Starting phenix.real_space_refine on Wed Mar 4 15:12:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l7i_23213/03_2026/7l7i_23213.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l7i_23213/03_2026/7l7i_23213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l7i_23213/03_2026/7l7i_23213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l7i_23213/03_2026/7l7i_23213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l7i_23213/03_2026/7l7i_23213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l7i_23213/03_2026/7l7i_23213.map" } resolution = 3.3 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= 0.002 sd= 0.053 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 72 5.16 5 C 9125 2.51 5 N 2447 2.21 5 O 2775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14425 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3229 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 396} Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 5107 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 15, 'TRANS': 612} Chain breaks: 1 Chain: "E" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 920 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.21 Number of scatterers: 14425 At special positions: 0 Unit cell: (102.564, 105.82, 142.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 6 15.00 O 2775 8.00 N 2447 7.00 C 9125 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: 0.97 Conformation dependent library (CDL) restraints added in 659.1 milliseconds 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 45.1% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 114 through 117 removed outlier: 4.274A pdb=" N GLY C 117 " --> pdb=" O GLY C 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 114 through 117' Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.665A pdb=" N ASP C 197 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 221 through 224 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 260 through 281 removed outlier: 4.019A pdb=" N LYS C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 300 removed outlier: 3.604A pdb=" N MET C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 330 removed outlier: 3.551A pdb=" N MET C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 347 removed outlier: 3.751A pdb=" N LYS C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 366 through 381 removed outlier: 3.565A pdb=" N GLY C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS C 376 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 410 Processing helix chain 'C' and resid 411 through 420 Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.768A pdb=" N SER A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 66 removed outlier: 4.190A pdb=" N ARG A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 405 through 428 removed outlier: 4.032A pdb=" N LEU A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 452 removed outlier: 4.574A pdb=" N GLN A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 463 removed outlier: 4.754A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 525 through 533 removed outlier: 4.304A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 568 Processing helix chain 'A' and resid 568 through 579 Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 674 removed outlier: 3.816A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 697 removed outlier: 3.582A pdb=" N HIS A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 36 removed outlier: 3.554A pdb=" N SER B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 43 through 63 Processing helix chain 'B' and resid 64 through 71 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.149A pdb=" N THR B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU B 196 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.770A pdb=" N GLN B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.776A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 3.782A pdb=" N LYS B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 3.764A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 525 through 533 removed outlier: 4.010A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 579 removed outlier: 5.054A pdb=" N ASN B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 621 through 629 removed outlier: 4.435A pdb=" N MET B 625 " --> pdb=" O ASP B 621 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 675 Processing helix chain 'B' and resid 680 through 697 removed outlier: 3.782A pdb=" N HIS B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 687 " --> pdb=" O THR B 683 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 690 " --> pdb=" O ASN B 686 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 