Starting phenix.real_space_refine on Fri Aug 22 23:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i39_35146/08_2025/8i39_35146_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i39_35146/08_2025/8i39_35146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i39_35146/08_2025/8i39_35146.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i39_35146/08_2025/8i39_35146.map" model { file = "/net/cci-nas-00/data/ceres_data/8i39_35146/08_2025/8i39_35146_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i39_35146/08_2025/8i39_35146_trim.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5495 2.51 5 N 1398 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8413 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4197 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 17, 'TRANS': 520} Chain breaks: 4 Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 3.25, per 1000 atoms: 0.39 Number of scatterers: 8413 At special positions: 0 Unit cell: (77.35, 103.53, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1470 8.00 N 1398 7.00 C 5495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 328.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 50.2% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.541A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.595A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.986A pdb=" N GLU A 195 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.618A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.809A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.543A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 300 removed outlier: 4.728A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.634A pdb=" N THR A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 397 removed outlier: 3.961A pdb=" N PHE A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.585A pdb=" N ARG A 402 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS A 403 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 438 through 455 removed outlier: 3.914A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.745A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.031A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.524A pdb=" N SER A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.874A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.766A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 561 removed outlier: 3.581A pdb=" N ALA A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.547A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 594 removed outlier: 3.538A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.576A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 3.541A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.595A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.986A pdb=" N GLU B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.618A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.809A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.542A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 4.728A pdb=" N MET B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.634A pdb=" N THR B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 397 removed outlier: 3.961A pdb=" N PHE B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.586A pdb=" N ARG B 402 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS B 403 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 438 through 455 removed outlier: 3.914A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.745A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 removed outlier: 4.031A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.524A pdb=" N SER B 498 " --> pdb=" O VAL B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.875A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.766A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 561 removed outlier: 3.581A pdb=" N ALA B 557 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 removed outlier: 3.547A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.538A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.576A pdb=" N ALA B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 5.317A pdb=" N SER A 85 " --> pdb=" O TYR A 47 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR A 47 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.141A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP