REVERT: B 488 ARG cc_start: 0.7088 (ttm170) cc_final: 0.6665 (ttm170) REVERT: B 578 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6155 (mmp) outliers start: 53 outliers final: 44 residues processed: 144 average time/residue: 0.1059 time to fit residues: 20.3497 Evaluate side-chains 151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 288 PHE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 HIS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.191741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159138 restraints weight = 10566.680| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.57 r_work: 0.3581 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8950 Z= 0.116 Angle : 0.563 9.386 12092 Z= 0.293 Chirality : 0.041 0.140 1440 Planarity : 0.003 0.034 1532 Dihedral : 4.974 28.750 1238 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.08 % Favored : 93.83 % Rotamer: Outliers : 5.27 % Allowed : 27.07 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.83 (0.26), residues: 1134 helix: -1.01 (0.20), residues: 722 sheet: -1.04 (0.66), residues: 78 loop : -1.31 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 530 TYR 0.006 0.001 TYR A 572 PHE 0.021 0.001 PHE B 115 TRP 0.012 0.001 TRP B 17 HIS 0.002 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8950) covalent geometry : angle 0.56292 (12092) hydrogen bonds : bond 0.03033 ( 311) hydrogen bonds : angle 3.98296 ( 894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 0.348 Fit side-chains REVERT: A 267 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 288 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: A 397 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 431 ASP cc_start: 0.7731 (t0) cc_final: 0.7487 (m-30) REVERT: B 48 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7879 (mp) REVERT: B 288 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: B 321 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8251 (mp) REVERT: B 322 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 397 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7217 (pm20) REVERT: B 488 ARG cc_start: 0.7073 (ttm170) cc_final: 0.6636 (ttm170) REVERT: B 578 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6100 (mmp) outliers start: 51 outliers final: 41 residues processed: 141 average time/residue: 0.0923 time to fit residues: 17.5313 Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 288 PHE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 HIS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 92 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 576 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.189825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156956 restraints weight = 10654.773| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.69 r_work: 0.3529 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8950 Z= 0.146 Angle : 0.601 9.077 12092 Z= 0.310 Chirality : 0.043 0.141 1440 Planarity : 0.004 0.049 1532 Dihedral : 5.100 28.103 1238 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 5.27 % Allowed : 26.96 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.90 (0.25), residues: 1134 helix: -1.08 (0.20), residues: 722 sheet: -1.19 (0.73), residues: 62 loop : -1.26 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 190 TYR 0.006 0.001 TYR A 572 PHE 0.021 0.001 PHE B 115 TRP 0.012 0.001 TRP B 17 HIS 0.002 0.000 HIS B 576 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8950) covalent geometry : angle 0.60089 (12092) hydrogen bonds : bond 0.03315 ( 311) hydrogen bonds : angle 4.03900 ( 894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 0.262 Fit side-chains REVERT: A 267 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 288 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: A 312 MET cc_start: 0.8341 (tpp) cc_final: 0.7453 (mmt) REVERT: A 431 ASP cc_start: 0.7833 (t0) cc_final: 0.7574 (m-30) REVERT: B 48 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7957 (mp) REVERT: B 288 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 321 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 322 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8260 (tt) REVERT: B 397 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7172 (pm20) REVERT: B 456 MET cc_start: 0.7828 (tpp) cc_final: 0.7492 (mmm) REVERT: B 488 ARG cc_start: 0.7153 (ttm170) cc_final: 0.6729 (ttm170) REVERT: B 578 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6116 (mmp) outliers start: 51 outliers final: 41 residues processed: 142 average time/residue: 0.0954 time to fit residues: 18.2729 Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 288 PHE Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 537 HIS Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 578 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 0.0000 chunk 30 optimal weight: 0.7980 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.160502 restraints weight = 10447.311| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.60 r_work: 0.3593 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8950 Z= 0.105 Angle : 0.564 8.812 12092 Z= 0.295 Chirality : 0.041 0.158 1440 Planarity : 0.004 0.061 1532 Dihedral : 4.944 28.191 1238 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 5.17 % Allowed : 27.17 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.68 (0.26), residues: 1134 helix: -0.87 (0.20), residues: 722 sheet: -0.97 (0.66), residues: 78 loop : -1.28 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 190 TYR 0.007 0.001 TYR A 572 PHE 0.020 0.001 PHE B 115 TRP 0.012 0.001 TRP B 17 HIS 0.003 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8950) covalent geometry : angle 0.56374 (12092) hydrogen bonds : bond 0.02914 ( 311) hydrogen bonds : angle 3.95935 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.53 seconds wall clock time: 43 minutes 59.03 seconds (2639.03 seconds total)