Starting phenix.real_space_refine on Thu Feb 13 10:38:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmo_27545/02_2025/8dmo_27545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmo_27545/02_2025/8dmo_27545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmo_27545/02_2025/8dmo_27545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmo_27545/02_2025/8dmo_27545.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmo_27545/02_2025/8dmo_27545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmo_27545/02_2025/8dmo_27545.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 5649 2.51 5 N 1549 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4459 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 13, 'TRANS': 561} Chain: "B" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4453 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 561} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.46, per 1000 atoms: 0.61 Number of scatterers: 8912 At special positions: 0 Unit cell: (89.46, 136.32, 136.32, 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 1660 8.00 N 1549 7.00 C 5649 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 4 sheets defined 71.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 23 through 47 removed outlier: 3.570A pdb=" N LEU A 27 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.580A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 109 Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 112 through 119 removed outlier: 4.278A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.773A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 130 through 164 Processing helix chain 'A' and resid 164 through 212 Proline residue: A 176 - end of helix removed outlier: 4.233A pdb=" N GLN A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 removed outlier: 3.748A pdb=" N ILE A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 272 removed outlier: 4.441A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.836A pdb=" N PHE A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.818A pdb=" N ASP A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 removed outlier: 4.537A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 3.563A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 323 removed outlier: 3.585A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.928A pdb=" N THR A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.090A pdb=" N ALA A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.545A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.532A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.618A pdb=" N ARG A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.973A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.649A pdb=" N THR B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 23 through 47 removed outlier: 3.599A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.681A pdb=" N LEU B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.545A pdb=" N GLN B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 removed outlier: 3.756A pdb=" N ILE B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 200 removed outlier: 8.040A pdb=" N GLN B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 200 through 212 removed outlier: 4.056A pdb=" N THR B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 5.161A pdb=" N ILE B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.598A pdb=" N GLN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.641A pdb=" N ILE B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.811A pdb=" N ASP B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.725A pdb=" N ILE B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 303 through 323 removed outlier: 3.618A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.724A pdb=" N THR B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.869A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.631A pdb=" N ASP B 471 " --> pdb=" O ASN B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 497 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.818A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 6.401A pdb=" N ARG A 360 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR A 348 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 362 