A 231 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A 145 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER A 263 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 230 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 88 removed outlier: 5.316A pdb=" N SER B 85 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 47 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.140A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP B 231 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B 145 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 840 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: 1.11 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1279 1.30 - 1.42: 2251 1.42 - 1.55: 4961 1.55 - 1.68: 12 1.68 - 1.81: 84 Bond restraints: 8587 Sorted by residual: bond pdb=" C1 A8S B 701 " pdb=" O11 A8S B 701 " ideal model delta sigma weight residual 1.250 1.167 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C3 A8S B 701 " pdb=" C4 A8S B 701 " ideal model delta sigma weight residual 1.463 1.381 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 A8S B 701 " pdb=" O12 A8S B 701 " ideal model delta sigma weight residual 1.249 1.173 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 A8S B 701 " pdb=" C2 A8S B 701 " ideal model delta sigma weight residual 1.512 1.457 0.055 2.00e-02 2.50e+03 7.63e+00 bond pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.29e+00 ... (remaining 8582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 11506 2.94 - 5.87: 108 5.87 - 8.81: 16 8.81 - 11.75: 5 11.75 - 14.68: 6 Bond angle restraints: 11641 Sorted by residual: angle pdb=" CA GLU B 183 " pdb=" CB GLU B 183 " pdb=" CG GLU B 183 " ideal model delta sigma weight residual 114.10 128.78 -14.68 2.00e+00 2.50e-01 5.39e+01 angle pdb=" CA GLU A 183 " pdb=" CB GLU A 183 " pdb=" CG GLU A 183 " ideal model delta sigma weight residual 114.10 128.74 -14.64 2.00e+00 2.50e-01 5.36e+01 angle pdb=" CA GLU A 188 " pdb=" CB GLU A 188 " pdb=" CG GLU A 188 " ideal model delta sigma weight residual 114.10 127.95 -13.85 2.00e+00 2.50e-01 4.79e+01 angle pdb=" CA GLU B 188 " pdb=" CB GLU B 188 " pdb=" CG GLU B 188 " ideal model delta sigma weight residual 114.10 127.94 -13.84 2.00e+00 2.50e-01 4.79e+01 angle pdb=" N HIS A 403 " pdb=" CA HIS A 403 " pdb=" C HIS A 403 " ideal model delta sigma weight residual 114.04 105.48 8.56 1.24e+00 6.50e-01 4.77e+01 ... (remaining 11636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.95: 4722 19.95 - 39.91: 275 39.91 - 59.86: 40 59.86 - 79.81: 9 79.81 - 99.76: 12 Dihedral angle restraints: 5058 sinusoidal: 1976 harmonic: 3082 Sorted by residual: dihedral pdb=" CA MET B 310 " pdb=" C MET B 310 " pdb=" N ASN B 311 " pdb=" CA ASN B 311 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA MET A 310 " pdb=" C MET A 310 " pdb=" N ASN A 311 " pdb=" CA ASN A 311 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LYS A 133 " pdb=" C LYS A 133 " pdb=" N ILE A 134 " pdb=" CA ILE A 134 " ideal model delta harmonic sigma weight residual -180.00 -157.72 -22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1222 0.073 - 0.146: 156 0.146 - 0.219: 8 0.219 - 0.292: 0 0.292 - 0.364: 1 Chirality restraints: 1387 Sorted by residual: chirality pdb=" C7 A8S B 701 " pdb=" C12 A8S B 701 " pdb=" C8 A8S B 701 " pdb=" O7 A8S B 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.32 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA GLU A 188 " pdb=" N GLU A 188 " pdb=" C GLU A 188 " pdb=" CB GLU A 188 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA GLU B 188 " pdb=" N GLU B 188 " pdb=" C GLU B 188 " pdb=" CB GLU B 188 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1384 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 A8S B 701 " -0.244 2.00e-02 2.50e+03 2.51e-01 6.31e+02 pdb=" C4 A8S B 701 " 0.202 2.00e-02 2.50e+03 pdb=" C5 A8S B 701 " 0.296 2.00e-02 2.50e+03 pdb=" C7 A8S B 701 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 A8S B 701 " -0.128 2.00e-02 2.50e+03 1.07e-01 1.42e+02 pdb=" C2 A8S B 701 " 0.175 2.00e-02 2.50e+03 pdb=" C3 A8S B 701 " 0.030 2.00e-02 2.50e+03 pdb=" C4 A8S B 701 " 0.016 2.00e-02 2.50e+03 pdb=" C6 A8S B 701 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 450 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO B 451 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " 0.037 