23 through 24 removed outlier: 4.020A pdb=" N LEU C 34 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE C 102 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 54 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE C 137 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS C 52 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 140 through 141 removed outlier: 6.376A pdb=" N GLN C 214 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR C 243 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG C 175 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL C 245 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU C 173 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU C 247 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS C 171 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 182 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS C 176 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET C 180 " --> pdb=" O CYS C 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.631A pdb=" N LYS B 147 " --> pdb=" O HIS B 189 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU B 223 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE B 285 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.838A pdb=" N GLN A 23 " --> pdb=" O ILE B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.450A pdb=" N ILE A 78 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 221 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 80 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.787A pdb=" N ALA A 325 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 365 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 466 through 467 removed outlier: 4.225A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N ILE A 519 " --> pdb=" O HIS A 490 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TYR A 492 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N MET A 521 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 494 " --> pdb=" O MET A 521 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.471A pdb=" N LYS A 585 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE A 636 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 323 through 332 removed outlier: 6.748A pdb=" N VAL B 343 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 326 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 341 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N HIS B 328 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA B 339 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER B 330 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B 337 " --> pdb=" O SER B 330 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 365 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 474 through 475 removed outlier: 4.098A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.543A pdb=" N LYS B 585 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE B 636 " --> pdb=" O LYS B 585 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 587 " --> pdb=" O ILE B 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 65 through 68 Processing sheet with id=AB5, first strand: chain 'E' and resid 25 through 32 removed outlier: 4.442A pdb=" N VAL E 27 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER E 39 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL E 29 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR E 37 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE E 31 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 1917 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: 2.17 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2489 1.28 - 1.41: 3548 1.41 - 1.55: 8492 1.55 - 1.69: 31 1.69 - 1.82: 117 Bond restraints: 14677 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.527 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.537 0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" C ARG B 182 " pdb=" O ARG B 182 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.25e-02 6.40e+03 5.65e+01 bond pdb=" N ARG C 175 " pdb=" CA ARG C 175 " ideal model delta sigma weight residual 1.457 1.368 0.088 1.24e-02 6.50e+03 5.09e+01 bond pdb=" C ARG B 591 " pdb=" O ARG B 591 " ideal model delta sigma weight residual 1.236 1.166 0.071 1.28e-02 6.10e+03 3.06e+01 ... (remaining 14672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 18277 3.15 - 6.29: 1407 6.29 - 9.44: 30 9.44 - 12.59: 5 12.59 - 15.73: 4 Bond angle restraints: 19723 Sorted by residual: angle pdb=" CA ARG B 182 " pdb=" C ARG B 182 " pdb=" N GLY B 183 " ideal model delta sigma weight residual 116.38 126.19 -9.81 1.35e+00 5.49e-01 5.28e+01 angle pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sigma