Starting phenix.real_space_refine on Fri Aug 7 07:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lck_66772/08_2026/9lck_66772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lck_66772/08_2026/9lck_66772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lck_66772/08_2026/9lck_66772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lck_66772/08_2026/9lck_66772.map" model { file = "/net/cci-nas-00/data/ceres_data/9lck_66772/08_2026/9lck_66772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lck_66772/08_2026/9lck_66772.cif" } resolution = 2.98 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= 0.003 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: 6 Type Number sf(0) Gaussians P 27 5.49 5 S 71 5.16 5 C 6172 2.51 5 N 1715 2.21 5 O 1945 1.98 5 H 9620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19550 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 8258 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 28, 'TRANS': 487} Chain: "B" Number of atoms: 9825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 9825 Classifications: {'peptide': 618} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 589} Chain breaks: 2 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 600 Classifications: {'peptide': 36} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 283 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 584 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Time building chain proxies: 2.64, per 1000 atoms: 0.14 Number of scatterers: 19550 At special positions: 0 Unit cell: (112.554, 95.316, 99.372, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 27 15.00 O 1945 8.00 N 1715 7.00 C 6172 6.00 H 9620 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 468.8 milliseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 48.8% alpha, 14.1% beta 8 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.523A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.870A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.549A pdb=" N ASP A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 removed outlier: 4.068A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.822A pdb=" N ILE A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.648A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.892A pdb=" N GLU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.608A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.535A pdb=" N LEU A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Proline residue: A 534 - end of helix removed outlier: 3.935A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 578 through 581 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.924A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 removed outlier: 4.384A pdb=" N GLU A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.759A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 removed outlier: 3.977A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.520A pdb=" N LEU A 701 " --> pdb=" O ASP A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.525A pdb=" N VAL B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.594A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.536A pdb=" N THR B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.538A pdb=" N ASN B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.986A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 176 removed outlier: 3.503A pdb=" N VAL B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 5.431A pdb=" N ILE B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.849A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.594A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 3.844A pdb=" N ILE B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.687A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.691A pdb=" N LYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.995A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.532A pdb=" N LYS B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.981A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.664A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.881A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 324 removed outlier: 9.574A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 549 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL A 557 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.412A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.638A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 619 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.515A pdb=" N MET B 179 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 