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 138 2.67 - 3.23: 8252 3.23 - 3.79: 11946 3.79 - 4.34: 19065 4.34 - 4.90: 29642 Nonbonded interactions: 69043 Sorted by model distance: nonbonded pdb=" O TYR B 298 " pdb=" OG SER B 301 " model vdw 2.116 3.040 nonbonded pdb=" O TYR A 298 " pdb=" OG SER A 301 " model vdw 2.117 3.040 nonbonded pdb=" O PRO A 102 " pdb=" OG SER A 105 " model vdw 2.136 3.040 nonbonded pdb=" O PRO B 102 " pdb=" OG SER B 105 " model vdw 2.137 3.040 nonbonded pdb=" OE2 GLU B 300 " pdb=" OG SER B 305 " model vdw 2.209 3.040 ... (remaining 69038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 36 through 660) } 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: 0.590 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.009 0.083 8587 Z= 0.371 Angle : 0.901 14.682 11641 Z= 0.504 Chirality : 0.050 0.364 1387 Planarity : 0.009 0.251 1424 Dihedral : 14.167 99.764 3078 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.22 % Allowed : 4.81 % Favored : 94.97 % 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: -5.71 (0.19), residues: 1056 helix: -4.67 (0.10), residues: 572 sheet: -2.41 (0.57), residues: 56 loop : -2.36 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 48 TYR 0.027 0.003 TYR A 475 PHE 0.028 0.002 PHE B 499 TRP 0.018 0.003 TRP A 426 HIS 0.011 0.003 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00867 ( 8587) covalent geometry : angle 0.90088 (11641) hydrogen bonds : bond 0.32277 ( 290) hydrogen bonds : angle 12.27655 ( 840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.7579 (ttm) cc_final: 0.7282 (ttm) REVERT: A 148 ASP cc_start: 0.7773 (m-30) cc_final: 0.7547 (m-30) REVERT: A 180 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6950 (mtm180) REVERT: A 224 ASN cc_start: 0.7914 (t0) cc_final: 0.7490 (t0) REVERT: A 227 LEU cc_start: 0.8199 (tp) cc_final: 0.7943 (tp) REVERT: A 424 MET cc_start: 0.7713 (mmm) cc_final: 0.7447 (mmm) REVERT: A 430 TYR cc_start: 0.7900 (p90) cc_final: 0.7597 (p90) REVERT: A 469 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 474 MET cc_start: 0.8257 (ttt) cc_final: 0.7957 (ttt) REVERT: A 475 TYR cc_start: 0.8743 (p90) cc_final: 0.8529 (p90) REVERT: A 555 MET cc_start: 0.8615 (mmm) cc_final: 0.8270 (mmm) REVERT: A 568 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7568 (mmmt) REVERT: B 97 MET cc_start: 0.7163 (ttm) cc_final: 0.6756 (ttm) REVERT: B 139 LEU cc_start: 0.8547 (mt) cc_final: 0.8344 (tp) REVERT: B 180 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7017 (mtm180) REVERT: B 270 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6311 (mtt180) REVERT: B 291 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7067 (tptp) REVERT: B 430 TYR cc_start: 0.7819 (p90) cc_final: 0.7342 (p90) REVERT: B 474 MET cc_start: 0.8242 (ttt) cc_final: 0.7922 (ttt) REVERT: B 506 MET cc_start: 0.7258 (mtp) cc_final: 0.7027 (mtp) REVERT: B 545 LYS cc_start: 0.7742 (mptt) cc_final: 0.7504 (pttm) REVERT: B 555 MET cc_start: 0.8237 (mmm) cc_final: 0.7888 (mmm) REVERT: B 568 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7812 (mmmt) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.6294 time to fit residues: 98.3593 Evaluate side-chains 114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 321 ASN A 454 ASN B 130 ASN B 321 ASN B 325 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.182633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133593 restraints weight = 8615.899| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.85 r_work: 0.3424 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8587 Z= 0.137 Angle : 0.615 5.287 11641 Z= 0.319 Chirality : 0.042 0.131 1387 Planarity : 0.005 0.038 1424 Dihedral : 6.802 45.911 1188 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.30 % Allowed : 9.08 % Favored : 88.62 % 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: -4.48 (0.22), residues: 1056 helix: -3.29 (0.15), residues: 634 sheet: -2.10 (0.55), residues: 76 loop : -2.02 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.020 0.001 TYR B 475 PHE 0.021 0.001 PHE A 144 TRP 0.011 0.002 TRP B 447 HIS 0.006 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8587) covalent geometry : angle 0.61514 (11641) hydrogen bonds : bond 0.03648 ( 290) hydrogen bonds : angle 5.47107 ( 840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6861 (tmm) REVERT: A 97 MET cc_start: 0.6753 (ttm) cc_final: 0.6460 (ttm) REVERT: A 148 ASP cc_start: 0.7804 (m-30) cc_final: 0.7545 (m-30) REVERT: A 180 ARG cc_start: 0.7071 (mtp180) cc_final: 0.6673 (mtm180) REVERT: A 232 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: A 291 LYS cc_start: 0.6462 (mmmt) cc_final: 0.5083 (ttpp) REVERT: A 424 MET cc_start: 0.8120 (mmm) cc_final: 0.7919 (mmm) REVERT: A 430 TYR cc_start: 0.7801 (p90) cc_final: 0.7594 (p90) REVERT: A 469 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 474 MET cc_start: 0.8020 (ttt) cc_final: 0.7756 (ttt) REVERT: A 475 TYR cc_start: 0.8393 (p90) cc_final: 0.8044 (p90) REVERT: A 555 MET cc_start: 0.8631 (mmm) cc_final: 0.8283 (mmm) REVERT: A 576 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7691 (ttm) REVERT: B 97 MET cc_start: 0.6595 (ttm) cc_final: 0.6287 (ttm) REVERT: B 158 ARG cc_start: 0.7336 (ttp80) cc_final: 0.7057 (ttp80) REVERT: B 180 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6492 (mtm180) REVERT: B 291 LYS cc_start: 0.6633 (mmmt) cc_final: 0.6109 (tptp) REVERT: B 395 HIS cc_start: 0.7548 (t-170) cc_final: 0.6357 (m90) REVERT: B 430 TYR cc_start: 0.7795 (p90) cc_final: 0.7453 (p90) REVERT: B 474 MET cc_start: 0.7724 (ttt) cc_final: 0.7493 (ttt) REVERT: B 545 LYS cc_start: 0.7660 (mptt) cc_final: 0.6869 (pttm) REVERT: B 555 MET cc_start: 0.8377 (mmm) cc_final: 0.8097 (mmm) REVERT: B 658 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7393 (mtm180) outliers start: 21 outliers final: 6 residues processed: 153 average time/residue: 0.6367 time to fit residues: 103.2631 Evaluate side-chains 134 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 658 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.181439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120238 restraints weight = 8390.767| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.78 r_work: 0.3386 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8587 Z= 0.112 Angle : 0.547 5.990 11641 Z= 0.282 Chirality : 0.040 0.142 1387 Planarity : 0.004 0.037 1424 Dihedral : 5.097 24.636 1188 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.28 % Allowed : 11.05 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.23), residues: 1056 helix: -2.20 (0.18), residues: 634 sheet: -1.82 (0.54), residues: 80 loop : -2.01 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 293 TYR 0.032 0.001 TYR B 475 PHE 0.020 0.001 PHE B 42 TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8587) covalent geometry : angle 0.54720 (11641) hydrogen bonds : bond 0.03099 ( 290) hydrogen bonds : angle 4.61922 ( 840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.5458 (tt0) cc_final: 0.5208 (tt0) REVERT: A 97 MET cc_start: 0.6544 (ttm) cc_final: 0.6221 (ttm) REVERT: A 148 ASP cc_start: 0.7752 (m-30) cc_final: 0.7518 (m-30) REVERT: A 158 ARG cc_start: 0.7295 (ttp80) cc_final: 0.6973 (ttp80) REVERT: A 180 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6633 (mtm180) REVERT: A 188 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7568 (pp20) REVERT: A 196 ASN cc_start: 0.8191 (m-40) cc_final: 0.7972 (m-40) REVERT: A 280 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.5763 (mm) REVERT: A 291 LYS cc_start: 0.6063 (mmmt) cc_final: 0.5643 (tptp) REVERT: A 430 TYR cc_start: 0.7708 (p90) cc_final: 0.7418 (p90) REVERT: A 474 MET cc_start: 0.7821 (ttt) cc_final: 0.7590 (ttp) REVERT: A 505 TRP cc_start: 0.8256 (m100) cc_final: 0.7846 (m100) REVERT: A 555 MET cc_start: 0.8524 (mmm) cc_final: 0.8279 (mmp) REVERT: A 587 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7630 (mmp-170) REVERT: A 658 ARG cc_start: 0.7552 (ttt180) cc_final: 0.7331 (mmm160) REVERT: B 97 MET cc_start: 0.6705 (ttm) cc_final: 0.6458 (ttm) REVERT: B 180 ARG cc_start: 0.6914 (mtp180) cc_final: 0.6445 (mtm180) REVERT: B 232 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6211 (mp0) REVERT: B 291 LYS cc_start: 0.6105 (mmmt) cc_final: 0.5621 (tptp) REVERT: B 395 HIS cc_start: 0.7506 (t-170) cc_final: 0.6289 (m90) REVERT: B 505 TRP cc_start: 0.8273 (m100) cc_final: 0.7867 (m100) REVERT: B 545 LYS cc_start: 0.7530 (mptt) cc_final: 0.6732 (pttm) REVERT: B 555 MET cc_start: 0.8432 (mmm) cc_final: 0.8167 (mmp) outliers start: 30 outliers final: 9 residues processed: 156 average time/residue: 0.6271 time to fit residues: 103.9862 Evaluate side-chains 145 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.180446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116887 