weight residual 113.80 120.16 -6.36 1.00e+00 1.00e+00 4.05e+01 angle pdb=" CA ASP C 195 " pdb=" CB ASP C 195 " pdb=" CG ASP C 195 " ideal model delta sigma weight residual 112.60 118.77 -6.17 1.00e+00 1.00e+00 3.81e+01 angle pdb=" N ARG C 184 " pdb=" CA ARG C 184 " pdb=" C ARG C 184 " ideal model delta sigma weight residual 108.60 117.55 -8.95 1.46e+00 4.69e-01 3.76e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 19718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.46: 8800 29.46 - 58.91: 197 58.91 - 88.37: 50 88.37 - 117.83: 0 117.83 - 147.29: 2 Dihedral angle restraints: 9049 sinusoidal: 3864 harmonic: 5185 Sorted by residual: dihedral pdb=" CA GLU C 192 " pdb=" C GLU C 192 " pdb=" N GLY C 193 " pdb=" CA GLY C 193 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLN A 287 " pdb=" C GLN A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta harmonic sigma weight residual -180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU A 392 " pdb=" C GLU A 392 " pdb=" N ASP A 393 " pdb=" CA ASP A 393 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 9046 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1327 0.078 - 0.155: 658 0.155 - 0.233: 127 0.233 - 0.311: 27 0.311 - 0.388: 11 Chirality restraints: 2150 Sorted by residual: chirality pdb=" CA ARG B 367 " pdb=" N ARG B 367 " pdb=" C ARG B 367 " pdb=" CB ARG B 367 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA ARG B 591 " pdb=" N ARG B 591 " pdb=" C ARG B 591 " pdb=" CB ARG B 591 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA ARG A 367 " pdb=" N ARG A 367 " pdb=" C ARG A 367 " pdb=" CB ARG A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 2147 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 109 " -0.134 2.00e-02 2.50e+03 6.96e-02 1.21e+02 pdb=" CG TRP E 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 109 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 109 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP E 109 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP E 109 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP E 109 " 0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 109 " -0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 109 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP E 109 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 297 " -0.078 2.00e-02 2.50e+03 6.04e-02 9.13e+01 pdb=" CG TRP A 297 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 297 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 297 " 0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP A 297 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 TRP A 297 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP A 297 " 0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 297 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 297 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 297 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 401 " 0.093 2.00e-02 2.50e+03 6.94e-02 7.22e+01 pdb=" CG HIS C 401 " -0.100 2.00e-02 2.50e+03 pdb=" ND1 HIS C 401 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 HIS C 401 " -0.051 2.00e-02 2.50e+03 pdb=" CE1 HIS C 401 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS C 401 " 0.054 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2885 2.82 - 3.34: 14157 3.34 - 3.86: 23867 3.86 - 4.38: 29744 4.38 - 4.90: 49461 Nonbonded interactions: 120114 Sorted by model distance: nonbonded pdb=" CD ARG B 510 " pdb=" O ASN B 590 " model vdw 2.300 3.440 nonbonded pdb=" ND2 ASN B 51 " pdb=" O1A ANP B 801 " model vdw 2.339 3.120 nonbonded pdb=" ND2 ASN A 51 " pdb=" O1A ANP A 801 " model vdw 2.381 3.120 nonbonded pdb=" O1B ANP A 801 " pdb=" O3' ANP A 801 " model vdw 2.479 3.040 nonbonded pdb=" O1B ANP B 801 " pdb=" O3' ANP B 801 " model vdw 2.532 3.040 ... (remaining 120109 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' } 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: 3.460 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.160 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 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 : 0.013 0.173 14677 Z= 0.742 Angle : 1.762 15.733 19723 Z= 1.160 Chirality : 0.092 0.388 2150 Planarity : 0.013 0.130 2520 Dihedral : 14.115 147.285 5701 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.74 % Favored : 96.09 % Rotamer: Outliers : 0.76 % Allowed : 2.85 % Favored : 96.39 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: -1.40 (0.18), residues: 1763 helix: -1.69 (0.16), residues: 660 sheet: 0.19 (0.32), residues: 265 loop : -0.48 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 464 TYR 0.109 0.019 TYR C 223 PHE 0.092 0.015 PHE A 329 TRP 0.134 0.025 TRP