243 removed outlier: 4.571A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 489 through 491 426 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9600 1.03 - 1.23: 51 1.23 - 1.42: 4257 1.42 - 1.62: 5782 1.62 - 1.81: 122 Bond restraints: 19812 Sorted by residual: bond pdb=" NZ LYS B 577 " pdb=" HZ1 LYS B 577 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 577 " pdb=" HZ2 LYS B 577 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS B 308 " pdb=" HZ2 LYS B 308 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS B 209 " pdb=" HZ3 LYS B 209 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS B 586 " pdb=" HZ2 LYS B 586 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 19807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.53: 35805 8.53 - 17.06: 0 17.06 - 25.59: 0 25.59 - 34.12: 1 34.12 - 42.65: 2 Bond angle restraints: 35808 Sorted by residual: angle pdb=" CA MET C 90 " pdb=" N MET C 90 " pdb=" H MET C 90 " ideal model delta sigma weight residual 114.00 156.65 -42.65 3.00e+00 1.11e-01 2.02e+02 angle pdb=" CA GLY B 206 " pdb=" N GLY B 206 " pdb=" H GLY B 206 " ideal model delta sigma weight residual 114.00 154.47 -40.47 3.00e+00 1.11e-01 1.82e+02 angle pdb=" CA ALA B 661 " pdb=" N ALA B 661 " pdb=" H ALA B 661 " ideal model delta sigma weight residual 114.00 141.48 -27.48 3.00e+00 1.11e-01 8.39e+01 angle pdb=" O5' U E 18 " pdb=" C5' U E 18 " pdb=" C4' U E 18 " ideal model delta sigma weight residual 109.40 112.84 -3.44 8.00e-01 1.56e+00 1.85e+01 angle pdb=" N ASP A 674 " pdb=" CA ASP A 674 " pdb=" C ASP A 674 " ideal model delta sigma weight residual 113.16 108.41 4.75 1.24e+00 6.50e-01 1.47e+01 ... (remaining 35803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 9069 36.00 - 71.99: 238 71.99 - 107.99: 20 107.99 - 143.99: 0 143.99 - 179.99: 6 Dihedral angle restraints: 9333 sinusoidal: 5376 harmonic: 3957 Sorted by residual: dihedral pdb=" CA SER B 585 " pdb=" C SER B 585 " pdb=" N LYS B 586 " pdb=" CA LYS B 586 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ARG B 215 " pdb=" C ARG B 215 " pdb=" N SER B 216 " pdb=" CA SER B 216 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG B 602 " pdb=" C ARG B 602 " pdb=" N ASN B 603 " pdb=" CA ASN B 603 " ideal model delta harmonic sigma weight residual 180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 9330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 967 0.033 - 0.067: 395 0.067 - 0.100: 118 0.100 - 0.134: 47 0.134 - 0.167: 11 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA ILE A 201 " pdb=" N ILE A 201 " pdb=" C ILE A 201 " pdb=" CB ILE A 201 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1535 not shown) Planarity restraints: 2815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 144 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C ALA B 144 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA B 144 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 145 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 559 " 0.009 2.00e-02 2.50e+03 1.48e-02 6.53e+00 pdb=" CG TYR B 559 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 559 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 559 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 559 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 559 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 559 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 559 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR B 559 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR B 559 " -0.033 2.00e-02 2.50e+03 pdb=" HE1 TYR B 559 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 559 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 496 " 0.174 9.50e-02 1.11e+02 5.88e-02 4.94e+00 pdb=" NE ARG A 496 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 496 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 496 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 496 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 496 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG A 496 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG A 496 " -0.013 2.00e-02 2.50e+03 pdb="HH22 ARG A 496 " 0.008 2.00e-02 2.50e+03 ... (remaining 2812 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 253 2.09 - 2.72: 32443 2.72 - 3.35: 54492 3.35 - 3.97: 70902 3.97 - 4.60: 111707 Nonbonded interactions: 269797 Sorted by model distance: nonbonded pdb=" H61 A E 1 " pdb="HO2' A E 10 " model vdw 1.468 2.100 nonbonded pdb=" HG SER B 173 " pdb=" HH TYR B 217 " model vdw 1.535 2.100 nonbonded pdb="HE22 GLN A 217 " pdb=" OD1 ASN B 58 " model vdw 