restraints weight = 8424.353| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.94 r_work: 0.3298 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8587 Z= 0.145 Angle : 0.563 6.693 11641 Z= 0.288 Chirality : 0.041 0.165 1387 Planarity : 0.004 0.034 1424 Dihedral : 5.006 25.311 1188 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.06 % Allowed : 13.24 % Favored : 83.70 % 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: -2.58 (0.25), residues: 1056 helix: -1.63 (0.20), residues: 614 sheet: -1.19 (0.56), residues: 76 loop : -1.66 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 158 TYR 0.040 0.002 TYR B 475 PHE 0.012 0.001 PHE A 499 TRP 0.010 0.001 TRP B 447 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8587) covalent geometry : angle 0.56257 (11641) hydrogen bonds : bond 0.03224 ( 290) hydrogen bonds : angle 4.47326 ( 840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 95 GLU cc_start: 0.5339 (tt0) cc_final: 0.5077 (tt0) REVERT: A 176 ASP cc_start: 0.7150 (t0) cc_final: 0.5819 (p0) REVERT: A 180 ARG cc_start: 0.7011 (mtp180) cc_final: 0.6529 (mtm180) REVERT: A 232 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: A 280 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5681 (mm) REVERT: A 288 PHE cc_start: 0.6946 (t80) cc_final: 0.6657 (t80) REVERT: A 291 LYS cc_start: 0.6216 (mmmt) cc_final: 0.5833 (tptp) REVERT: A 315 PHE cc_start: 0.7169 (t80) cc_final: 0.6918 (t80) REVERT: A 474 MET cc_start: 0.7804 (ttt) cc_final: 0.7573 (ttt) REVERT: A 475 TYR cc_start: 0.8267 (p90) cc_final: 0.8033 (p90) REVERT: A 555 MET cc_start: 0.8375 (mmm) cc_final: 0.8146 (mmp) REVERT: A 587 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7553 (mmp-170) REVERT: A 654 TYR cc_start: 0.8067 (t80) cc_final: 0.7829 (t80) REVERT: A 658 ARG cc_start: 0.7370 (ttt180) cc_final: 0.7122 (mmm160) REVERT: B 158 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6941 (ttp80) REVERT: B 180 ARG cc_start: 0.6777 (mtp180) cc_final: 0.6306 (mtm180) REVERT: B 291 LYS cc_start: 0.5977 (mmmt) cc_final: 0.5477 (tptp) REVERT: B 387 PHE cc_start: 0.7359 (m-80) cc_final: 0.6906 (m-80) REVERT: B 395 HIS cc_start: 0.7376 (t-170) cc_final: 0.6214 (m90) REVERT: B 430 TYR cc_start: 0.7655 (p90) cc_final: 0.7436 (p90) REVERT: B 545 LYS cc_start: 0.7487 (mptt) cc_final: 0.6612 (pttm) REVERT: B 555 MET cc_start: 0.8368 (mmm) cc_final: 0.8130 (mmp) outliers start: 28 outliers final: 10 residues processed: 151 average time/residue: 0.6119 time to fit residues: 98.1944 Evaluate side-chains 142 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.180799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117609 restraints weight = 8326.032| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.93 r_work: 0.3285 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8587 Z= 0.130 Angle : 0.535 6.475 11641 Z= 0.273 Chirality : 0.041 0.155 1387 Planarity : 0.004 0.032 1424 Dihedral : 4.679 20.867 1188 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.72 % Allowed : 14.11 % Favored : 82.17 % 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 (0.25), residues: 1056 helix: -1.27 (0.20), residues: 616 sheet: -1.03 (0.56), residues: 76 loop : -1.47 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.037 0.002 TYR B 475 PHE 0.022 0.001 PHE B 42 TRP 0.010 0.001 TRP B 447 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8587) covalent geometry : angle 0.53504 (11641) hydrogen bonds : bond 0.02979 ( 290) hydrogen bonds : angle 4.26319 ( 840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7019 (mmmm) REVERT: A 158 ARG cc_start: 0.7065 (ttp80) cc_final: 0.6829 (ttp80) REVERT: A 180 ARG cc_start: 0.7126 (mtp180) cc_final: 0.6677 (mtm180) REVERT: A 232 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6523 (mt-10) REVERT: A 280 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5621 (mm) REVERT: A 291 LYS cc_start: 0.6118 (mmmt) cc_final: 0.5775 (tptp) REVERT: A 475 TYR cc_start: 0.8286 (p90) cc_final: 0.8056 (p90) REVERT: A 505 TRP cc_start: 0.8245 (m100) cc_final: 0.7814 (m100) REVERT: A 587 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7546 (mmp-170) REVERT: A 654 TYR cc_start: 0.8088 (t80) cc_final: 0.7838 (t80) REVERT: A 658 ARG cc_start: 0.7423 (ttt180) cc_final: 0.7162 (mmm160) REVERT: B 90 MET cc_start: 0.8177 (tmm) cc_final: 