Starting phenix.real_space_refine on Thu Feb 5 20:28:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lck_66772/02_2026/9lck_66772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lck_66772/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lck_66772/02_2026/9lck_66772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lck_66772/02_2026/9lck_66772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lck_66772/02_2026/9lck_66772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lck_66772/02_2026/9lck_66772.map" } 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-2.0-5952/lib/python3.9/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: 3.60, per 1000 atoms: 0.18 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: 1.81 Conformation dependent library (CDL) restraints added in 518.1 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: 3.26 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: 4.49 Time building geometry restraints manager: 2.48 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=" 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 angle pdb=" N GLU B 148 " pdb=" CA GLU B 148 " pdb=" CB GLU B 148 " ideal model delta sigma weight residual 110.28 116.02 -5.74 1.55e+00 4.16e-01 1.37e+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: 978 0.033 - 0.067: 414 0.067 - 0.100: 93 0.100 - 0.134: 42 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: 1.230 Set stop_for_unknowns flag: 0.010 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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= 0.196 Angle : 0.733 6.876 13883 Z= 0.395 Chirality : 0.041 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 covalent geometry : bond 0.00429 (10192) covalent geometry : angle 0.73350 (13883) hydrogen bonds : bond 0.16411 ( 444) hydrogen bonds : angle 6.41648 ( 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 : 0.437 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: 0.8077 (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: 1.7753 time to fit residues: 373.8304 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 : 0.494 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 412 ASN B 284 ASN B 582 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126549 restraints weight = 33001.531| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.96 r_work: 0.3308 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10192 Z= 0.127 Angle : 0.553 6.114 13883 Z= 0.289 Chirality : 0.038 0.138 1538 Planarity : 0.005 0.049 1688 Dihedral : 11.862 92.440 1665 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.84 % Allowed : 10.53 % Favored : 87.63 % 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: -0.65 (0.24), residues: 1158 helix: 0.81 (0.23), residues: 502 sheet: -0.84 (0.46), residues: 107 loop : -1.54 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 269 TYR 0.014 0.001 TYR B 620 PHE 0.012 0.001 PHE A 611 TRP 0.009 0.001 TRP B 613 HIS 0.002 0.001 HIS B 456 Details of bonding type rmsd covalent geometry : bond 0.00289 (10192) covalent geometry : angle 0.55256 (13883) hydrogen bonds : bond 0.04590 ( 444) hydrogen bonds : angle 4.67292 ( 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 172 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: A 674 ASP cc_start: 0.8017 (t0) cc_final: 0.7602 (t0) REVERT: B 146 THR cc_start: 0.8960 (t) cc_final: 0.8601 (m) REVERT: B 174 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7766 (mpp) REVERT: B 227 MET cc_start: 0.8558 (ptt) cc_final: 0.8130 (ptt) REVERT: B 529 VAL cc_start: 0.8079 (p) cc_final: 0.7726 (m) REVERT: C 71 ASN cc_start: 0.6363 (p0) cc_final: 0.6129 (p0) outliers start: 19 outliers final: 7 residues processed: 161 average time/residue: 1.4186 time to fit residues: 243.7342 Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 692 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 477 MET Chi-restraints excluded: chain B residue 507 MET 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: 1.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 536 ASN C 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120755 restraints weight = 33121.116| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.95 r_work: 0.3125 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10192 Z= 0.219 Angle : 0.596 6.304 13883 Z= 0.316 Chirality : 0.041 0.158 1538 Planarity : 0.005 0.051 1688 Dihedral : 11.961 95.507 1665 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 3.57 % Allowed : 12.08 % Favored : 84.35 % 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: -0.68 (0.25), residues: 1158 helix: 0.88 (0.24), residues: 499 sheet: -0.74 (0.45), residues: 120 loop : -1.70 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 204 TYR 0.020 0.002 TYR A 564 PHE 0.016 0.002 PHE B 412 TRP 0.014 0.002 TRP B 613 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00517 (10192) covalent geometry : angle 0.59632 (13883) hydrogen bonds : bond 0.05113 ( 444) hydrogen bonds : angle 4.48941 ( 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 184 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: B 146 THR cc_start: 0.8889 (t) cc_final: 0.8551 (m) REVERT: B 227 MET cc_start: 0.8572 (ptt) cc_final: 0.8135 (ptt) REVERT: B 317 MET