E 109 HIS 0.015 0.004 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.01259 (14677) covalent geometry : angle 1.76186 (19723) hydrogen bonds : bond 0.16167 ( 693) hydrogen bonds : angle 7.72043 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 184 average time/residue: 0.1603 time to fit residues: 40.3797 Evaluate side-chains 94 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 591 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN C 163 ASN ** A 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 633 HIS B 77 HIS B 79 ASN B 359 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.124897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.079782 restraints weight = 31384.055| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.40 r_work: 0.3137 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14677 Z= 0.134 Angle : 0.593 8.353 19723 Z= 0.328 Chirality : 0.043 0.151 2150 Planarity : 0.004 0.034 2520 Dihedral : 7.948 139.576 1997 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.27 % Allowed : 5.76 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.29 (0.20), residues: 1763 helix: 0.46 (0.19), residues: 692 sheet: 0.32 (0.28), residues: 323 loop : 0.07 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 464 TYR 0.016 0.002 TYR A 434 PHE 0.027 0.002 PHE E 103 TRP 0.025 0.002 TRP B 162 HIS 0.003 0.001 HIS C 401 Details of bonding type rmsd covalent geometry : bond 0.00293 (14677) covalent geometry : angle 0.59283 (19723) hydrogen bonds : bond 0.04357 ( 693) hydrogen bonds : angle 5.05770 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8732 (tpp) cc_final: 0.8289 (tmm) REVERT: A 109 THR cc_start: 0.8485 (m) cc_final: 0.8233 (p) REVERT: A 287 GLN cc_start: 0.7243 (tp40) cc_final: 0.6669 (mm-40) REVERT: A 628 MET cc_start: 0.6905 (ptm) cc_final: 0.6656 (ptp) REVERT: E 9 TYR cc_start: 0.6159 (p90) cc_final: 0.5936 (p90) outliers start: 20 outliers final: 7 residues processed: 122 average time/residue: 0.1325 time to fit residues: 23.6256 Evaluate side-chains 92 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 40.0000 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 77 HIS B 79 ASN B 306 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.120707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.073436 restraints weight = 32803.161| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.52 r_work: 0.3006 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 14677 Z= 0.292 Angle : 0.670 7.952 19723 Z= 0.357 Chirality : 0.046 0.159 2150 Planarity : 0.004 0.044 2520 Dihedral : 7.537 133.567 1990 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.58 % Allowed : 7.22 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.15 (0.20), residues: 1763 helix: 0.72 (0.19), residues: 674 sheet: -0.11 (0.27), residues: 331 loop : -0.22 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 464 TYR 0.026 0.002 TYR A 434 PHE 0.034 0.002 PHE A 329 TRP 0.033 0.003 TRP C 297 HIS 0.007 0.002 HIS B 490 Details of bonding type rmsd covalent geometry : bond 0.00687 (14677) covalent geometry : angle 0.67047 (19723) hydrogen bonds : bond 0.04544 ( 693) hydrogen bonds : angle 5.12452 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.8812 (tpp) cc_final: 0.8466 (mmm) REVERT: A 127 ASP cc_start: 0.8309 (t0) cc_final: 0.8078 (p0) REVERT: A 287 GLN cc_start: 0.7374 (tp40) cc_final: 0.6893 (mm-40) REVERT: A 457 LYS cc_start: 0.8647 (tppt) cc_final: 0.8353 (tppt) REVERT: B 287 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 581 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7810 (pttm) outliers start: 25 outliers final: 13 residues processed: 109 average time/residue: 0.1370 time to fit residues: 21.5846 Evaluate side-chains 95 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 356 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 166 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 HIS B 77 HIS B 79 ASN B 189 HIS B 514 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.124738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080761 restraints weight = 32443.999| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.96 r_work: 0.3140 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14677 Z= 0.113 Angle : 0.507 7.134 19723 Z= 0.275 Chirality : 0.041 0.151 2150 Planarity : 0.003 0.034 2520 Dihedral : 7.004 129.091 1990 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.46 % Allowed : 7.78 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.49 (0.20), residues: 1763 helix: 1.10 (0.20), residues: 688 sheet: -0.08 (0.27), residues: 342 loop : -0.07 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.017 0.001 TYR A 434 PHE 0.010 0.001 PHE A 329 TRP 