Starting phenix.real_space_refine on Sun Jun 8 00:13:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqg_60791/06_2025/9iqg_60791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqg_60791/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9iqg_60791/06_2025/9iqg_60791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqg_60791/06_2025/9iqg_60791.map" model { file = "/net/cci-nas-00/data/ceres_data/9iqg_60791/06_2025/9iqg_60791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqg_60791/06_2025/9iqg_60791.cif" } resolution = 2.7 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= 0.113 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.87, per 1000 atoms: 0.64 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: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.02 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: 2.84 Time building geometry restraints manager: 3.27 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.240 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- 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 (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: 2.07 (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 TRP 0.010 0.001 TRP B 246 HIS 0.006 0.001 HIS A 88 PHE 0.015 0.001 PHE B 509 TYR 0.013 0.001 TYR B 400 ARG 0.009 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.11506 ( 644) hydrogen bonds : angle 4.83304 ( 1905) covalent geometry : bond 0.00365 ( 9292) covalent geometry : angle 0.56186 (12662) *********************** 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 : 1.160 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: 1.5108 time to fit residues: 218.9792 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 : 0.933 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.155549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126107 restraints weight = 10365.600| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.78 r_work: 0.3376 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0589 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= 0.132 Angle : 0.534 10.267 12662 Z= 0.277 Chirality : 0.040 0.148 1522 Planarity : 0.004 0.052 1616 Dihedral : 8.745 137.318 1369 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.36 % Favored : 97.47 % Rotamer: Outliers : 3.87 % Allowed : 14.87 % Favored : 81.26 % 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 (0.24), residues: 1187 helix: 2.33 (0.18), residues: 810 sheet: 0.52 (0.70), residues: 48 loop : -0.72 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 246 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE B 509 TYR 0.011 0.001 TYR B 400 ARG 0.008 0.000 ARG B 624 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 644) hydrogen bonds : angle 4.07630 ( 1905) covalent geometry : bond 0.00278 ( 9292) covalent geometry : angle 0.53392 (12662) *********************** 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 169 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.170 Fit side-chains REVERT: A 48 LYS cc_start: 0.8638 (mttp) cc_final: 0.8332 (mttp) REVERT: A 215 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8323 (mt) REVERT: A 290 MET cc_start: 0.7653 (ttm) cc_final: 0.7441 (ttp) REVERT: A 293 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 394 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 515 ARG cc_start: 0.7434 (ttm110) cc_final: 0.6962 (mtm-85) REVERT: B 115 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7758 (mtt180) REVERT: B 273 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7759 (mp0) REVERT: B 327 GLN cc_start: 0.8149 (mt0) cc_final: 0.7799 (mt0) REVERT: B 358 GLN cc_start: 0.8198 (tp40) cc_final: 0.7862 (tm-30) REVERT: B 458 VAL cc_start: 0.7734 (OUTLIER) cc_final: 0.7474 (m) REVERT: B 495 ASP cc_start: 0.7458 (m-30) cc_final: 0.6955 (t0) outliers start: 37 outliers final: 13 residues processed: 157 average time/residue: 1.5520 time to fit residues: 261.4572 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.156187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126943 restraints weight = 10568.241| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.79 r_work: 0.3369 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9292 Z= 0.140 Angle : 0.522 7.922 12662 Z= 0.271 Chirality : 0.040 0.140 1522 Planarity : 0.004 0.052 1616 Dihedral : 8.357 136.345 1359 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Rotamer: Outliers : 3.56 % Allowed : 15.18 % Favored : 81.26 % 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: 2.14 (0.24), residues: 1187 helix: 2.33 (0.17), residues: 808 sheet: 0.39 (0.70), residues: 48 loop : -0.76 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.015 0.001 PHE B 509 TYR 0.012 0.001 TYR B 400 ARG 0.015 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04872 ( 644) hydrogen bonds : angle 3.98116 ( 1905) covalent geometry : bond 0.00306 ( 9292) covalent geometry : angle 0.52209 (12662) *********************** 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 159 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.040 Fit side-chains REVERT: A 48 LYS cc_start: 0.8603 (mttp) cc_final: 0.8297 (mttp) REVERT: A 215 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 290 MET cc_start: 0.7620 (ttm) cc_final: 0.7406 (ttp) REVERT: A 293 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6678 (t80) REVERT: A 394 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 515 ARG cc_start: 0.7445 (ttm110) cc_final: 0.6976 (mtm-85) REVERT: B 79 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 115 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7843 (mtm-85) REVERT: B 232 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7215 (ttm170) REVERT: B 327 GLN cc_start: 0.8106 (mt0) cc_final: 0.7766 (mt0) REVERT: B 358 GLN cc_start: 0.8201 (tp40) cc_final: 0.7864 (tm-30) REVERT: B 458 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7523 (m) REVERT: B 495 ASP cc_start: 0.7480 (m-30) cc_final: 0.6965 (t0) REVERT: B 545 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7540 (ptt180) outliers start: 