cc_start: 0.8089 (ptt) cc_final: 0.7792 (mmp) REVERT: B 348 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8447 (mtp) REVERT: B 481 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8646 (mtmt) outliers start: 37 outliers final: 17 residues processed: 164 average time/residue: 1.2905 time to fit residues: 225.5624 Evaluate side-chains 156 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 590 GLN 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 56 THR 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 298 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 592 SER 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: 0.7980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 104 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 591 GLN B 413 ASN B 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.159286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120051 restraints weight = 32842.067| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.82 r_work: 0.3143 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10192 Z= 0.114 Angle : 0.517 6.352 13883 Z= 0.270 Chirality : 0.037 0.138 1538 Planarity : 0.004 0.050 1688 Dihedral : 11.800 94.845 1665 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 3.09 % Allowed : 13.24 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.25), residues: 1158 helix: 1.11 (0.24), residues: 510 sheet: -0.47 (0.48), residues: 110 loop : -1.68 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.014 0.001 TYR B 620 PHE 0.011 0.001 PHE A 611 TRP 0.009 0.001 TRP B 613 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00268 (10192) covalent geometry : angle 0.51663 (13883) hydrogen bonds : bond 0.03875 ( 444) hydrogen bonds : angle 4.19202 ( 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 176 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7876 (mttt) REVERT: A 380 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: A 427 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: A 674 ASP cc_start: 0.8031 (t0) cc_final: 0.7406 (t0) REVERT: B 146 THR cc_start: 0.8761 (t) cc_final: 0.8478 (m) REVERT: B 227 MET cc_start: 0.8504 (ptt) cc_final: 0.8066 (ptt) REVERT: B 317 MET cc_start: 0.8093 (ptt) cc_final: 0.7782 (mmp) REVERT: B 577 LYS cc_start: 0.7000 (tmmt) cc_final: 0.6722 (tmmt) REVERT: C 61 LYS cc_start: 0.4027 (pttt) cc_final: 0.3418 (pptt) REVERT: C 72 GLU cc_start: 0.6004 (mp0) cc_final: 0.5299 (mp0) outliers start: 32 outliers final: 17 residues processed: 158 average time/residue: 1.2392 time to fit residues: 209.2941 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 : 0.396 ------------------------------------------------------------------------------- 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 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 298 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 628 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: 1.9990 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 587 GLN A 591 GLN B 533 ASN B 536 ASN ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121700 restraints weight = 32709.072| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.88 r_work: 0.3165 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10192 Z= 0.135 Angle : 0.527 6.136 13883 Z= 0.277 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.058 1688 Dihedral : 11.776 96.470 1665 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 2.80 % Allowed : 14.69 % Favored : 82.51 % 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: -0.37 (0.25), residues: 1158 helix: 1.20 (0.24), residues: 512 sheet: -0.41 (0.49), residues: 110 loop : -1.69 (0.26), residues: 536 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 B 613 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00321 (10192) covalent geometry : angle 0.52739 (13883) hydrogen bonds : bond 0.03973 ( 444) hydrogen bonds : angle 4.13373 ( 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 168 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7882 (mttt) REVERT: A 380 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7130 (m-30) REVERT: A 427 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 441 MET cc_start: 0.7744 (ttm) cc_final: 0.7397 (ttm) REVERT: B 61 THR cc_start: 0.9043 (m) cc_final: 0.8760 (p) REVERT: B 146 THR cc_start: 0.8864 (t) cc_final: 0.8565 (m) REVERT: B 227 MET cc_start: 0.8576 (ptt) cc_final: 0.8147 (ptt) REVERT: B 577 LYS cc_start: 0.7100 (tmmt) cc_final: 0.6893 (tmmt) REVERT: C 61 LYS cc_start: 0.4118 (pttt) cc_final: 0.3499 (pptt) REVERT: C 71 ASN cc_start: 0.6784 (p0) cc_final: 0.6573 (p0) outliers start: 29 outliers final: 17 residues processed: 155 average time/residue: 1.4092 time to fit residues: 232.7247 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 : 0.553 ------------------------------------------------------------------------------- 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 514 ASP Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 559 ARG 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 298 LEU Chi-restraints excluded: chain B residue 477 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 533 ASN B 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119673 restraints