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N PHE A 344 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 401 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASN A 346 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.780A 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 422 removed outlier: 6.239A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 372 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL A 375 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU A 552 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 366 removed outlier: 6.548A pdb=" N ARG B 360 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR B 348 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE B 362 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE B 344 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B 401 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ASN B 346 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.824A 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: 6.544A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 2.45 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: 2951 1.34 - 1.46: 1909 1.46 - 1.58: 4080 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 9044 Sorted by residual: bond pdb=" N ILE B 172 " pdb=" CA ILE B 172 " ideal model delta sigma weight residual 1.459 1.440 0.019 1.25e-02 6.40e+03 2.37e+00 bond pdb=" C VAL A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.330 1.346 -0.015 1.19e-02 7.06e+03 1.66e+00 bond pdb=" CB PRO A 297 " pdb=" CG PRO A 297 " ideal model delta sigma weight residual 1.492 1.446 0.046 5.00e-02 4.00e+02 8.34e-01 bond pdb=" CB GLU B 336 " pdb=" CG GLU B 336 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.36e-01 bond pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 1.459 1.470 -0.011 1.25e-02 6.40e+03 7.11e-01 ... (remaining 9039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11996 1.88 - 3.76: 181 3.76 - 5.64: 35 5.64 - 7.52: 6 7.52 - 9.40: 5 Bond angle restraints: 12223 Sorted by residual: angle pdb=" C ILE B 172 " pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 121.97 127.75 -5.78 1.80e+00 3.09e-01 1.03e+01 angle pdb=" CB MET B 111 " pdb=" CG MET B 111 " pdb=" SD MET B 111 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" CA MET B 466 " pdb=" CB MET B 466 " pdb=" CG MET B 466 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.51e+00 angle pdb=" CB MET B 196 " pdb=" CG MET B 196 " pdb=" SD MET B 196 " ideal model delta sigma weight residual 112.70 121.56 -8.86 3.00e+00 1.11e-01 8.71e+00 angle pdb=" CA MET A 466 " pdb=" CB MET A 466 " pdb=" CG MET A 466 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.70e+00 ... (remaining 12218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4942 17.92 - 35.85: 458 35.85 - 53.77: 72 53.77 - 71.70: 17 71.70 - 89.62: 10 Dihedral angle restraints: 5499 sinusoidal: 2177 harmonic: 3322 Sorted by residual: dihedral pdb=" CA MET B 111 " pdb=" C MET B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta harmonic sigma weight residual -180.00 -153.69 -26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA MET A 466 " pdb=" C MET A 466 " pdb=" N ASP A 467 " pdb=" CA ASP A 467 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET B 466 " pdb=" C MET B 466 " pdb=" N ASP B 467 " pdb=" CA ASP B 467 " ideal model delta harmonic sigma weight residual -180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 921 0.033 - 0.066: 361 0.066 - 0.099: 119 0.099 - 0.132: 49 0.132 - 0.165: 4 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB ILE A 501 " pdb=" CA ILE A 501 " pdb=" CG1 ILE A 501 " pdb=" CG2 ILE A 501 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA TRP B 17 " pdb=" N TRP B 17 " pdb=" C TRP B 17 " pdb=" CB TRP B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA MET A 109 " pdb=" N MET A 109 " pdb=" C MET A 109 " pdb=" CB MET A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 1451 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 296 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO A 297 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 297 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 297 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 296 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO B 297 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 252 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 253 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.021 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1636 2.77 - 3.30: 9524 3.30 - 3.84: 14652 3.84 - 4.37: 15871 4.37 - 4.90: 27705 Nonbonded interactions: 69388 Sorted by model distance: nonbonded pdb=" OG SER B 46 " pdb=" OH TYR B 163 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 12 " pdb=" OE1 GLN B 316 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR B 351 " pdb=" OG1 THR B 384 " model vdw 2.242 3.040 nonbonded pdb=" O THR A 280 " pdb=" OG1 THR A 283 " model vdw 2.243 3.040 nonbonded pdb=" O ASN B 363 " pdb=" NH2 ARG B 559 " model vdw 2.267 3.120 ... (remaining 69383 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 496 or (resid 497 and (name N or name CA or name \ C or name O or name CB )) or resid 498 through 581)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.930 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9044 Z= 0.204 Angle : 0.626 9.395 12223 Z= 0.324 Chirality : 0.042 0.165 1454 Planarity : 0.004 0.042 1547 Dihedral : 14.363 89.619 3351 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.25), residues: 1146 helix: 2.06 (0.20), residues: 682 sheet: 1.07 (0.61), residues: 76 loop : -0.37 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 10 HIS 0.005 0.001 HIS A 214 PHE 0.017 0.002 PHE B 115 TYR 0.015 0.001 TYR B 439 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2384 time to fit residues: 33.2854 Evaluate side-chains 67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 326 GLN A 436 ASN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 GLN B 316 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.035256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.025264 restraints weight = 81511.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.026083 restraints weight = 51008.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.026634 restraints weight = 37962.768| |-----------------------------------------------------------------------------| r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9044 Z= 0.202 Angle : 0.608 9.465 12223 Z= 0.311 Chirality : 0.041 0.135 1454 Planarity : 0.004 0.041 1547 Dihedral : 3.895 18.833 1249 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.86 % Rotamer: Outliers : 1.13 % Allowed : 10.03 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1146 helix: 2.01 (0.20), residues: 728 sheet: 1.60 (0.59), residues: 70 loop : -0.41 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 10 HIS 0.005 0.001 HIS A 427 PHE 0.011 0.001 PHE A 462 TYR 0.011 0.001 TYR B 439 ARG 0.004 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9473 (tpp) cc_final: 0.9146 (mmp) REVERT: A 98 MET cc_start: 0.9124 (tpp) cc_final: 0.8667 (tpt) REVERT: A 160 MET cc_start: 0.9605 (mtm) cc_final: 0.9222 (mtp) REVERT: A 196 MET cc_start: 0.9375 (tpp) cc_final: 0.7958 (tpp) REVERT: A 200 MET cc_start: 0.9514 (tpp) cc_final: 0.9083 (mpp) REVERT: A 244 MET cc_start: 0.9448 (mtt) cc_final: 0.8740 (mmt) REVERT: A 276 MET cc_start: 0.8875 (ptm) cc_final: 0.8347 (ptt) REVERT: A 524 ASP cc_start: 0.9468 (t0) cc_final: 0.9222 (m-30) REVERT: B 98 MET cc_start: 0.9079 (ttm) cc_final: 0.8693 (tpt) REVERT: B 111 MET cc_start: 0.9422 (OUTLIER) cc_final: 0.8865 (tmm) REVERT: B 160 MET cc_start: 0.9534 (ttm) cc_final: 0.9325 (ttm) REVERT: B 196 MET cc_start: 0.9481 (tpt) cc_final: 0.8993 (tpp) REVERT: B 210 MET cc_start: 0.9260 (mmm) cc_final: 0.8994 (mmt) REVERT: B 244 MET cc_start: 0.9784 (ttm) cc_final: 0.9225 (ttt) outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 0.2058 time to fit residues: 23.1800 Evaluate side-chains 72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.035228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.025588 restraints weight = 82951.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.026405 restraints weight = 51880.