0.7634 (tmt) REVERT: B 180 ARG cc_start: 0.6963 (mtp180) cc_final: 0.6497 (mtm180) REVERT: B 188 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7323 (pp20) REVERT: B 291 LYS cc_start: 0.6026 (mmmt) cc_final: 0.5619 (tptp) REVERT: B 395 HIS cc_start: 0.7347 (t-170) cc_final: 0.6182 (m90) REVERT: B 505 TRP cc_start: 0.8259 (m100) cc_final: 0.7807 (m100) REVERT: B 542 MET cc_start: 0.7818 (mmt) cc_final: 0.7458 (mmt) REVERT: B 545 LYS cc_start: 0.7441 (mptt) cc_final: 0.6493 (pttm) outliers start: 34 outliers final: 14 residues processed: 150 average time/residue: 0.6268 time to fit residues: 99.9100 Evaluate side-chains 142 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.128938 restraints weight = 8440.520| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.00 r_work: 0.3274 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8587 Z= 0.159 Angle : 0.567 7.021 11641 Z= 0.287 Chirality : 0.042 0.151 1387 Planarity : 0.004 0.043 1424 Dihedral : 4.716 25.783 1188 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.05 % Allowed : 14.00 % Favored : 81.95 % 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: -2.04 (0.25), residues: 1056 helix: -1.17 (0.20), residues: 618 sheet: -1.15 (0.55), residues: 80 loop : -1.42 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 293 TYR 0.040 0.002 TYR B 475 PHE 0.013 0.001 PHE A 499 TRP 0.010 0.002 TRP B 447 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8587) covalent geometry : angle 0.56744 (11641) hydrogen bonds : bond 0.03187 ( 290) hydrogen bonds : angle 4.30331 ( 840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7125 (mmmm) REVERT: A 180 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6725 (mtm180) REVERT: A 232 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: A 280 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.5825 (mm) REVERT: A 291 LYS cc_start: 0.6436 (mmmt) cc_final: 0.6102 (tptp) REVERT: A 469 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7551 (mt-10) REVERT: A 475 TYR cc_start: 0.8578 (p90) cc_final: 0.8378 (p90) REVERT: A 658 ARG cc_start: 0.7602 (ttt180) cc_final: 0.7345 (mmm160) REVERT: B 90 MET cc_start: 0.8279 (tmm) cc_final: 0.7768 (tmt) REVERT: B 158 ARG cc_start: 0.7343 (ttp80) cc_final: 0.7046 (ttp80) REVERT: B 180 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6690 (mtm180) REVERT: B 188 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: B 291 LYS cc_start: 0.6337 (mmmt) cc_final: 0.5907 (tptp) REVERT: B 395 HIS cc_start: 0.7581 (t-170) cc_final: 0.6432 (m90) REVERT: B 542 MET cc_start: 0.7892 (mmt) cc_final: 0.7565 (mmt) REVERT: B 545 LYS cc_start: 0.7777 (mptt) cc_final: 0.6891 (pttm) outliers start: 37 outliers final: 15 residues processed: 146 average time/residue: 0.5946 time to fit residues: 92.4700 Evaluate side-chains 140 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.177623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113597 restraints weight = 8384.352| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.89 r_work: 0.3065 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8587 Z= 0.202 Angle : 0.622 8.411 11641 Z= 0.309 Chirality : 0.044 0.151 1387 Planarity : 0.004 0.058 1424 Dihedral : 4.892 38.851 1188 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.94 % Allowed : 14.66 % Favored : 81.40 % 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: -2.09 (0.25), residues: 1056 helix: -1.23 (0.20), residues: 618 sheet: -1.03 (0.55), residues: 78 loop : -1.42 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 244 TYR 0.043 0.002 TYR B 475 PHE 0.022 0.002 PHE B 42 TRP 0.012 0.002 TRP B 426 HIS 0.004 0.001 HIS A 403 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8587) covalent geometry : angle 0.62198 (11641) hydrogen bonds : bond 0.03463 ( 290) hydrogen bonds : angle 4.43998 ( 840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.7019 (mmmm) REVERT: A 158 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6844 (ttp80) REVERT: A 180 ARG cc_start: 0.7037 (mtp180) cc_final: 0.6566 (mtm180) REVERT: A 280 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5719 (mm) REVERT: A 291 LYS cc_start: 0.6184 (mmmt) cc_final: 0.5866 (tptp) REVERT: A 658 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7236 (mmm160) REVERT: B 90 MET cc_start: 0.8071 (tmm) cc_final: 0.7784 (tmt) REVERT: B 158 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6838 (ttp80) REVERT: B 180 ARG cc_start: 0.6974 (mtp180) cc_final: 0.6468 (mtm180) REVERT: B 291 LYS cc_start: 0.6233 (mmmt) cc_final: 0.5825 (tptp) REVERT: B 395 HIS cc_start: 0.7557 (t-170) cc_final: 0.6400 (m90) REVERT: B 542 MET cc_start: 0.7894 (mmt) cc_final: 0.7673 (mmt) outliers start: 36 outliers final: 18 residues processed: 145 average time/residue: 0.5816 time to fit residues: 89.8024 Evaluate side-chains 135 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 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 = 0.4034 r_free = 0.4034 target = 0.179670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115845 restraints weight = 8241.675| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.88 r_work: 0.3288 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8587 Z= 0.137 Angle : 0.557 8.383 11641 Z= 0.280 Chirality : 0.041 0.152 1387 Planarity : 0.004 0.041 1424 Dihedral : 4.610 37.364 1188 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.61 % Allowed : 15.32 % Favored : 81.07 % 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: -1.77 (0.26), residues: 1056 helix: -0.95 (0.20), residues: 620 sheet: -1.05 (0.55), residues: 80 loop : -1.28 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 293 TYR 0.038 0.002 TYR A 475 PHE 0.017 0.001 PHE A 275 TRP 0.010 0.002 TRP B 447 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8587) covalent geometry : angle 0.55705 (11641) hydrogen bonds : bond 0.03023 ( 290) hydrogen bonds : angle 4.19776 ( 840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7134 (mmmm) REVERT: A 158 ARG cc_start: 0.6986 (ttp80) cc_final: 0.6660 (ttp80) REVERT: A 180 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6683 (mtm180) REVERT: A 280 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5681 (mm) REVERT: A 291 LYS cc_start: 0.6116 (mmmt) cc_final: 0.5814 (tptp) REVERT: A 505 TRP cc_start: 0.8212 (m100) cc_final: 0.7646 (m100) REVERT: A 555 MET cc_start: 0.8184 (mmm) cc_final: 0.7972 (mmp) REVERT: A 587 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7521 (mmp-170) REVERT: A 658 ARG cc_start: 0.7407 (ttt180) cc_final: 0.7058 (mmm160) REVERT: B 90 MET cc_start: 0.8119 (tmm) cc_final: 0.7792 (tmt) REVERT: B 158 ARG cc_start: 0.6965 (ttp80) cc_final: 0.6671 (ttp80) REVERT: B 180 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6443 (mtm180) REVERT: B 244 ARG cc_start: 0.5777 (mmm160) cc_final: 0.5505 (mmp-170) REVERT: B 291 LYS cc_start: 0.6064 (mmmt) cc_final: 0.5685 (tptp) REVERT: B 395 HIS cc_start: 0.7271 (t-170) cc_final: 0.6110 (m90) REVERT: B 542 MET cc_start: 0.7760 (mmt) cc_final: 0.7546 (mmm) REVERT: B 555 MET cc_start: 0.8173 (mmm) cc_final: 0.7944 (mmp) outliers start: 33 outliers final: 16 residues processed: 143 average time/residue: 0.5872 time to fit residues: 89.4407 Evaluate side-chains 135 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.177859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114069 restraints weight = 8245.864| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.87 r_work: 0.3069 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8587 Z= 0.193 Angle : 0.620 11.055 11641 Z= 0.307 Chirality : 0.044 0.147 1387 Planarity : 0.004 0.039 1424 Dihedral : 4.814 43.952 1188 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.50 % Allowed : 16.19 % 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 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: -1.81 (0.26), residues: 1056 helix: -0.99 (0.20), residues: 618 sheet: -0.99 (0.55), residues: 80 loop : -1.32 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 293 TYR 0.045 0.002 TYR A 475 PHE 0.023 0.002 PHE A 275 TRP 0.013 0.002 TRP B 426 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8587) covalent geometry : angle 0.61983 (11641) hydrogen bonds : bond 0.03423 ( 290) hydrogen bonds : angle 4.38509 ( 840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7507 (tmt) REVERT: A 136 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7103 (mmmm) REVERT: A 158 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6849 (ttp80) REVERT: A 180 ARG cc_start: 0.7079 (mtp180) cc_final: 0.6602 (mtm180) REVERT: A 237 LEU cc_start: 0.8263 (mt) cc_final: 0.7930 (tp) REVERT: A 280 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5742 (mm) REVERT: A 291 LYS cc_start: 0.6136 (mmmt) cc_final: 0.5811 (tptp) REVERT: A 469 