1.672 2.450 nonbonded pdb=" OE2 GLU B 491 " pdb=" H SER B 494 " model vdw 1.701 2.450 nonbonded pdb=" O ASP A 426 " pdb="HE21 GLN B 549 " model vdw 1.719 2.450 ... (remaining 269792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.050 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10192 Z= 0.204 Angle : 0.749 6.876 13883 Z= 0.436 Chirality : 0.043 0.167 1538 Planarity : 0.005 0.071 1688 Dihedral : 14.032 95.109 4042 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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 are not related in a simple way. whole: -1.10 (0.24), residues: 1158 helix: 0.13 (0.23), residues: 507 sheet: -0.83 (0.45), residues: 109 loop : -1.51 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 496 TYR 0.014 0.002 TYR B 559 PHE 0.021 0.002 PHE A 611 TRP 0.017 0.002 TRP B 613 HIS 0.002 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (10192) covalent geometry : angle 0.74913 / 0.44 (13883) hydrogen bonds : bond 0.16411 / 11.35 ( 444) hydrogen bonds : angle 6.41648 / 4.47 ( 1229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.8490 (ptt) cc_final: 0.8076 (ptt) REVERT: B 311 GLU cc_start: 0.8096 (mp0) cc_final: 0.7875 (mp0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 1.3970 time to fit residues: 296.9754 Evaluate side-chains 144 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 284 ASN B 533 ASN ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.164700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127634 restraints weight = 32949.292| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.93 r_work: 0.3234 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10192 Z= 0.136 Angle : 0.582 5.804 13883 Z= 0.306 Chirality : 0.039 0.140 1538 Planarity : 0.005 0.047 1688 Dihedral : 11.880 92.167 1665 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.74 % Allowed : 10.43 % Favored : 87.83 % 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 are not related in a simple way. whole: -0.75 (0.24), residues: 1158 helix: 0.66 (0.23), residues: 510 sheet: -0.71 (0.47), residues: 105 loop : -1.60 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 211 TYR 0.013 0.001 TYR B 555 PHE 0.015 0.001 PHE A 611 TRP 0.008 0.001 TRP C 98 HIS 0.002 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10192) covalent geometry : angle 0.58211 / 0.31 (13883) hydrogen bonds : bond 0.05529 / 3.90 ( 444) hydrogen bonds : angle 4.96101 / 3.49 ( 1229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: B 227 MET cc_start: 0.8436 (ptt) cc_final: 0.8000 (ptt) REVERT: C 71 ASN cc_start: 0.6430 (p0) cc_final: 0.6168 (p0) outliers start: 18 outliers final: 10 residues processed: 157 average time/residue: 1.2303 time to fit residues: 208.1028 Evaluate side-chains 147 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 533 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 412 ASN B 533 ASN B 536 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.160902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123284 restraints weight = 33033.231| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.96 r_work: 0.3212 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 10192 Z= 0.203 Angle : 0.584 5.867 13883 Z= 0.309 Chirality : 0.040 0.137 1538 Planarity : 0.005 0.060 1688 Dihedral : 11.886 91.878 1665 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 2.71 % Allowed : 11.59 % Favored : 85.70 % 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 are not related in a simple way. whole: -0.74 (0.24), residues: 1158 helix: 0.69 (0.23), residues: 507 sheet: -0.76 (0.45), residues: 118 loop : -1.60 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 269 TYR 0.012 0.002 TYR A 564 PHE 0.016 0.001 PHE A 611 TRP 0.009 0.001 TRP C 98 HIS 0.003 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (10192) covalent geometry : angle 0.58400 / 0.31 (13883) hydrogen bonds : bond 0.05238 / 3.64 ( 444) hydrogen bonds : angle 4.69678 / 3.28 ( 1229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: B 148 GLU cc_start: 0.8219 (mp0) cc_final: 0.7926 (mp0) REVERT: B 227 MET cc_start: 0.8555 (ptt) cc_final: 0.8194 (ptt) REVERT: B 331 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8236 (tp30) REVERT: B 481 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8576 (mtmt) REVERT: B 529 VAL cc_start: 0.8070 (p) cc_final: 0.7701 (m) REVERT: B 577 LYS cc_start: 0.6998 (tmmt) cc_final: 0.6792 (tmmt) REVERT: C 67 ILE cc_start: 0.7228 (mt) cc_final: 0.6965 (tt) REVERT: C 71 ASN cc_start: 0.6430 (p0) cc_final: 0.6196 (p0) outliers start: 28 outliers final: 15 residues processed: 156 average time/residue: 