Starting phenix.real_space_refine on Wed Sep 17 14:25:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqg_60791/09_2025/9iqg_60791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqg_60791/09_2025/9iqg_60791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iqg_60791/09_2025/9iqg_60791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqg_60791/09_2025/9iqg_60791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iqg_60791/09_2025/9iqg_60791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqg_60791/09_2025/9iqg_60791.map" } resolution = 2.7 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= 0.001 sd= 0.113 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 5 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 5778 2.51 5 N 1612 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 9137 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4357 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 19, 'TRANS': 555} Chain: "B" Number of atoms: 4715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4715 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 18, 'TRANS': 597} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 9137 At special positions: 0 Unit cell: (71.552, 86.528, 151.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 33 16.00 P 5 15.00 Mg 2 11.99 O 1706 8.00 N 1612 7.00 C 5778 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: 1.03 Conformation dependent library (CDL) restraints added in 395.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 71.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid -1 through 10 Processing helix chain 'A' and resid 13 through 45 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 50 through 99 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.871A pdb=" N ASP A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 Processing helix chain 'A' and resid 157 through 203 removed outlier: 4.313A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 166 - end of helix Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 212 through 239 Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.739A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.929A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 313 removed outlier: 3.710A pdb=" N ARG A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 382 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.506A pdb=" N GLY A 396 " --> pdb=" O ARG A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 425 through 431 removed outlier: 3.630A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.581A pdb=" N VAL A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.644A pdb=" N ARG A 488 " --> pdb=" O ARG A 484 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.626A pdb=" N VAL A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 560 removed outlier: 3.583A pdb=" N ALA A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 16 through 29 Processing helix chain 'B' and resid 34 through 71 removed outlier: 3.719A pdb=" N GLY B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Proline residue: B 53 - end of helix removed outlier: 3.982A pdb=" N GLU B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.864A pdb=" N ASP B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 160 Processing helix chain 'B' and resid 161 through 167 removed outlier: 3.956A pdb=" N PHE B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 178 through 213 removed outlier: 5.833A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLN B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.662A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 271 through 299 Processing helix chain 'B' and resid 299 through 326 Processing helix chain 'B' and resid 329 through 353 Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.550A pdb=" N VAL B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 481 through 487 Processing helix chain 'B' and resid 493 through 504 Processing helix chain 'B' and resid 505 through 511 removed outlier: 4.130A pdb=" N PHE B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.580A pdb=" N ALA B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 removed outlier: 3.656A pdb=" N LEU B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 572 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 616 through 628 removed outlier: 3.689A pdb=" N TRP B 620 " --> pdb=" O HIS B 616 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS B 626 " --> pdb=" O MET B 622 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 627 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 354 removed outlier: 5.464A pdb=" N GLN A 352 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 341 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP A 338 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER A 391 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414 removed outlier: 6.163A pdb=" N TYR A 493 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL A 526 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE A 495 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 363 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 540 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 365 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 542 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 367 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AA4, first strand: chain 'B' and resid 407 through 414 removed outlier: 6.385A pdb=" N GLU B 408 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER B 397 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU B 410 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 393 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR B 449 " --> pdb=" O PHE B 393 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N HIS B 395 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ARG B 447 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 467 through 470 removed outlier: 6.787A pdb=" N LEU B 549 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ILE B 582 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 551 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 421 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET B 598 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 423 " --> pdb=" O MET B 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 479 through 480 644 hydrogen bonds defined for protein. 1905 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: 1.50 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3109 1.36 - 1.50: 2250 1.50 - 1.63: 3868 1.63 - 1.77: 0 1.77 - 1.91: 65 Bond restraints: 9292 Sorted by residual: bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C5 ADP B 701 " pdb=" C6 ADP B 701 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C8 ADP B 701 " pdb=" N7 ADP B 701 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C5 ADP B 701 " pdb=" N7 ADP B 701 " ideal model delta sigma weight residual 1.350 1.388 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C4 ADP B 701 " pdb=" N9 ADP B 701 " ideal model delta sigma weight residual 1.337 1.374 -0.037 2.00e-02 2.50e+03 3.47e+00 ... (remaining 9287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12513 2.03 - 4.06: 113 4.06 - 6.08: 27 6.08 - 8.11: 6 8.11 - 10.14: 3 Bond angle restraints: 12662 Sorted by residual: angle pdb=" PA ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " ideal model delta sigma weight residual 120.50 130.64 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N1 ADP B 701 " pdb=" C2 ADP B 701 " pdb=" N3 ADP B 701 " ideal model delta sigma weight residual 120.00 129.34 -9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" C2 ADP B 701 " pdb=" N3 ADP B 701 " pdb=" C4 ADP B 701 " ideal model delta sigma weight residual 120.00 110.94 9.06 3.00e+00 1.11e-01 9.12e+00 angle pdb=" CG ARG B 624 " pdb=" CD ARG B 624 " pdb=" NE ARG B 624 " ideal model delta sigma weight residual 112.00 118.17 -6.17 2.20e+00 2.07e-01 7.86e+00 angle pdb=" O1B ADP B 701 " pdb=" PB ADP B 701 " pdb=" O3B ADP B 701 " ideal model delta sigma weight residual 119.90 112.12 7.78 3.00e+00 1.11e-01 6.72e+00 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 5237 28.59 - 57.18: 259 57.18 - 85.77: 31 85.77 - 114.36: 2 114.36 - 142.95: 2 Dihedral angle restraints: 5531 sinusoidal: 2128 harmonic: 3403 Sorted by residual: dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 82.95 -142.95 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 70.20 -130.20 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" CA ILE A 404 " pdb=" C ILE A 404 " pdb=" N GLU A 405 " pdb=" CA GLU A 405 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1077 0.039 - 0.078: 335 0.078 - 0.117: 93 0.117 - 0.155: 15 0.155 - 0.194: 2 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CB ILE A 330 " pdb=" CA ILE A 330 " pdb=" CG1 ILE A 330 " pdb=" CG2 ILE A 330 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA ASP B 591 " pdb=" N ASP B 591 " pdb=" C ASP B 591 " pdb=" CB ASP B 591 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1519 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 52 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 53 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 424 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO B 425 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 425 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 425 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 