weight = 32761.538| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.81 r_work: 0.3158 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10192 Z= 0.133 Angle : 0.519 6.036 13883 Z= 0.272 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.063 1688 Dihedral : 11.774 98.192 1665 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 3.00 % Allowed : 14.69 % 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: -0.29 (0.25), residues: 1158 helix: 1.26 (0.24), residues: 518 sheet: -0.34 (0.50), residues: 107 loop : -1.69 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 204 TYR 0.014 0.001 TYR B 620 PHE 0.009 0.001 PHE B 490 TRP 0.009 0.001 TRP B 613 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00318 (10192) covalent geometry : angle 0.51893 (13883) hydrogen bonds : bond 0.03845 ( 444) hydrogen bonds : angle 4.06001 ( 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 165 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7885 (mttt) REVERT: A 380 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7157 (m-30) REVERT: A 427 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 441 MET cc_start: 0.7781 (ttm) cc_final: 0.7428 (ttm) REVERT: B 61 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8660 (p) REVERT: B 146 THR cc_start: 0.8875 (t) cc_final: 0.8577 (m) REVERT: B 227 MET cc_start: 0.8598 (ptt) cc_final: 0.8159 (ptt) REVERT: C 61 LYS cc_start: 0.4142 (pttt) cc_final: 0.3516 (pptt) outliers start: 31 outliers final: 19 residues processed: 149 average time/residue: 1.3162 time to fit residues: 209.2949 Evaluate side-chains 157 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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 61 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 67 ILE 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: 4.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 428 GLN 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 = 0.3850 r_free = 0.3850 target = 0.157705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118688 restraints weight = 32814.525| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.82 r_work: 0.3106 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10192 Z= 0.148 Angle : 0.529 6.536 13883 Z= 0.278 Chirality : 0.037 0.137 1538 Planarity : 0.005 0.067 1688 Dihedral : 11.785 100.696 1665 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 2.61 % Allowed : 15.36 % Favored : 82.03 % 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: -0.24 (0.25), residues: 1158 helix: 1.33 (0.24), residues: 518 sheet: -0.37 (0.50), residues: 107 loop : -1.67 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 204 TYR 0.013 0.001 TYR B 559 PHE 0.010 0.001 PHE B 490 TRP 0.011 0.001 TRP B 613 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00354 (10192) covalent geometry : angle 0.52944 (13883) hydrogen bonds : bond 0.03925 ( 444) hydrogen bonds : angle 4.04133 ( 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 164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7809 (mttt) REVERT: A 427 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: A 441 MET cc_start: 0.7747 (ttm) cc_final: 0.7360 (ttm) REVERT: B 61 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8788 (p) REVERT: B 146 THR cc_start: 0.8736 (t) cc_final: 0.8458 (m) REVERT: B 227 MET cc_start: 0.8559 (ptt) cc_final: 0.8085 (ptt) REVERT: C 61 LYS cc_start: 0.3917 (pttt) cc_final: 0.3388 (pptt) outliers start: 27 outliers final: 20 residues processed: 150 average time/residue: 1.1972 time to fit residues: 192.3161 Evaluate side-chains 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET 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 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 61 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 67 ILE 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: 3.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 7 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118865 restraints weight = 32794.455| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.89 r_work: 0.3219 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10192 Z= 0.131 Angle : 0.527 6.216 13883 Z= 0.275 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.077 1688 Dihedral : 11.765 102.425 1665 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 2.42 % Allowed : 16.04 % Favored : 81.55 % 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: -0.21 (0.25), residues: 1158 helix: 1.36 (0.24), residues: 522 sheet: -0.38 (0.49), residues: 107 loop : -1.68 (0.26), residues: 529 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 0.009 0.001 PHE B 490 TRP 0.014 0.001 TRP B 613 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00316 (10192) covalent geometry : angle 0.52693 (13883) hydrogen bonds : bond 0.03732 ( 444) hydrogen bonds : angle 3.97824 ( 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 160 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7863 (mttt) REVERT: A 427 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: A 441 MET cc_start: 0.7832 (ttm) cc_final: 0.7477 (ttm) REVERT: B 146 THR cc_start: 0.8902 (t) cc_final: 0.8604 (m) REVERT: B 227 MET cc_start: 0.8636 (ptt) cc_final: 0.8174 (ptt) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 1.3581 time to fit residues: 214.6120 Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET 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 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 282 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 477 MET 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: 0.