1.3623 time to fit residues: 228.4057 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 591 GLN B 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122964 restraints weight = 32819.371| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.80 r_work: 0.3184 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10192 Z= 0.157 Angle : 0.548 7.636 13883 Z= 0.288 Chirality : 0.039 0.138 1538 Planarity : 0.005 0.060 1688 Dihedral : 11.878 92.476 1665 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 3.00 % Allowed : 12.56 % Favored : 84.44 % 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 are not related in a simple way. whole: -0.66 (0.25), residues: 1158 helix: 0.83 (0.23), residues: 506 sheet: -0.74 (0.45), residues: 120 loop : -1.65 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 204 TYR 0.013 0.001 TYR B 620 PHE 0.011 0.001 PHE B 490 TRP 0.008 0.001 TRP A 368 HIS 0.003 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (10192) covalent geometry : angle 0.54843 / 0.29 (13883) hydrogen bonds : bond 0.04636 / 3.23 ( 444) hydrogen bonds : angle 4.48065 / 3.14 ( 1229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: B 227 MET cc_start: 0.8526 (ptt) cc_final: 0.8131 (ptt) REVERT: B 317 MET cc_start: 0.8032 (ptt) cc_final: 0.7770 (mmp) REVERT: B 481 LYS cc_start: 0.8909 (mtpt) cc_final: 0.8556 (mtmt) REVERT: C 67 ILE cc_start: 0.7216 (mt) cc_final: 0.6999 (tt) outliers start: 31 outliers final: 19 residues processed: 159 average time/residue: 1.3684 time to fit residues: 233.7814 Evaluate side-chains 162 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 64 optimal weight: 0.0770 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 587 GLN A 591 GLN B 536 ASN B 537 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.161704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123776 restraints weight = 32819.322| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.96 r_work: 0.3187 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10192 Z= 0.108 Angle : 0.520 6.904 13883 Z= 0.272 Chirality : 0.037 0.139 1538 Planarity : 0.005 0.065 1688 Dihedral : 11.792 91.686 1665 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 2.51 % Allowed : 13.91 % Favored : 83.57 % 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 are not related in a simple way. whole: -0.44 (0.25), residues: 1158 helix: 1.10 (0.24), residues: 507 sheet: -0.71 (0.45), residues: 120 loop : -1.60 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 204 TYR 0.013 0.001 TYR B 620 PHE 0.010 0.001 PHE B 490 TRP 0.010 0.001 TRP C 98 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10192) covalent geometry : angle 0.52033 / 0.27 (13883) hydrogen bonds : bond 0.04075 / 2.83 ( 444) hydrogen bonds : angle 4.28185 / 3.02 ( 1229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6835 (ptm160) REVERT: A 427 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: A 674 ASP cc_start: 0.7991 (t0) cc_final: 0.7636 (t0) REVERT: B 146 THR cc_start: 0.8868 (t) cc_final: 0.8526 (m) REVERT: B 227 MET cc_start: 0.8514 (ptt) cc_final: 0.8112 (ptt) REVERT: B 317 MET cc_start: 0.8045 (ptt) cc_final: 0.7789 (mmp) REVERT: B 481 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8567 (mtmt) REVERT: C 67 ILE cc_start: 0.7214 (mt) cc_final: 0.6996 (tt) outliers start: 26 outliers final: 13 residues processed: 159 average time/residue: 1.1728 time to fit residues: 200.6289 Evaluate side-chains 152 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.0020 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 0.0050 chunk 11 optimal weight: 2.9990 overall best weight: 0.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.160872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123106 restraints weight = 32820.115| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.95 r_work: 0.3160 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10192 Z= 0.129 Angle : 0.520 5.761 13883 Z= 0.274 Chirality : 0.037 0.138 1538 Planarity : 0.004 0.065 1688 Dihedral : 11.770 92.101 1665 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 2.42 % Allowed : 14.49 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.36 (0.25), residues: 1158 helix: 1.18 (0.24), residues: 511 sheet: -0.42 (0.48), residues: 110 loop : -1.65 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 269 TYR 0.015 0.001 TYR B 620 PHE 0.009 0.001 PHE B 490 TRP 0.008 0.001 TRP A 368 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10192) covalent geometry : angle 0.52010 / 0.27 (13883) hydrogen bonds : bond 0.04049 / 2.80 ( 444) hydrogen bonds : angle 4.17881 / 2.94 ( 