34 outliers final: 16 residues processed: 144 average time/residue: 1.3056 time to fit residues: 199.9987 Evaluate side-chains 136 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 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 587 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 18 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.157061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127780 restraints weight = 10359.994| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.79 r_work: 0.3386 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0932 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= 0.127 Angle : 0.505 7.576 12662 Z= 0.263 Chirality : 0.040 0.138 1522 Planarity : 0.004 0.052 1616 Dihedral : 8.089 134.190 1359 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.86 % Favored : 96.97 % Rotamer: Outliers : 3.35 % Allowed : 15.50 % 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 (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 (0.24), residues: 1187 helix: 2.38 (0.18), residues: 807 sheet: 0.29 (0.70), residues: 48 loop : -0.80 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE B 509 TYR 0.011 0.001 TYR B 400 ARG 0.009 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 644) hydrogen bonds : angle 3.89297 ( 1905) covalent geometry : bond 0.00269 ( 9292) covalent geometry : angle 0.50542 (12662) *********************** 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 163 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.951 Fit side-chains REVERT: A 48 LYS cc_start: 0.8619 (mttp) cc_final: 0.8296 (mttp) REVERT: A 215 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (mt) REVERT: A 290 MET cc_start: 0.7544 (ttm) cc_final: 0.7328 (ttp) REVERT: A 293 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6633 (t80) REVERT: A 515 ARG cc_start: 0.7432 (ttm110) cc_final: 0.6938 (mtm-85) REVERT: B 115 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7775 (mtm-85) REVERT: B 232 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7174 (ttm170) REVERT: B 273 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7744 (mp0) REVERT: B 327 GLN cc_start: 0.8125 (mt0) cc_final: 0.7785 (mt0) REVERT: B 358 GLN cc_start: 0.8151 (tp40) cc_final: 0.7809 (tm-30) REVERT: B 458 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7551 (m) REVERT: B 495 ASP cc_start: 0.7516 (m-30) cc_final: 0.6942 (t0) REVERT: B 563 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6807 (tm-30) outliers start: 32 outliers final: 17 residues processed: 152 average time/residue: 1.2548 time to fit residues: 203.2571 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 : 1.065 ------------------------------------------------------------------------------- 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 414 VAL Chi-restraints excluded: chain B residue 50 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 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 = 0.3801 r_free = 0.3801 target = 0.158206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129605 restraints weight = 10560.454| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.79 r_work: 0.3388 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9292 Z= 0.125 Angle : 0.506 7.477 12662 Z= 0.262 Chirality : 0.040 0.145 1522 Planarity : 0.004 0.058 1616 Dihedral : 7.790 131.175 1357 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 3.98 % Allowed : 14.97 % 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 (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: 2.20 (0.24), residues: 1187 helix: 2.41 (0.18), residues: 806 sheet: 0.31 (0.72), residues: 48 loop : -0.83 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE B 509 TYR 0.011 0.001 TYR B 400 ARG 0.014 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 644) hydrogen bonds : angle 3.85793 ( 1905) covalent geometry : bond 0.00264 ( 9292) covalent geometry : angle 0.50596 (12662) *********************** 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 165 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8585 (mttp) cc_final: 0.8267 (mttp) REVERT: A 215 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8325 (mt) REVERT: A 293 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.6666 (t80) REVERT: A 511 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7544 (mtm-85) REVERT: A 515 ARG cc_start: 0.7427 (ttm110) cc_final: 0.6938 (mtm-85) REVERT: B 79 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: B 115 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7789 (mtm-85) REVERT: B 232 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7188 (ttm170) REVERT: B 273 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7744 (mp0) REVERT: B 327 GLN cc_start: 0.8106 (mt0) cc_final: 0.7785 (mt0) REVERT: B 358 GLN cc_start: 0.8139 (tp40) cc_final: 0.7774 (tm-30) REVERT: B 458 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7520 (m) REVERT: B 495 ASP cc_start: 0.7550 (m-30) cc_final: 0.6919 (t0) REVERT: B 563 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6795 (tm-30) outliers start: 38 outliers final: 18 residues processed: 151 average time/residue: 1.5086 time to fit residues: 242.5983 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 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 = 0.3748 r_free = 0.3748 target = 0.153506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124786 restraints weight = 10596.966| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.71 r_work: 0.3333 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9292 Z= 0.219 Angle : 0.579 8.594 12662 Z= 0.303 Chirality : 0.044 0.188 1522 Planarity : 0.004 0.054 1616 Dihedral : 8.153 142.136 1357 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.77 % Allowed : 15.50 % 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 (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: 1.70 (0.24), residues: 1187 helix: 1.98 (0.17), residues: 808 sheet: 0.23 (0.71), residues: 48 loop : -0.89 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 HIS 0.009 0.001 HIS A 88 PHE 0.023 