386 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C VAL B 386 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL B 386 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG B 387 " 0.008 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 47 2.51 - 3.11: 6813 3.11 - 3.71: 14912 3.71 - 4.30: 21109 4.30 - 4.90: 35493 Nonbonded interactions: 78374 Sorted by model distance: nonbonded pdb=" OE1 GLN A 416 " pdb="MG MG A 602 " model vdw 1.913 2.170 nonbonded pdb=" OG1 THR B 431 " pdb="MG MG B 703 " model vdw 1.932 2.170 nonbonded pdb=" OG SER A 375 " pdb="MG MG A 602 " model vdw 1.936 2.170 nonbonded pdb=" O4 VO4 B 702 " pdb="MG MG B 703 " model vdw 1.952 2.170 nonbonded pdb=" OE1 GLN B 472 " pdb="MG MG B 703 " model vdw 2.014 2.170 ... (remaining 78369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.240 Find NCS groups from input model: 0.070 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.004 0.110 9292 Z= 0.171 Angle : 0.562 10.140 12662 Z= 0.288 Chirality : 0.041 0.194 1522 Planarity : 0.004 0.052 1616 Dihedral : 16.544 142.954 3341 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 1.99 % Allowed : 17.28 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.07 (0.24), residues: 1187 helix: 2.23 (0.18), residues: 802 sheet: 0.73 (0.71), residues: 48 loop : -0.65 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 624 TYR 0.013 0.001 TYR B 400 PHE 0.015 0.001 PHE B 509 TRP 0.010 0.001 TRP B 246 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9292) covalent geometry : angle 0.56186 (12662) hydrogen bonds : bond 0.11506 ( 644) hydrogen bonds : angle 4.83304 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.366 Fit side-chains REVERT: A 48 LYS cc_start: 0.8507 (mttp) cc_final: 0.8197 (mttp) REVERT: A 290 MET cc_start: 0.7690 (ttm) cc_final: 0.7411 (ttp) REVERT: A 333 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7237 (p0) REVERT: A 352 GLN cc_start: 0.7901 (mt0) cc_final: 0.7597 (mt0) REVERT: A 391 SER cc_start: 0.8389 (p) cc_final: 0.8080 (p) REVERT: A 437 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7253 (p) REVERT: A 515 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6710 (mtm-85) REVERT: B 79 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: B 115 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7651 (mtm-85) REVERT: B 273 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7556 (mp0) REVERT: B 327 GLN cc_start: 0.8162 (mt0) cc_final: 0.7780 (mt0) REVERT: B 358 GLN cc_start: 0.8294 (tp40) cc_final: 0.7827 (tm-30) REVERT: B 621 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7236 (mt-10) outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 0.6333 time to fit residues: 91.4618 Evaluate side-chains 135 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 294 GLN B 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129186 restraints weight = 10589.364| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.78 r_work: 0.3380 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9292 Z= 0.137 Angle : 0.537 10.264 12662 Z= 0.278 Chirality : 0.041 0.145 1522 Planarity : 0.004 0.052 1616 Dihedral : 8.758 137.598 1369 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.27 % Favored : 97.56 % Rotamer: Outliers : 3.87 % Allowed : 15.08 % Favored : 81.05 % 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: 2.14 (0.24), residues: 1187 helix: 2.30 (0.18), residues: 810 sheet: 0.55 (0.71), residues: 48 loop : -0.73 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 624 TYR 0.011 0.001 TYR B 400 PHE 0.015 0.001 PHE B 509 TRP 0.006 0.001 TRP B 246 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9292) covalent geometry : angle 0.53659 (12662) hydrogen bonds : bond 0.04991 ( 644) hydrogen bonds : angle 4.07511 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.415 Fit side-chains REVERT: A 48 LYS cc_start: 0.8558 (mttp) cc_final: 0.8244 (mttp) REVERT: A 215 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8265 (mt) REVERT: A 290 MET cc_start: 0.7606 (ttm) cc_final: 0.7381 (ttp) REVERT: A 293 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 394 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7662 (tt) REVERT: A 515 ARG cc_start: 0.7386 (ttm110) cc_final: 0.6901 (mtm-85) REVERT: B 115 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7661 (mtt180) REVERT: B 273 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7628 (mp0) REVERT: B 327 GLN cc_start: 0.8127 (mt0) cc_final: 0.7762 (mt0) REVERT: B 358 GLN cc_start: 0.8177 (tp40) cc_final: 0.7769 (tm-30) REVERT: B 458 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7439 (m) REVERT: B 494 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: B 495 ASP cc_start: 0.7417 (m-30) cc_final: 0.6892 (t0) outliers start: 37 outliers final: 13 residues processed: 154 average time/residue: 0.6772 time to fit residues: 110.7775 Evaluate side-chains 135 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123712 restraints weight = 10412.080| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.76 r_work: 0.3346 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9292 Z= 0.168 Angle : 0.545 8.308 12662 Z= 0.284 Chirality : 0.042 0.147 1522 Planarity : 0.004 0.052 1616 Dihedral : 8.480 140.572 1359 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 4.19 % Allowed : 14.66 % Favored : 81.15 % 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: 1.97 (0.24), residues: 1187 helix: 2.20 (0.17), residues: 807 sheet: 0.39 (0.70), residues: 48 loop : -0.82 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 624 TYR 0.013 0.002 TYR B 400 PHE 0.018 0.002 PHE B 509 TRP 0.005 0.001 TRP B 132 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9292) covalent geometry : angle 0.54542 (12662) hydrogen bonds : bond 0.05235 ( 644) hydrogen bonds : angle 4.04759 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.382 Fit side-chains REVERT: A 215 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 290 MET cc_start: 0.7623 (ttm) cc_final: 0.7396 (ttp) REVERT: A 293 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 394 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7730 (tt) REVERT: A 511 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7574 (mtm-85) REVERT: A 515 ARG cc_start: 0.7380 (ttm110) cc_final: 0.6900 (mtm-85) REVERT: B 79 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: B 115 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7800 (mtm-85) REVERT: B 232 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7183 (ttm170) REVERT: B 327 GLN cc_start: 0.8135 (mt0) cc_final: 0.7788 (mt0) REVERT: B 358 GLN cc_start: 0.8180 (tp40) cc_final: 0.7832 (tm-30) REVERT: B 458 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (m) REVERT: B 563 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6849 (tm-30) outliers start: 40 outliers final: 18 residues processed: 150 average time/residue: 0.7344 time to fit residues: 116.8249 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 94 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 186 ASN B 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122876 restraints weight = 10661.590| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.82 r_work: 0.3264 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9292 Z= 0.125 Angle : 0.508 7.581 12662 Z= 0.265 Chirality : 0.040 0.146 1522 Planarity : 0.004 0.051 1616 Dihedral : 8.122 137.567 1359 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 3.46 % Allowed : 15.50 % Favored : 81.05 % 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: 2.11 (0.24), residues: 1187 helix: 2.33 (0.17), residues: 807 sheet: 0.32 (0.69), residues: 48 loop : -0.84 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 624 TYR 0.011 0.001 TYR B 400 PHE 0.013 0.001 PHE B 509 TRP 0.005 0.001 TRP B 620 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9292) covalent geometry : angle 0.50824 (12662) hydrogen bonds : bond 0.04725 ( 644) hydrogen bonds : angle 3.91938 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.368 Fit side-chains REVERT: A 48 LYS cc_start: 0.8483 (mttp) cc_final: 0.8180 (mttp) REVERT: A 215 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 286 MET cc_start: 0.7254 (tmt) cc_final: 0.6952 (tmt) REVERT: A 293 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6686 (t80) REVERT: A 511 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7469 (mtm-85) REVERT: A 515 ARG cc_start: 0.7404 (ttm110) cc_final: 0.6876 (mtm-85) REVERT: B 115 ARG cc_start: 0.8025 (mtp180) cc_final: 0.7695 (mtm-85) REVERT: B 185 GLN cc_start: 0.8282 (tt0) cc_final: 0.8061 (tp40) REVERT: B 232 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7135 (ttm170) REVERT: B 237 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7050 (ttm-80) REVERT: B 273 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7625 (mp0) REVERT: B 327 GLN cc_start: 0.8141 (mt0) cc_final: 0.7762 (mt0) REVERT: B 358 GLN cc_start: 0.8171 (tp40) cc_final: 0.7761 (tm-30) REVERT: B 458 VAL cc_start: 0.7701 (OUTLIER) cc_final: 0.7497 (m) REVERT: B 495 ASP cc_start: 0.7502 (m-30) cc_final: 0.6935 (t0) REVERT: B 563 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6694 (tm-30) outliers start: 33 outliers final: 17 residues processed: 149 average time/residue: 0.7385 time to fit residues: 116.4239 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122869 restraints weight = 10710.663| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.82 r_work: 0.3259 