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 555 MET cc_start: 0.8306 (mmm) cc_final: 0.8098 (mmp) REVERT: A 587 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7747 (mmp-170) REVERT: A 658 ARG cc_start: 0.7567 (ttt180) cc_final: 0.7207 (mmm160) REVERT: B 90 MET cc_start: 0.8075 (tmm) cc_final: 0.7791 (tmt) REVERT: B 180 ARG cc_start: 0.6975 (mtp180) cc_final: 0.6488 (mtm180) REVERT: B 291 LYS cc_start: 0.6191 (mmmt) cc_final: 0.5807 (tptp) REVERT: B 395 HIS cc_start: 0.7551 (t-170) cc_final: 0.6392 (m90) REVERT: B 542 MET cc_start: 0.7885 (mmt) cc_final: 0.7673 (mmt) REVERT: B 555 MET cc_start: 0.8326 (mmm) cc_final: 0.8120 (mmp) outliers start: 32 outliers final: 18 residues processed: 139 average time/residue: 0.5507 time to fit residues: 81.5546 Evaluate side-chains 134 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 0.0370 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 71 optimal weight: 0.8980 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.182405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118508 restraints weight = 8222.367| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.89 r_work: 0.3339 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8587 Z= 0.098 Angle : 0.523 7.416 11641 Z= 0.265 Chirality : 0.039 0.143 1387 Planarity : 0.004 0.051 1424 Dihedral : 4.312 35.532 1188 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.08 % Allowed : 18.27 % Favored : 79.65 % 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: -1.13 (0.26), residues: 1056 helix: -0.48 (0.21), residues: 604 sheet: -0.90 (0.56), residues: 80 loop : -0.91 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 293 TYR 0.036 0.001 TYR A 475 PHE 0.018 0.001 PHE A 275 TRP 0.010 0.001 TRP A 447 HIS 0.003 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8587) covalent geometry : angle 0.52260 (11641) hydrogen bonds : bond 0.02672 ( 290) hydrogen bonds : angle 3.98390 ( 840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8050 (tmm) cc_final: 0.7691 (tmt) REVERT: A 136 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7174 (mmmm) REVERT: A 158 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6652 (ttp80) REVERT: A 180 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6686 (mtm180) REVERT: A 237 LEU cc_start: 0.8215 (mt) cc_final: 0.7881 (tp) REVERT: A 280 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5762 (mm) REVERT: A 395 HIS cc_start: 0.7218 (t70) cc_final: 0.6067 (m90) REVERT: A 469 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7250 (mt-10) REVERT: A 505 TRP cc_start: 0.8225 (m100) cc_final: 0.7812 (m100) REVERT: A 587 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7559 (mmp-170) REVERT: B 90 MET cc_start: 0.8028 (tmm) cc_final: 0.7749 (tmt) REVERT: B 158 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6662 (ttp80) REVERT: B 180 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6642 (mtm180) REVERT: B 291 LYS cc_start: 0.5963 (mmmt) cc_final: 0.5574 (tptp) REVERT: B 395 HIS cc_start: 0.7281 (t-170) cc_final: 0.6130 (m90) REVERT: B 542 MET cc_start: 0.7564 (mmt) cc_final: 0.7292 (mmm) outliers start: 19 outliers final: 11 residues processed: 137 average time/residue: 0.5528 time to fit residues: 80.7195 Evaluate side-chains 129 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.180996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117087 restraints weight = 8198.408| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.89 r_work: 0.3318 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8587 Z= 0.132 Angle : 0.558 8.373 11641 Z= 0.280 Chirality : 0.041 0.143 1387 Planarity : 0.004 0.057 1424 Dihedral : 4.399 34.590 1188 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.84 % Allowed : 17.83 % Favored : 79.32 % 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: -1.03 (0.26), residues: 1056 helix: -0.35 (0.21), residues: 604 sheet: -0.89 (0.56), residues: 80 loop : -0.94 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 293 TYR 0.039 0.002 TYR B 475 PHE 0.025 0.001 PHE B 42 TRP 0.011 0.001 TRP B 447 HIS 0.004 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8587) covalent geometry : angle 0.55842 (11641) hydrogen bonds : bond 0.02946 ( 290) hydrogen bonds : angle 4.06584 ( 840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.04 seconds wall clock time: 59 minutes 58.88 seconds (3598.88 seconds total)