0.002 PHE B 509 TYR 0.018 0.002 TYR A 9 ARG 0.012 0.001 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 644) hydrogen bonds : angle 4.09439 ( 1905) covalent geometry : bond 0.00519 ( 9292) covalent geometry : angle 0.57879 (12662) *********************** 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 155 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 1.128 Fit side-chains REVERT: A 215 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 293 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.6710 (t80) REVERT: A 393 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6570 (mtt90) REVERT: A 511 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7362 (mtm-85) REVERT: B 79 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: B 115 ARG cc_start: 0.8057 (mtp180) cc_final: 0.7652 (mtt90) REVERT: B 185 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: B 232 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7034 (ttm170) REVERT: B 273 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7557 (mp0) REVERT: B 327 GLN cc_start: 0.8136 (mt0) cc_final: 0.7774 (mt0) REVERT: B 358 GLN cc_start: 0.8036 (tp40) cc_final: 0.7544 (tm-30) REVERT: B 563 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6595 (tm-30) outliers start: 36 outliers final: 18 residues processed: 145 average time/residue: 2.0230 time to fit residues: 313.7610 Evaluate side-chains 139 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 185 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126536 restraints weight = 10613.579| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.84 r_work: 0.3340 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1133 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= 0.146 Angle : 0.533 7.942 12662 Z= 0.278 Chirality : 0.041 0.139 1522 Planarity : 0.004 0.051 1616 Dihedral : 7.992 144.623 1356 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.77 % Allowed : 15.92 % Favored : 80.31 % 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: 1.84 (0.24), residues: 1187 helix: 2.12 (0.17), residues: 806 sheet: 0.20 (0.72), residues: 48 loop : -0.92 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.018 0.001 PHE B 509 TYR 0.013 0.001 TYR B 400 ARG 0.019 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.05067 ( 644) hydrogen bonds : angle 3.98911 ( 1905) covalent geometry : bond 0.00324 ( 9292) covalent geometry : angle 0.53284 (12662) *********************** 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 154 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8331 (mt) REVERT: A 293 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6730 (t80) REVERT: A 393 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6618 (mtt90) REVERT: A 511 ARG cc_start: 0.7889 (mtp180) cc_final: 0.7601 (mtm-85) REVERT: B 79 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 115 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7926 (mtm-85) REVERT: B 185 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: B 232 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7206 (ttm170) REVERT: B 273 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7768 (mp0) REVERT: B 327 GLN cc_start: 0.8194 (mt0) cc_final: 0.7850 (mt0) REVERT: B 549 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 563 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6775 (tm-30) outliers start: 36 outliers final: 19 residues processed: 143 average time/residue: 1.7919 time to fit residues: 277.2254 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 413 LEU 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 185 GLN 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 519 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 549 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 49 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120056 restraints weight = 10758.156| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.85 r_work: 0.3219 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1142 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= 0.140 Angle : 0.526 7.827 12662 Z= 0.274 Chirality : 0.040 0.139 1522 Planarity : 0.004 0.052 1616 Dihedral : 7.936 145.047 1356 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.25 % Allowed : 16.34 % 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 (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: 1.93 (0.24), residues: 1187 helix: 2.20 (0.17), residues: 806 sheet: 0.21 (0.72), residues: 48 loop : -0.91 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.016 0.001 PHE B 509 TYR 0.012 0.001 TYR B 400 ARG 0.014 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 644) hydrogen bonds : angle 3.93779 ( 1905) covalent geometry : bond 0.00309 ( 9292) covalent geometry : angle 0.52605 (12662) *********************** 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 150 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.556 Fit side-chains REVERT: A 215 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 293 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 393 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6624 (mtt90) REVERT: A 511 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7360 (mtm-85) REVERT: B 79 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 115 ARG cc_start: 0.8038 (mtp180) cc_final: 0.7774 (mtm-85) REVERT: B 185 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: B 232 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7120 (ttm170) REVERT: B 273 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7638 (mp0) REVERT: B 327 GLN cc_start: 0.8213 (mt0) cc_final: 0.7840 (mt0) REVERT: B 495 ASP cc_start: 0.7405 (m-30) cc_final: 0.6925 (t0) REVERT: B 563 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6632 (tm-30) outliers start: 31 outliers final: 18 residues processed: 140 average time/residue: 1.4977 time to fit residues: 223.5375 Evaluate side-chains 137 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 185 GLN 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 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 