0.041 0.002 TRP C 297 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00249 (14677) covalent geometry : angle 0.50660 (19723) hydrogen bonds : bond 0.03581 ( 693) hydrogen bonds : angle 4.66443 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.2027 (tt0) cc_final: 0.1586 (mm-30) REVERT: C 209 MET cc_start: -0.1126 (ttp) cc_final: -0.1551 (ptp) REVERT: A 30 MET cc_start: 0.8657 (tpp) cc_final: 0.8393 (mmm) REVERT: A 287 GLN cc_start: 0.7225 (tp40) cc_final: 0.6740 (mm-40) REVERT: B 142 TYR cc_start: 0.8943 (m-80) cc_final: 0.8555 (m-80) REVERT: B 287 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7311 (tm-30) REVERT: E 84 GLN cc_start: 0.6876 (tm-30) cc_final: 0.6496 (tm-30) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.1221 time to fit residues: 20.0505 Evaluate side-chains 94 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 148 optimal weight: 0.8980 chunk 121 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 40.0000 chunk 5 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 HIS A 633 HIS B 77 HIS B 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.124896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079091 restraints weight = 32445.800| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.45 r_work: 0.3178 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14677 Z= 0.115 Angle : 0.501 8.490 19723 Z= 0.268 Chirality : 0.041 0.141 2150 Planarity : 0.003 0.035 2520 Dihedral : 6.607 129.230 1986 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.58 % Allowed : 8.29 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.60 (0.20), residues: 1763 helix: 1.31 (0.20), residues: 686 sheet: -0.06 (0.27), residues: 347 loop : -0.12 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 78 TYR 0.017 0.001 TYR A 434 PHE 0.010 0.001 PHE A 329 TRP 0.030 0.002 TRP C 297 HIS 0.014 0.001 HIS A 633 Details of bonding type rmsd covalent geometry : bond 0.00260 (14677) covalent geometry : angle 0.50070 (19723) hydrogen bonds : bond 0.03448 ( 693) hydrogen bonds : angle 4.54368 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.2075 (tt0) cc_final: 0.1650 (mm-30) REVERT: C 48 MET cc_start: 0.6931 (mtp) cc_final: 0.6264 (mmt) REVERT: C 209 MET cc_start: -0.1056 (ttp) cc_final: -0.1264 (ptp) REVERT: A 30 MET cc_start: 0.8579 (tpp) cc_final: 0.8273 (mmm) REVERT: A 287 GLN cc_start: 0.7168 (tp40) cc_final: 0.6684 (mm-40) REVERT: A 625 MET cc_start: 0.3951 (ptt) cc_final: 0.3650 (ptp) REVERT: B 142 TYR cc_start: 0.8990 (m-80) cc_final: 0.8602 (m-80) REVERT: B 287 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 572 CYS cc_start: 0.9126 (m) cc_final: 0.8876 (m) REVERT: B 581 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7738 (pttm) outliers start: 25 outliers final: 13 residues processed: 107 average time/residue: 0.1144 time to fit residues: 18.8262 Evaluate side-chains 95 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 147 optimal weight: 0.0000 chunk 119 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 79 ASN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.122669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077425 restraints weight = 32415.603| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.82 r_work: 0.3106 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14677 Z= 0.181 Angle : 0.540 9.212 19723 Z= 0.287 Chirality : 0.042 0.145 2150 Planarity : 0.004 0.053 2520 Dihedral : 6.708 131.093 1986 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.58 % Allowed : 8.73 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.51 (0.20), residues: 1763 helix: 1.31 (0.20), residues: 686 sheet: -0.10 (0.28), residues: 347 loop : -0.27 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 78 TYR 0.025 0.002 TYR E 9 PHE 0.019 0.001 PHE A 329 TRP 0.042 0.002 TRP C 297 HIS 0.004 0.001 HIS B 490 Details of bonding type rmsd covalent geometry : bond 0.00423 (14677) covalent geometry : angle 0.54040 (19723) hydrogen bonds : bond 0.03641 ( 693) hydrogen bonds : angle 4.65562 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.2292 (tt0) cc_final: 0.1799 (mm-30) REVERT: A 30 MET cc_start: 0.8720 (tpp) cc_final: 0.8417 (mmm) REVERT: A 287 GLN cc_start: 0.7221 (tp40) cc_final: 0.6763 (mm-40) REVERT: A 625 MET cc_start: 0.3873 (ptt) cc_final: 0.3530 (ptp) REVERT: B 142 TYR cc_start: 0.8965 (m-80) cc_final: 0.8471 (m-80) REVERT: B 287 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7338 (tm-30) REVERT: B 581 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7837 (pttm) REVERT: E 9 TYR cc_start: 0.5595 (p90) cc_final: 0.5343 (p90) REVERT: E 84 GLN cc_start: 0.6898 (tm-30) cc_final: 0.6557 (tm-30) outliers start: 25 outliers final: 13 residues processed: 