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9292 Z= 0.129 Angle : 0.510 7.600 12662 Z= 0.265 Chirality : 0.040 0.146 1522 Planarity : 0.004 0.052 1616 Dihedral : 7.861 135.316 1357 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.98 % Allowed : 15.08 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.12 (0.24), residues: 1187 helix: 2.34 (0.17), residues: 808 sheet: 0.29 (0.70), residues: 48 loop : -0.85 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 624 TYR 0.012 0.001 TYR B 400 PHE 0.015 0.001 PHE B 509 TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9292) covalent geometry : angle 0.50988 (12662) hydrogen bonds : bond 0.04703 ( 644) hydrogen bonds : angle 3.88269 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.381 Fit side-chains REVERT: A 215 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8252 (mt) REVERT: A 293 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6702 (t80) REVERT: A 393 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6526 (mtt90) REVERT: A 511 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7485 (mtm-85) REVERT: A 515 ARG cc_start: 0.7402 (ttm110) cc_final: 0.6871 (mtm-85) REVERT: B 79 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 115 ARG cc_start: 0.8044 (mtp180) cc_final: 0.7719 (mtm-85) REVERT: B 185 GLN cc_start: 0.8293 (tt0) cc_final: 0.8054 (tp40) REVERT: B 232 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7146 (ttm170) REVERT: B 237 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7055 (ttm-80) REVERT: B 273 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7652 (mp0) REVERT: B 327 GLN cc_start: 0.8161 (mt0) cc_final: 0.7785 (mt0) REVERT: B 358 GLN cc_start: 0.8181 (tp40) cc_final: 0.7748 (tm-30) REVERT: B 495 ASP cc_start: 0.7493 (m-30) cc_final: 0.6897 (t0) REVERT: B 563 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6662 (tm-30) outliers start: 38 outliers final: 18 residues processed: 149 average time/residue: 0.7277 time to fit residues: 114.8711 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 13 optimal weight: 0.0970 chunk 114 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123245 restraints weight = 10661.214| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.82 r_work: 0.3268 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9292 Z= 0.125 Angle : 0.503 7.487 12662 Z= 0.262 Chirality : 0.040 0.145 1522 Planarity : 0.004 0.057 1616 Dihedral : 7.666 131.818 1356 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Rotamer: Outliers : 3.35 % Allowed : 15.92 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.18 (0.24), residues: 1187 helix: 2.39 (0.17), residues: 806 sheet: 0.36 (0.71), residues: 48 loop : -0.83 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 545 TYR 0.012 0.001 TYR B 400 PHE 0.014 0.001 PHE B 509 TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9292) covalent geometry : angle 0.50328 (12662) hydrogen bonds : bond 0.04615 ( 644) hydrogen bonds : angle 3.85330 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8406 (mttp) cc_final: 0.8141 (mttp) REVERT: A 215 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8244 (mt) REVERT: A 293 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6711 (t80) REVERT: A 393 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6540 (mtt90) REVERT: A 511 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7355 (mtm-85) REVERT: A 515 ARG cc_start: 0.7409 (ttm110) cc_final: 0.6855 (mtm-85) REVERT: B 79 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: B 115 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7708 (mtm-85) REVERT: B 232 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7130 (ttm170) REVERT: B 273 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7643 (mp0) REVERT: B 327 GLN cc_start: 0.8145 (mt0) cc_final: 0.7786 (mt0) REVERT: B 358 GLN cc_start: 0.8193 (tp40) cc_final: 0.7758 (tm-30) REVERT: B 495 ASP cc_start: 0.7476 (m-30) cc_final: 0.6863 (t0) outliers start: 32 outliers final: 17 residues processed: 148 average time/residue: 0.6977 time to fit residues: 109.7915 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.150726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120130 restraints weight = 10709.900| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.82 r_work: 0.3222 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9292 Z= 0.172 Angle : 0.546 8.059 12662 Z= 0.285 Chirality : 0.042 0.156 1522 Planarity : 0.004 0.053 1616 Dihedral : 7.793 134.426 1355 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.46 % Allowed : 16.13 % Favored : 80.42 % 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 (0.24), residues: 1187 helix: 2.15 (0.17), residues: 808 sheet: 0.35 (0.72), residues: 48 loop : -0.83 