98 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 528 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120022 restraints weight = 10522.791| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.83 r_work: 0.3189 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1176 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= 0.144 Angle : 0.531 7.860 12662 Z= 0.277 Chirality : 0.041 0.137 1522 Planarity : 0.004 0.051 1616 Dihedral : 7.945 146.433 1356 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.35 % Allowed : 16.54 % Favored : 80.10 % 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: 1.92 (0.24), residues: 1187 helix: 2.19 (0.17), residues: 807 sheet: 0.19 (0.71), residues: 48 loop : -0.91 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.017 0.001 PHE B 509 TYR 0.012 0.001 TYR B 400 ARG 0.020 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 644) hydrogen bonds : angle 3.93113 ( 1905) covalent geometry : bond 0.00320 ( 9292) covalent geometry : angle 0.53135 (12662) *********************** 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 151 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 293 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 393 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6569 (mtt90) REVERT: A 511 ARG cc_start: 0.7693 (mtp180) cc_final: 0.7265 (mtm-85) REVERT: A 515 ARG cc_start: 0.7422 (ttm110) cc_final: 0.6850 (mtm-85) REVERT: B 79 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 115 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7754 (mtm-85) REVERT: B 185 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: B 232 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7094 (ttm170) REVERT: B 273 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7612 (mp0) REVERT: B 327 GLN cc_start: 0.8203 (mt0) cc_final: 0.7820 (mt0) REVERT: B 563 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6611 (tm-30) outliers start: 32 outliers final: 17 residues processed: 141 average time/residue: 1.6238 time to fit residues: 243.3044 Evaluate side-chains 138 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 185 GLN 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 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 79 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.152421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121552 restraints weight = 10707.228| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.75 r_work: 0.3248 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1233 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= 0.151 Angle : 0.539 7.923 12662 Z= 0.281 Chirality : 0.041 0.138 1522 Planarity : 0.004 0.052 1616 Dihedral : 7.949 148.127 1355 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 2.62 % Allowed : 17.28 % Favored : 80.10 % 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: 1.89 (0.24), residues: 1187 helix: 2.17 (0.17), residues: 806 sheet: 0.17 (0.71), residues: 48 loop : -0.91 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.006 0.001 HIS A 88 PHE 0.018 0.001 PHE B 509 TYR 0.012 0.001 TYR B 400 ARG 0.017 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 644) hydrogen bonds : angle 3.94137 ( 1905) covalent geometry : bond 0.00340 ( 9292) covalent geometry : angle 0.53918 (12662) ********************** 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 144 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.946 Fit side-chains REVERT: A 215 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8268 (mt) REVERT: A 293 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6748 (t80) REVERT: A 393 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6587 (mtt90) REVERT: A 511 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7367 (mtm-85) REVERT: A 515 ARG cc_start: 0.7497 (ttm110) cc_final: 0.6947 (mtm-85) REVERT: B 79 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: B 115 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7809 (mtm-85) REVERT: B 185 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: B 232 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7137 (ttm170) REVERT: B 273 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7597 (mp0) REVERT: B 327 GLN cc_start: 0.8208 (mt0) cc_final: 0.7859 (mt0) REVERT: B 545 ARG cc_start: 0.7989 (mtm110) cc_final: 0.7425 (ptp-110) REVERT: B 563 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6687 (tm-30) outliers start: 25 outliers final: 17 residues processed: 137 average time/residue: 1.3135 time to fit residues: 191.2721 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 : 0.976 ------------------------------------------------------------------------------- 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 185 GLN 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 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 67 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.153460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122755 restraints weight = 10595.455| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.74 r_work: 0.3262 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1245 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= 0.133 Angle : 0.526 7.714 12662 Z= 0.274 Chirality : 0.040 0.135 1522 Planarity : 0.004 0.051 1616 Dihedral : 7.891 147.961 1355 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 2.93 % Allowed : 17.28 % 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 (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 (0.24), residues: 1187 helix: 2.25 (0.18), residues: 807 sheet: 0.15 (0.71), residues: 48 loop : -0.89 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 174 HIS 0.005 0.001 HIS A 88 PHE 0.016 0.001 PHE B 509 TYR 0.012 0.001 TYR B 400 ARG 0.018 0.000 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 644) hydrogen bonds : angle 3.89778 ( 1905) covalent geometry : bond 0.00290 ( 9292) covalent geometry : angle 0.52644 (12662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7903.05 seconds wall clock time: 141 minutes 13.98 seconds (8473.98 seconds total)