1229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6938 (m-30) REVERT: A 427 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: A 674 ASP cc_start: 0.8026 (t0) cc_final: 0.7547 (t0) REVERT: B 146 THR cc_start: 0.8799 (t) cc_final: 0.8482 (m) REVERT: B 227 MET cc_start: 0.8490 (ptt) cc_final: 0.7975 (ptt) REVERT: B 311 GLU cc_start: 0.7873 (mp0) cc_final: 0.7609 (mp0) REVERT: B 317 MET cc_start: 0.8085 (ptt) cc_final: 0.7762 (mmp) REVERT: B 367 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7772 (tp40) REVERT: B 481 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8584 (mtmt) REVERT: C 61 LYS cc_start: 0.3935 (pttt) cc_final: 0.3396 (pptt) REVERT: C 67 ILE cc_start: 0.7181 (mt) cc_final: 0.6938 (tt) outliers start: 25 outliers final: 17 residues processed: 149 average time/residue: 1.2423 time to fit residues: 199.1635 Evaluate side-chains 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122946 restraints weight = 32970.925| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.95 r_work: 0.3162 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10192 Z= 0.137 Angle : 0.523 6.549 13883 Z= 0.275 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.077 1688 Dihedral : 11.768 92.626 1665 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 2.61 % Allowed : 15.07 % Favored : 82.32 % 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 are not related in a simple way. whole: -0.32 (0.25), residues: 1158 helix: 1.23 (0.24), residues: 512 sheet: -0.33 (0.49), residues: 107 loop : -1.66 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 204 TYR 0.015 0.001 TYR B 620 PHE 0.010 0.001 PHE B 490 TRP 0.011 0.001 TRP C 98 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10192) covalent geometry : angle 0.52311 / 0.28 (13883) hydrogen bonds : bond 0.04034 / 2.79 ( 444) hydrogen bonds : angle 4.13860 / 2.91 ( 1229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.7206 (mtp-110) cc_final: 0.6797 (ptm160) REVERT: A 380 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 427 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: B 146 THR cc_start: 0.8811 (t) cc_final: 0.8503 (m) REVERT: B 227 MET cc_start: 0.8515 (ptt) cc_final: 0.7998 (ptt) REVERT: B 311 GLU cc_start: 0.7917 (mp0) cc_final: 0.7658 (mp0) REVERT: B 317 MET cc_start: 0.8113 (ptt) cc_final: 0.7834 (mmp) REVERT: B 481 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8598 (mtmt) REVERT: C 61 LYS cc_start: 0.4005 (pttt) cc_final: 0.3409 (pptt) REVERT: C 67 ILE cc_start: 0.7310 (mt) cc_final: 0.7110 (tt) REVERT: C 75 GLN cc_start: 0.6053 (tp-100) cc_final: 0.5785 (tp40) outliers start: 27 outliers final: 18 residues processed: 151 average time/residue: 1.2329 time to fit residues: 200.1695 Evaluate side-chains 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121997 restraints weight = 32777.700| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.85 r_work: 0.3161 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10192 Z= 0.141 Angle : 0.524 6.365 13883 Z= 0.276 Chirality : 0.038 0.138 1538 Planarity : 0.005 0.079 1688 Dihedral : 11.776 93.852 1665 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 2.80 % Allowed : 15.07 % Favored : 82.13 % 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 are not related in a simple way. whole: -0.31 (0.25), residues: 1158 helix: 1.24 (0.24), residues: 515 sheet: -0.30 (0.50), residues: 107 loop : -1.69 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 269 TYR 0.016 0.001 TYR B 559 PHE 0.010 0.001 PHE B 412 TRP 0.011 0.001 TRP C 98 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (10192) covalent geometry : angle 0.52358 / 0.28 (13883) hydrogen bonds : bond 0.04033 / 2.78 ( 444) hydrogen bonds : angle 4.08692 / 2.88 ( 1229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6980 (m-30) REVERT: A 427 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 441 MET cc_start: 0.7702 (ttm) cc_final: 0.7359 (ttm) REVERT: B 146 THR cc_start: 0.8853 (t) cc_final: 0.8565 (m) REVERT: B 227 MET cc_start: 0.8571 (ptt) cc_final: 0.8156 (ptt) REVERT: B 311 GLU cc_start: 0.7925 (mp0) cc_final: 0.7676 (mp0) REVERT: B 317 MET cc_start: 0.8088 (ptt) cc_final: 0.7879 (mmp) REVERT: B 481 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8606 (mtmt) REVERT: C 61 LYS cc_start: 0.4042 (pttt) cc_final: 0.3442 (pptt) outliers start: 29 outliers final: 19 residues processed: 149 average time/residue: 1.1934 time to fit residues: 191.8372 Evaluate side-chains 154 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 382 GLU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 533 ASN B 536 ASN B 621 