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 545 TYR 0.015 0.002 TYR A 9 PHE 0.019 0.002 PHE B 509 TRP 0.005 0.001 TRP B 132 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9292) covalent geometry : angle 0.54587 (12662) hydrogen bonds : bond 0.05220 ( 644) hydrogen bonds : angle 3.98045 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 293 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6736 (t80) REVERT: A 393 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6590 (mtt90) REVERT: A 511 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7425 (mtm-85) REVERT: B 79 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: B 115 ARG cc_start: 0.8106 (mtp180) cc_final: 0.7847 (mtm-85) REVERT: B 154 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: B 232 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7126 (ttm170) REVERT: B 273 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7673 (mp0) REVERT: B 327 GLN cc_start: 0.8189 (mt0) cc_final: 0.7841 (mt0) REVERT: B 408 GLU cc_start: 0.8140 (pm20) cc_final: 0.7909 (pm20) REVERT: B 563 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6624 (tm-30) outliers start: 33 outliers final: 17 residues processed: 147 average time/residue: 0.7004 time to fit residues: 109.5381 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122719 restraints weight = 10529.679| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.80 r_work: 0.3265 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9292 Z= 0.132 Angle : 0.517 7.558 12662 Z= 0.269 Chirality : 0.040 0.138 1522 Planarity : 0.004 0.051 1616 Dihedral : 7.651 131.497 1355 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 2.93 % Allowed : 17.17 % Favored : 79.90 % 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: 2.02 (0.24), residues: 1187 helix: 2.26 (0.18), residues: 807 sheet: 0.33 (0.73), residues: 48 loop : -0.87 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 545 TYR 0.012 0.001 TYR B 400 PHE 0.016 0.001 PHE B 509 TRP 0.005 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9292) covalent geometry : angle 0.51695 (12662) hydrogen bonds : bond 0.04778 ( 644) hydrogen bonds : angle 3.89788 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.363 Fit side-chains REVERT: A 48 LYS cc_start: 0.8452 (mttp) cc_final: 0.8181 (mttp) REVERT: A 215 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8229 (mt) REVERT: A 293 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 393 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6553 (mtt90) REVERT: A 511 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7312 (mtm-85) REVERT: A 515 ARG cc_start: 0.7428 (ttm110) cc_final: 0.6860 (mtm-85) REVERT: B 79 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: B 115 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7772 (mtm-85) REVERT: B 185 GLN cc_start: 0.8293 (tt0) cc_final: 0.8075 (tp40) REVERT: B 232 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7144 (ttm170) REVERT: B 273 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7590 (mp0) REVERT: B 327 GLN cc_start: 0.8133 (mt0) cc_final: 0.7744 (mt0) REVERT: B 408 GLU cc_start: 0.8143 (pm20) cc_final: 0.7905 (pm20) REVERT: B 447 ARG cc_start: 0.8064 (ptt-90) cc_final: 0.7863 (ptt-90) REVERT: B 495 ASP cc_start: 0.7446 (m-30) cc_final: 0.6915 (t0) REVERT: B 563 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6554 (tm-30) outliers start: 28 outliers final: 17 residues processed: 145 average time/residue: 0.7394 time to fit residues: 113.6234 Evaluate side-chains 142 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124232 restraints weight = 10370.335| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.68 r_work: 0.3337 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9292 Z= 0.119 Angle : 0.511 7.241 12662 Z= 0.264 Chirality : 0.039 0.135 1522 Planarity : 0.004 0.071 1616 Dihedral : 7.418 121.229 1355 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 3.04 % Allowed : 17.17 % Favored : 79.79 % 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: 2.15 (0.24), residues: 1187 helix: 2.37 (0.18), residues: 807 sheet: 0.31 (0.72), residues: 48 loop : -0.85 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 545 TYR 0.012 0.001 TYR B 400 PHE 0.015 0.001 PHE B 509 TRP 0.005 0.001 TRP B 233 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9292) covalent geometry : angle 0.51149 (12662) hydrogen bonds : bond 0.04481 ( 644) hydrogen bonds : angle 3.82264 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.372 Fit side-chains REVERT: A 48 LYS cc_start: 0.8323 (mttp) cc_final: 0.8033 (mttp) REVERT: A 215 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8102 (mt) REVERT: A 293 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 