97 average time/residue: 0.1036 time to fit residues: 15.7048 Evaluate side-chains 92 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 50.0000 chunk 142 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.0050 chunk 126 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.123704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078080 restraints weight = 32269.097| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.22 r_work: 0.3171 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14677 Z= 0.131 Angle : 0.498 9.738 19723 Z= 0.266 Chirality : 0.041 0.138 2150 Planarity : 0.003 0.063 2520 Dihedral : 6.577 129.919 1986 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.27 % Allowed : 9.30 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.60 (0.20), residues: 1763 helix: 1.48 (0.20), residues: 684 sheet: -0.05 (0.28), residues: 345 loop : -0.32 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.020 0.001 TYR E 9 PHE 0.012 0.001 PHE A 329 TRP 0.035 0.002 TRP C 297 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00303 (14677) covalent geometry : angle 0.49767 (19723) hydrogen bonds : bond 0.03388 ( 693) hydrogen bonds : angle 4.51274 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.2913 (tt0) cc_final: 0.2350 (mm-30) REVERT: C 48 MET cc_start: 0.6875 (mtp) cc_final: 0.6069 (mmt) REVERT: A 30 MET cc_start: 0.8636 (tpp) cc_final: 0.8332 (mmm) REVERT: A 287 GLN cc_start: 0.7131 (tp40) cc_final: 0.6662 (mm-40) REVERT: A 625 MET cc_start: 0.3880 (ptt) cc_final: 0.3597 (ptp) REVERT: B 142 TYR cc_start: 0.8954 (m-80) cc_final: 0.8465 (m-80) REVERT: B 287 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 572 CYS cc_start: 0.9134 (m) cc_final: 0.8851 (m) REVERT: B 581 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7807 (pttm) REVERT: E 84 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6970 (tm-30) outliers start: 20 outliers final: 16 residues processed: 96 average time/residue: 0.1079 time to fit residues: 15.9911 Evaluate side-chains 95 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.123684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.077931 restraints weight = 32305.081| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.29 r_work: 0.3167 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14677 Z= 0.131 Angle : 0.495 10.597 19723 Z= 0.265 Chirality : 0.041 0.140 2150 Planarity : 0.003 0.067 2520 Dihedral : 6.521 129.463 1986 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.20 % Allowed : 9.49 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.63 (0.20), residues: 1763 helix: 1.56 (0.20), residues: 682 sheet: -0.03 (0.28), residues: 351 loop : -0.36 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 78 TYR 0.019 0.001 TYR A 434 PHE 0.012 0.001 PHE A 329 TRP 0.033 0.002 TRP C 297 HIS 0.003 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00302 (14677) covalent geometry : angle 0.49511 (19723) hydrogen bonds : bond 0.03358 ( 693) hydrogen bonds : angle 4.46662 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.3039 (tt0) cc_final: 0.2572 (mm-30) REVERT: C 48 MET cc_start: 0.6857 (mtp) cc_final: 0.6074 (mmt) REVERT: A 30 MET cc_start: 0.8653 (tpp) cc_final: 0.8333 (mmm) REVERT: A 287 GLN cc_start: 0.7117 (tp40) cc_final: 0.6652 (mm-40) REVERT: A 625 MET cc_start: 0.3928 (ptt) cc_final: 0.3445 (ptp) REVERT: B 142 TYR cc_start: 0.8962 (m-80) cc_final: 0.8458 (m-80) REVERT: B 287 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 572 CYS cc_start: 0.9157 (m) cc_final: 0.8880 (m) REVERT: B 581 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7818 (pttm) REVERT: E 84 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7011 (tm-30) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.1074 time to fit residues: 16.1143 Evaluate side-chains 96 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 683 THR Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 164 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 79 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS B 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.121998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075880 restraints weight = 32693.637| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.34 r_work: 0.3121 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14677 Z= 0.216 Angle : 0.570 10.810 19723 Z= 0.300 Chirality : 0.043 0.146 2150 Planarity : 0.004 0.064 2520 Dihedral : 6.719 130.828 1986 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.20 % Allowed : 9.81 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.45 (0.20), residues: 1763 helix: 1.42 (0.20), residues: 680 sheet: -0.16 (0.28), residues: 344 loop : -0.43 