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120987 restraints weight = 32562.537| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.84 r_work: 0.3158 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10192 Z= 0.106 Angle : 0.512 6.663 13883 Z= 0.269 Chirality : 0.037 0.139 1538 Planarity : 0.005 0.089 1688 Dihedral : 11.736 94.149 1665 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 2.32 % Allowed : 15.94 % Favored : 81.74 % 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 are not related in a simple way. whole: -0.19 (0.25), residues: 1158 helix: 1.38 (0.24), residues: 514 sheet: -0.31 (0.49), residues: 107 loop : -1.66 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 204 TYR 0.017 0.001 TYR B 620 PHE 0.009 0.001 PHE A 520 TRP 0.018 0.001 TRP B 613 HIS 0.001 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10192) covalent geometry : angle 0.51154 / 0.27 (13883) hydrogen bonds : bond 0.03706 / 2.55 ( 444) hydrogen bonds : angle 4.02317 / 2.83 ( 1229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6979 (m-30) REVERT: A 427 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: A 441 MET cc_start: 0.7679 (ttm) cc_final: 0.7339 (ttm) REVERT: B 146 THR cc_start: 0.8799 (t) cc_final: 0.8527 (m) REVERT: B 227 MET cc_start: 0.8560 (ptt) cc_final: 0.8145 (ptt) REVERT: B 311 GLU cc_start: 0.7935 (mp0) cc_final: 0.7666 (mp0) REVERT: B 317 MET cc_start: 0.8101 (ptt) cc_final: 0.7892 (mmp) REVERT: B 481 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8618 (mtmt) REVERT: C 61 LYS cc_start: 0.3925 (pttt) cc_final: 0.3380 (pptt) REVERT: C 75 GLN cc_start: 0.5879 (tp-100) cc_final: 0.5652 (tp40) outliers start: 24 outliers final: 17 residues processed: 149 average time/residue: 1.2644 time to fit residues: 203.0257 Evaluate side-chains 152 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN B 533 ASN B 536 ASN B 621 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122286 restraints weight = 32880.046| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.96 r_work: 0.3167 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10192 Z= 0.124 Angle : 0.520 6.822 13883 Z= 0.274 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.087 1688 Dihedral : 11.737 94.986 1665 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 1.93 % Allowed : 16.43 % Favored : 81.64 % 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 are not related in a simple way. whole: -0.20 (0.25), residues: 1158 helix: 1.37 (0.24), residues: 514 sheet: -0.27 (0.50), residues: 107 loop : -1.66 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 204 TYR 0.016 0.001 TYR B 559 PHE 0.009 0.001 PHE B 412 TRP 0.015 0.001 TRP B 613 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (10192) covalent geometry : angle 0.51971 / 0.27 (13883) hydrogen bonds : bond 0.03779 / 2.61 ( 444) hydrogen bonds : angle 4.01475 / 2.82 ( 1229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: A 427 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: A 441 MET cc_start: 0.7674 (ttm) cc_final: 0.7334 (ttm) REVERT: B 146 THR cc_start: 0.8819 (t) cc_final: 0.8560 (m) REVERT: B 227 MET cc_start: 0.8581 (ptt) cc_final: 0.8152 (ptt) REVERT: B 311 GLU cc_start: 0.7938 (mp0) cc_final: 0.7672 (mp0) REVERT: B 481 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8617 (mtmt) REVERT: C 61 LYS cc_start: 0.3956 (pttt) cc_final: 0.3412 (pptt) outliers start: 20 outliers final: 15 residues processed: 143 average time/residue: 1.2923 time to fit residues: 198.6974 Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 533 ASN B 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122918 restraints weight = 32866.273| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.91 r_work: 0.3202 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10192 Z= 0.111 Angle : 0.515 6.814 13883 Z= 0.270 Chirality : 0.037 0.139 1538 Planarity : 0.005 0.089 1688 Dihedral : 11.717 95.633 1665 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 2.32 % Allowed : 16.43 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.25), residues: 1158 helix: 1.41 (0.24), residues: 514 sheet: -0.27 (0.49), residues: 107 loop : -1.65 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 204 TYR 0.014 0.001 TYR B 620 PHE 0.008 0.001 PHE A 520 TRP 0.024 0.001 TRP B 613 HIS 0.002 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (10192) covalent geometry : angle 0.51535 / 0.27 (13883) hydrogen bonds : bond 0.03643 / 2.50 ( 444) hydrogen bonds : angle 3.99510 / 2.81 ( 1229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7089.62 seconds wall clock time: 120 minutes 26.90 seconds (7226.90 seconds total)