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.026969 restraints weight = 38059.129| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9044 Z= 0.188 Angle : 0.561 9.138 12223 Z= 0.290 Chirality : 0.040 0.185 1454 Planarity : 0.003 0.039 1547 Dihedral : 3.727 17.404 1249 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 0.61 % Allowed : 14.02 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1146 helix: 2.04 (0.19), residues: 746 sheet: 1.58 (0.60), residues: 70 loop : -0.39 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 10 HIS 0.005 0.001 HIS A 427 PHE 0.011 0.001 PHE B 56 TYR 0.025 0.001 TYR A 572 ARG 0.003 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9545 (tpp) cc_final: 0.9056 (mmp) REVERT: A 98 MET cc_start: 0.8971 (tpp) cc_final: 0.8461 (tpt) REVERT: A 111 MET cc_start: 0.8722 (tmm) cc_final: 0.8297 (tmm) REVERT: A 160 MET cc_start: 0.9668 (mtm) cc_final: 0.9385 (mtt) REVERT: A 196 MET cc_start: 0.9494 (tpp) cc_final: 0.9187 (tpt) REVERT: A 276 MET cc_start: 0.8934 (ptm) cc_final: 0.8519 (ptm) REVERT: A 460 MET cc_start: 0.9264 (mmm) cc_final: 0.8801 (mmm) REVERT: B 98 MET cc_start: 0.9118 (ttm) cc_final: 0.8652 (tpp) REVERT: B 111 MET cc_start: 0.9247 (tmm) cc_final: 0.8809 (tmm) REVERT: B 196 MET cc_start: 0.9497 (tpt) cc_final: 0.9261 (tpt) REVERT: B 210 MET cc_start: 0.9273 (mmm) cc_final: 0.9001 (mmt) REVERT: B 244 MET cc_start: 0.9733 (ttm) cc_final: 0.9170 (ttt) REVERT: B 402 MET cc_start: 0.9164 (ppp) cc_final: 0.8835 (ppp) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2052 time to fit residues: 21.0266 Evaluate side-chains 69 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 390 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.035208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.025621 restraints weight = 82649.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.026455 restraints weight = 50119.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.027029 restraints weight = 36654.372| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9044 Z= 0.162 Angle : 0.548 8.849 12223 Z= 0.279 Chirality : 0.040 0.127 1454 Planarity : 0.003 0.037 1547 Dihedral : 3.641 14.542 1249 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 1.13 % Allowed : 16.79 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.26), residues: 1146 helix: 2.23 (0.19), residues: 730 sheet: 1.55 (0.60), residues: 70 loop : -0.27 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 10 HIS 0.005 0.001 HIS A 427 PHE 0.008 0.001 PHE B 56 TYR 0.016 0.001 TYR A 572 ARG 0.004 0.000 ARG B 569 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9596 (tpp) cc_final: 0.9075 (mmp) REVERT: A 98 MET cc_start: 0.8965 (tpp) cc_final: 0.8455 (tpt) REVERT: A 111 MET cc_start: 0.8819 (tmm) cc_final: 0.8550 (tmm) REVERT: A 160 MET cc_start: 0.9644 (mtm) cc_final: 0.9344 (mtt) REVERT: A 196 MET cc_start: 0.9529 (tpp) cc_final: 0.8769 (tpp) REVERT: A 200 MET cc_start: 0.9560 (tpp) cc_final: 0.9144 (mmm) REVERT: A 276 MET cc_start: 0.8933 (ptm) cc_final: 0.8502 (ptm) REVERT: B 98 MET cc_start: 0.9128 (ttm) cc_final: 0.8898 (ttm) REVERT: B 111 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8955 (tmm) REVERT: B 160 MET cc_start: 0.9588 (ttm) cc_final: 0.9260 (mmt) REVERT: B 196 MET cc_start: 0.9407 (tpt) cc_final: 0.8811 (tpt) REVERT: B 200 MET cc_start: 0.9483 (tpp) cc_final: 0.9080 (tpp) REVERT: B 244 MET cc_start: 0.9762 (ttm) cc_final: 0.8914 (ttt) REVERT: B 312 MET cc_start: 0.9284 (tpp) cc_final: 0.8627 (mmm) REVERT: B 402 MET cc_start: 0.9183 (ppp) cc_final: 0.8916 (ppp) REVERT: B 460 MET cc_start: 0.9057 (mmm) cc_final: 0.8783 (tpp) outliers start: 11 outliers final: 6 residues processed: 75 average time/residue: 0.1939 time to fit residues: 21.7546 Evaluate side-chains 72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.035060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.025535 restraints weight = 81759.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.026339 restraints weight = 51076.