393 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6467 (mtt90) REVERT: A 511 ARG cc_start: 0.7560 (mtp180) cc_final: 0.7111 (mtm-85) REVERT: A 515 ARG cc_start: 0.7318 (ttm110) cc_final: 0.6756 (mtm-85) REVERT: B 79 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 115 ARG cc_start: 0.7804 (mtp180) cc_final: 0.7435 (mtm-85) REVERT: B 194 GLN cc_start: 0.7599 (mp10) cc_final: 0.6696 (mp10) REVERT: B 232 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6976 (ttm170) REVERT: B 273 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7371 (mp0) REVERT: B 327 GLN cc_start: 0.8082 (mt0) cc_final: 0.7652 (mt0) REVERT: B 495 ASP cc_start: 0.7328 (m-30) cc_final: 0.6755 (t0) REVERT: B 545 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7433 (ptp-110) REVERT: B 563 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6487 (tm-30) outliers start: 29 outliers final: 17 residues processed: 147 average time/residue: 0.6878 time to fit residues: 107.5685 Evaluate side-chains 143 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 12 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.156846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126886 restraints weight = 10566.382| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.65 r_work: 0.3326 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9292 Z= 0.121 Angle : 0.515 7.168 12662 Z= 0.266 Chirality : 0.040 0.135 1522 Planarity : 0.004 0.061 1616 Dihedral : 7.235 112.652 1355 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.78 % Favored : 97.05 % Rotamer: Outliers : 2.62 % Allowed : 17.80 % Favored : 79.58 % 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: 2.17 (0.24), residues: 1187 helix: 2.40 (0.18), residues: 807 sheet: 0.32 (0.72), residues: 48 loop : -0.87 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 545 TYR 0.011 0.001 TYR B 400 PHE 0.015 0.001 PHE B 509 TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9292) covalent geometry : angle 0.51470 (12662) hydrogen bonds : bond 0.04492 ( 644) hydrogen bonds : angle 3.81017 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.349 Fit side-chains REVERT: A 215 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 293 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6491 (t80) REVERT: A 393 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6471 (mtt90) REVERT: A 511 ARG cc_start: 0.7527 (mtp180) cc_final: 0.7056 (mtm-85) REVERT: A 515 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6758 (mtm-85) REVERT: B 79 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: B 115 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7405 (mtm-85) REVERT: B 194 GLN cc_start: 0.7552 (mp10) cc_final: 0.6639 (mp10) REVERT: B 232 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6978 (ttm170) REVERT: B 237 ARG cc_start: 0.7610 (mtt180) cc_final: 0.6915 (ttm-80) REVERT: B 273 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7374 (mp0) REVERT: B 327 GLN cc_start: 0.8076 (mt0) cc_final: 0.7643 (mt0) REVERT: B 495 ASP cc_start: 0.7359 (m-30) cc_final: 0.6766 (t0) REVERT: B 511 HIS cc_start: 0.6739 (m-70) cc_final: 0.6512 (m-70) REVERT: B 545 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7321 (ptp-110) REVERT: B 563 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: B 624 ARG cc_start: 0.6841 (mmp80) cc_final: 0.6435 (mmp80) outliers start: 25 outliers final: 15 residues processed: 143 average time/residue: 0.6947 time to fit residues: 105.7328 Evaluate side-chains 140 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 563 GLU Chi-restraints excluded: chain B residue 587 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 108 optimal weight: 0.0070 chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.126540 restraints weight = 10531.964| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.65 r_work: 0.3322 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9292 Z= 0.126 Angle : 0.522 7.161 12662 Z= 0.270 Chirality : 0.040 0.134 1522 Planarity : 0.004 0.060 1616 Dihedral : 6.896 105.375 1351 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.70 % Favored : 97.14 % Rotamer: Outliers : 2.41 % Allowed : 18.22 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.13 (0.24), residues: 1187 helix: 2.38 (0.18), residues: 806 sheet: 0.28 (0.72), residues: 48 loop : -0.92 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 545 TYR 0.011 0.001 TYR B 400 PHE 0.014 0.001 PHE B 509 TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9292) covalent geometry : angle 0.52226 (12662) hydrogen bonds : bond 0.04557 ( 644) hydrogen bonds : angle 3.81359 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3774.91 seconds wall clock time: 65 minutes 7.68 seconds (3907.68 seconds total)