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 201 TYR 0.034 0.002 TYR E 9 PHE 0.023 0.001 PHE A 329 TRP 0.051 0.002 TRP C 297 HIS 0.005 0.001 HIS B 490 Details of bonding type rmsd covalent geometry : bond 0.00507 (14677) covalent geometry : angle 0.56981 (19723) hydrogen bonds : bond 0.03680 ( 693) hydrogen bonds : angle 4.68217 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.3186 (tt0) cc_final: 0.2716 (mm-30) REVERT: C 48 MET cc_start: 0.6835 (mtp) cc_final: 0.6111 (mmt) REVERT: A 30 MET cc_start: 0.8697 (tpp) cc_final: 0.8376 (mmm) REVERT: A 287 GLN cc_start: 0.7240 (tp40) cc_final: 0.6784 (mm-40) REVERT: A 457 LYS cc_start: 0.8687 (tppt) cc_final: 0.8484 (tppt) REVERT: A 620 ARG cc_start: 0.7208 (mpt180) cc_final: 0.6624 (mmt-90) REVERT: B 142 TYR cc_start: 0.8962 (m-80) cc_final: 0.8355 (m-80) REVERT: B 287 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 581 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7745 (pttm) REVERT: E 12 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7599 (tpp80) REVERT: E 84 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6734 (tm-30) outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 0.1168 time to fit residues: 17.0425 Evaluate side-chains 93 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.123039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.077139 restraints weight = 32296.229| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.33 r_work: 0.3149 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14677 Z= 0.154 Angle : 0.527 10.412 19723 Z= 0.280 Chirality : 0.041 0.142 2150 Planarity : 0.003 0.064 2520 Dihedral : 6.609 129.450 1986 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.08 % Allowed : 9.81 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.50 (0.20), residues: 1763 helix: 1.47 (0.20), residues: 682 sheet: -0.16 (0.28), residues: 346 loop : -0.42 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 620 TYR 0.020 0.001 TYR A 434 PHE 0.016 0.001 PHE A 329 TRP 0.049 0.002 TRP C 297 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00358 (14677) covalent geometry : angle 0.52715 (19723) hydrogen bonds : bond 0.03456 ( 693) hydrogen bonds : angle 4.57043 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3526 Ramachandran restraints generated. 1763 Oldfield, 0 Emsley, 1763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 23 GLU cc_start: 0.3315 (tt0) cc_final: 0.2850 (mm-30) REVERT: C 48 MET cc_start: 0.6810 (mtp) cc_final: 0.6081 (mmt) REVERT: A 30 MET cc_start: 0.8674 (tpp) cc_final: 0.8329 (mmm) REVERT: A 287 GLN cc_start: 0.7195 (tp40) cc_final: 0.6727 (mm-40) REVERT: A 620 ARG cc_start: 0.7217 (mpt180) cc_final: 0.6602 (mmt-90) REVERT: B 142 TYR cc_start: 0.8968 (m-80) cc_final: 0.8426 (m-80) REVERT: B 287 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 572 CYS cc_start: 0.9138 (m) cc_final: 0.8849 (m) REVERT: B 581 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7769 (pttm) REVERT: E 84 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6762 (tm-30) outliers start: 17 outliers final: 15 residues processed: 95 average time/residue: 0.1191 time to fit residues: 17.2150 Evaluate side-chains 94 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 472 ASP Chi-restraints excluded: chain A residue 581 LYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 284 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 581 LYS Chi-restraints excluded: chain B residue 677 SER Chi-restraints excluded: chain B residue 694 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 137 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.123634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.078046 restraints weight = 32215.503| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.27 r_work: 0.3171 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14677 Z= 0.130 Angle : 0.517 9.991 19723 Z= 0.274 Chirality : 0.041 0.148 2150 Planarity : 0.003 0.064 2520 Dihedral : 6.490 128.820 1986 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.95 % Allowed : 10.00 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 are not related in a simple way. whole: 0.58 (0.20), residues: 1763 helix: 1.57 (0.20), residues: 682 sheet: -0.14 (0.28), residues: 356 loop : -0.40 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.018 0.001 TYR A 434 PHE 0.012 0.001 PHE A 329 TRP 0.047 0.002 TRP C 297 HIS 0.004 0.001 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00301 (14677) covalent geometry : angle 0.51704 (19723) hydrogen bonds : bond 0.03324 ( 693) hydrogen bonds : angle 4.47232 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3798.03 seconds wall clock time: 65 minutes 44.84 seconds (3944.84 seconds total)