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.026882 restraints weight = 37912.837| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9044 Z= 0.157 Angle : 0.543 8.959 12223 Z= 0.275 Chirality : 0.040 0.141 1454 Planarity : 0.003 0.036 1547 Dihedral : 3.582 15.882 1249 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 1.13 % Allowed : 17.50 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.26), residues: 1146 helix: 2.37 (0.19), residues: 728 sheet: 1.43 (0.60), residues: 70 loop : -0.24 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 10 HIS 0.005 0.001 HIS A 427 PHE 0.009 0.001 PHE B 429 TYR 0.013 0.001 TYR A 572 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9554 (tpp) cc_final: 0.9101 (mmp) REVERT: A 98 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8539 (tpt) REVERT: A 111 MET cc_start: 0.8920 (tmm) cc_final: 0.8597 (tmm) REVERT: A 160 MET cc_start: 0.9655 (mtm) cc_final: 0.9432 (mtt) REVERT: A 196 MET cc_start: 0.9588 (tpp) cc_final: 0.9026 (tpp) REVERT: A 200 MET cc_start: 0.9537 (tpp) cc_final: 0.9150 (mmm) REVERT: A 276 MET cc_start: 0.8923 (ptm) cc_final: 0.8435 (ptm) REVERT: A 460 MET cc_start: 0.9183 (mmm) cc_final: 0.8840 (mmm) REVERT: B 98 MET cc_start: 0.9143 (ttm) cc_final: 0.8918 (ttm) REVERT: B 196 MET cc_start: 0.9440 (tpt) cc_final: 0.8053 (tpp) REVERT: B 200 MET cc_start: 0.9531 (tpp) cc_final: 0.8923 (mmm) REVERT: B 210 MET cc_start: 0.9262 (mmm) cc_final: 0.8792 (ttt) REVERT: B 244 MET cc_start: 0.9754 (ttm) cc_final: 0.8150 (ttt) REVERT: B 312 MET cc_start: 0.9345 (tpp) cc_final: 0.8604 (mmm) REVERT: B 402 MET cc_start: 0.9147 (ppp) cc_final: 0.8879 (ppp) REVERT: B 460 MET cc_start: 0.9043 (mmm) cc_final: 0.8808 (tpp) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.1935 time to fit residues: 20.7581 Evaluate side-chains 72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.033887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.024124 restraints weight = 82005.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.024876 restraints weight = 53104.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.025392 restraints weight = 40138.360| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9044 Z= 0.190 Angle : 0.554 9.379 12223 Z= 0.284 Chirality : 0.040 0.153 1454 Planarity : 0.003 0.039 1547 Dihedral : 3.606 15.088 1249 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.88 % Favored : 97.03 % Rotamer: Outliers : 1.54 % Allowed : 17.40 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.26), residues: 1146 helix: 2.29 (0.19), residues: 736 sheet: 1.42 (0.61), residues: 70 loop : -0.16 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 10 HIS 0.005 0.001 HIS A 427 PHE 0.011 0.001 PHE B 429 TYR 0.010 0.001 TYR A 572 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9580 (tpp) cc_final: 0.9131 (mmp) REVERT: A 98 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8577 (tpt) REVERT: A 196 MET cc_start: 0.9631 (tpp) cc_final: 0.9051 (tpp) REVERT: A 200 MET cc_start: 0.9547 (tpp) cc_final: 0.9071 (tpp) REVERT: A 276 MET cc_start: 0.8941 (ptm) cc_final: 0.8501 (ptm) REVERT: A 460 MET cc_start: 0.9217 (mmm) cc_final: 0.8907 (mmm) REVERT: B 98 MET cc_start: 0.9138 (ttm) cc_final: 0.8882 (ttm) REVERT: B 196 MET cc_start: 0.9457 (tpt) cc_final: 0.7990 (tpp) REVERT: B 200 MET cc_start: 0.9605 (tpp) cc_final: 0.8875 (mmm) REVERT: B 244 MET cc_start: 0.9798 (ttm) cc_final: 0.8281 (ttt) REVERT: B 312 MET cc_start: 0.9353 (tpp) cc_final: 0.8638 (mmm) REVERT: B 402 MET cc_start: 0.9216 (ppp) cc_final: 0.8688 (ppp) REVERT: B 456 MET cc_start: 0.9660 (ptp) cc_final: 0.9234 (ptp) REVERT: B 460 MET cc_start: 0.9081 (mmm) cc_final: 0.8877 (tpp) outliers start: 15 outliers final: 9 residues processed: 73 average time/residue: 0.1945 time to fit residues: 21.1407 Evaluate side-chains 71 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.034833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.024937 restraints weight = 81897.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.025725 restraints weight = 52515.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.026245 restraints weight = 39448.620| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9044 Z= 0.140 Angle : 0.567 9.723 12223 Z= 0.284 Chirality : 0.040 0.189 1454 Planarity : 0.003 0.040 1547 Dihedral : 3.587 14.666 1249 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.53 % Favored : 97.38 % Rotamer: Outliers : 1.02 % Allowed : 18.22 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1146 helix: 2.28 (0.19), residues: 742 sheet: 1.61 (0.62), residues: 70 loop : -0.33 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 10 HIS 0.003 0.001 HIS B 427 PHE 0.006 0.001 PHE B 220 TYR 0.010 0.001 TYR A 572 ARG 0.003 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9592 (tpp) cc_final: 0.9121 (mmp) REVERT: A 98 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8645 (tpt) REVERT: A 111 MET cc_start: 0.8836 (tmm) cc_final: 0.8407 (tmm) REVERT: A 196 MET cc_start: 0.9643 (tpp) cc_final: 0.9397 (tpp) REVERT: A 200 MET cc_start: 0.9531 (tpp) cc_final: 0.9299 (tpp) REVERT: A 276 MET cc_start: 0.8941 (ptm) cc_final: 0.8517 (ptm) REVERT: A 460 MET cc_start: 0.9196 (mmm) cc_final: 0.8872 (mmm) REVERT: B 98 MET cc_start: 0.9098 (ttm) cc_final: 0.8836 (ttm) REVERT: B 196 MET cc_start: 0.9475 (tpt) cc_final: 0.8097 (tpp) REVERT: B 200 MET cc_start: 0.9601 (tpp) cc_final: 0.8749 (mmm) REVERT: B 244 MET cc_start: 0.9809 (ttm) cc_final: 0.8373 (ttt) REVERT: B 312 MET cc_start: 0.9341 (tpp) cc_final: 0.8636 (mmm) REVERT: B 402 MET cc_start: 0.9202 (ppp) cc_final: 0.8678 (ppp) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.2118 time to fit residues: 24.6640 Evaluate side-chains 72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 543 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.033861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.024042 restraints weight = 84863.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.024818 restraints weight = 54275.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.025354 restraints weight = 40762.554| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9044 Z= 0.193 Angle : 0.609 10.698 12223 Z= 0.302 Chirality : 0.041 0.177 1454 Planarity : 0.003 0.042 1547 Dihedral : 3.650 14.913 1249 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.97 % Favored : 96.95 % Rotamer: Outliers : 1.33 % Allowed : 18.53 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.25), residues: 1146 helix: 2.15 (0.19), residues: 748 sheet: 1.50 (0.61), residues: 70 loop : -0.33 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 10 HIS 0.005 0.001 HIS A 214 PHE 0.009 0.001 PHE B 429 TYR 0.010 0.001 TYR A 572 ARG 0.004 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9602 (tpp) cc_final: 0.9177 (mmp) REVERT: A 98 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8608 (tpt) REVERT: A 111 MET cc_start: 0.8924 (tmm) cc_final: 0.8664 (tmm) REVERT: A 196 MET cc_start: 0.9653 (tpp) cc_final: 0.9399 (tpp) REVERT: A 200 MET cc_start: 0.9547 (tpp) cc_final: 0.9297 (tpp) REVERT: A 276 MET cc_start: 0.8913 (ptm) cc_final: 0.8495 (ptm) REVERT: A 402 MET cc_start: 0.9489 (ppp) cc_final: 0.9252 (ppp) REVERT: B 98 MET cc_start: 0.9139 (ttm) cc_final: 0.8800 (ttm) REVERT: B 196 MET cc_start: 0.9476 (tpt) cc_final: 0.8021 (tpp) REVERT: B 200 MET cc_start: 0.9630 (tpp) cc_final: 0.8716 (mmm) REVERT: B 244 MET cc_start: 0.9807 (ttm) cc_final: 0.8297 (ttt) REVERT: B 312 MET cc_start: 0.9378 (tpp) cc_final: 0.8651 (mmm) REVERT: B 402 MET cc_start: 0.9273 (ppp) cc_final: 0.8779 (ppp) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.2090 time to fit residues: 22.3575 Evaluate side-chains 73 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.033574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.023851 restraints weight = 83469.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.024598 restraints weight = 54110.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.025122 restraints weight = 40901.792| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9044 Z= 0.201 Angle : 0.646 12.176 12223 Z= 0.315 Chirality : 0.041 0.182 1454 Planarity : 0.003 0.039 1547 Dihedral : 3.715 15.012 1249 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.71 % Favored : 97.21 % Rotamer: Outliers : 1.74 % Allowed : 18.32 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1146 helix: 2.03 (0.19), residues: 756 sheet: 1.49 (0.61), residues: 70 loop : -0.41 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 10 HIS 0.005 0.001 HIS A 427 PHE 0.009 0.001 PHE B 220 TYR 0.009 0.001 TYR A 572 ARG 0.004 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9597 (tpp) cc_final: 0.9191 (mmp) REVERT: A 98 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8564 (tpt) REVERT: A 111 MET cc_start: 0.8966 (tmm) cc_final: 0.8685 (tmm) REVERT: A 196 MET cc_start: 0.9660 (tpp) cc_final: 0.9402 (tpp) REVERT: A 200 MET cc_start: 0.9535 (tpp) cc_final: 0.9281 (tpp) REVERT: A 223 GLN cc_start: 0.9416 (OUTLIER) cc_final: 0.9164 (mp10) REVERT: A 276 MET cc_start: 0.8887 (ptm) cc_final: 0.8444 (ptm) REVERT: A 402 MET cc_start: 0.9477 (ppp) cc_final: 0.9214 (ppp) REVERT: A 460 MET cc_start: 0.9218 (mmm) cc_final: 0.9011 (mmm) REVERT: B 98 MET cc_start: 0.9144 (ttm) cc_final: 0.8820 (ttm) REVERT: B 196 MET cc_start: 0.9481 (tpt) cc_final: 0.8021 (tpp) REVERT: B 200 MET cc_start: 0.9618 (tpp) cc_final: 0.8711 (mmm) REVERT: B 244 MET cc_start: 0.9798 (ttm) cc_final: 0.8238 (ttt) REVERT: B 257 LEU cc_start: 0.9846 (tp) cc_final: 0.9518 (pp) REVERT: B 312 MET cc_start: 0.9405 (tpp) cc_final: 0.8695 (mmm) REVERT: B 402 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8768 (ppp) outliers start: 17 outliers final: 10 residues processed: 76 average time/residue: 0.1969 time to fit residues: 22.1413 Evaluate side-chains 75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.4980 chunk 112 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 chunk 98 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.024829 restraints weight = 82311.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.025611 restraints weight = 53815.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.026148 restraints weight = 40845.486| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9044 Z= 0.150 Angle : 0.652 12.982 12223 Z= 0.312 Chirality : 0.041 0.192 1454 Planarity : 0.003 0.037 1547 Dihedral : 3.709 17.342 1249 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 0.92 % Allowed : 19.34 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1146 helix: 2.00 (0.19), residues: 756 sheet: 1.58 (0.61), residues: 70 loop : -0.41 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 10 HIS 0.003 0.000 HIS A 427 PHE 0.025 0.001 PHE B 115 TYR 0.008 0.001 TYR A 572 ARG 0.002 0.000 ARG A 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2292 Ramachandran restraints generated. 1146 Oldfield, 0 Emsley, 1146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9554 (tpp) cc_final: 0.9148 (mmp) REVERT: A 98 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8663 (tpp) REVERT: A 111 MET cc_start: 0.8929 (tmm) cc_final: 0.8650 (tmm) REVERT: A 196 MET cc_start: 0.9672 (tpp) cc_final: 0.9425 (tpp) REVERT: A 200 MET cc_start: 0.9526 (tpp) cc_final: 0.9291 (tpp) REVERT: A 257 LEU cc_start: 0.9875 (tt) cc_final: 0.9568 (pp) REVERT: A 276 MET cc_start: 0.8900 (ptm) cc_final: 0.8465 (ptm) REVERT: A 402 MET cc_start: 0.9463 (ppp) cc_final: 0.9200 (ppp) REVERT: A 460 MET cc_start: 0.9234 (mmm) cc_final: 0.9028 (mmm) REVERT: A 562 HIS cc_start: 0.9600 (t70) cc_final: 0.9372 (t70) REVERT: B 98 MET cc_start: 0.9046 (ttm) cc_final: 0.8744 (ttm) REVERT: B 196 MET cc_start: 0.9475 (tpt) cc_final: 0.8077 (tpp) REVERT: B 200 MET cc_start: 0.9621 (tpp) cc_final: 0.8765 (mmm) REVERT: B 244 MET cc_start: 0.9804 (ttm) cc_final: 0.8392 (ttt) REVERT: B 257 LEU cc_start: 0.9848 (tp) cc_final: 0.9518 (pp) REVERT: B 312 MET cc_start: 0.9370 (tpp) cc_final: 0.8645 (mmm) REVERT: B 402 MET cc_start: 0.9286 (ppp) cc_final: 0.8783 (ppp) REVERT: B 460 MET cc_start: 0.9031 (mmm) cc_final: 0.8826 (mmm) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.1882 time to fit residues: 21.9951 Evaluate side-chains 75 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.0000 chunk 106 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 50 optimal weight: 8.9990 overall best weight: 0.7066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.034764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.024864 restraints weight = 82515.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.025654 restraints weight = 53820.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.026205 restraints weight = 40737.583| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9044 Z= 0.153 Angle : 0.646 12.454 12223 Z= 0.311 Chirality : 0.041 0.203 1454 Planarity : 0.003 0.038 1547 Dihedral : 3.644 15.772 1249 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.62 % Favored : 97.29 % Rotamer: Outliers : 1.02 % Allowed : 19.86 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1146 helix: 1.99 (0.19), residues: 756 sheet: 1.61 (0.61), residues: 70 loop : -0.38 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 10 HIS 0.003 0.001 HIS A 427 PHE 0.019 0.001 PHE B 115 TYR 0.007 0.001 TYR A 572 ARG 0.003 0.000 ARG B 455 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2539.97 seconds wall clock time: 46 minutes 27.48 seconds (2787.48 seconds total)