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122789 restraints weight = 32821.942| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.86 r_work: 0.3265 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2949 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= 0.126 Angle : 0.528 6.596 13883 Z= 0.275 Chirality : 0.037 0.139 1538 Planarity : 0.005 0.082 1688 Dihedral : 11.745 104.246 1665 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 2.42 % Allowed : 16.33 % 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: -0.14 (0.25), residues: 1158 helix: 1.43 (0.24), residues: 522 sheet: -0.32 (0.49), residues: 107 loop : -1.66 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 204 TYR 0.011 0.001 TYR B 620 PHE 0.009 0.001 PHE B 490 TRP 0.021 0.001 TRP C 98 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00303 (10192) covalent geometry : angle 0.52753 (13883) hydrogen bonds : bond 0.03634 ( 444) hydrogen bonds : angle 3.93049 ( 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 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7873 (mttt) REVERT: A 427 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7136 (pm20) REVERT: A 441 MET cc_start: 0.7842 (ttm) cc_final: 0.7510 (ttm) REVERT: A 656 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: B 146 THR cc_start: 0.8981 (t) cc_final: 0.8708 (m) REVERT: B 211 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7421 (mtt-85) REVERT: B 219 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 227 MET cc_start: 0.8716 (ptt) cc_final: 0.8261 (ptt) REVERT: B 593 ASP cc_start: 0.8426 (p0) cc_final: 0.8116 (p0) outliers start: 25 outliers final: 19 residues processed: 144 average time/residue: 1.4090 time to fit residues: 216.0805 Evaluate side-chains 150 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 656 GLU 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 219 ILE Chi-restraints excluded: chain B residue 282 LEU 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 67 ILE 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: 1.9990 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122575 restraints weight = 32949.730| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.85 r_work: 0.3143 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3027 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= 0.134 Angle : 0.534 6.460 13883 Z= 0.278 Chirality : 0.037 0.139 1538 Planarity : 0.005 0.086 1688 Dihedral : 11.759 106.010 1665 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 2.51 % Allowed : 16.33 % Favored : 81.16 % 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: -0.12 (0.25), residues: 1158 helix: 1.44 (0.24), residues: 522 sheet: -0.34 (0.49), residues: 107 loop : -1.64 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 204 TYR 0.011 0.001 TYR A 464 PHE 0.009 0.001 PHE B 490 TRP 0.020 0.001 TRP C 98 HIS 0.002 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00324 (10192) covalent geometry : angle 0.53385 (13883) hydrogen bonds : bond 0.03692 ( 444) hydrogen bonds : angle 3.94564 ( 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 159 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7809 (mttt) REVERT: A 427 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: A 441 MET cc_start: 0.7805 (ttm) cc_final: 0.7450 (ttm) REVERT: A 656 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 146 THR cc_start: 0.8804 (t) cc_final: 0.8542 (m) REVERT: B 211 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7469 (mtt-85) REVERT: B 227 MET cc_start: 0.8614 (ptt) cc_final: 0.8141 (ptt) REVERT: B 615 LEU cc_start: 0.8796 (mm) cc_final: 0.8563 (mp) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 1.5025 time to fit residues: 235.5441 Evaluate side-chains 154 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 656 GLU 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 282 LEU 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 67 ILE 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: 1.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122602 restraints weight = 33034.578| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.87 r_work: 0.3198 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10192 Z= 0.132 Angle : 0.532 6.386 13883 Z= 0.277 Chirality : 0.037 0.137 1538 Planarity : 0.005 0.086 1688 Dihedral : 11.754 107.873 1665 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 2.22 % Allowed : 16.62 % Favored : 81.16 % 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: -0.08 (0.25), residues: 1158 helix: 1.43 (0.24), residues: 525 sheet: -0.32 (0.49), residues: 107 loop : -1.60 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 204 TYR 0.011 0.001 TYR A 464 PHE 0.009 0.001 PHE B 490 TRP 0.022 0.001 TRP C 98 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00317 (10192) covalent geometry : angle 0.53166 (13883) hydrogen bonds : bond 0.03647 ( 444) hydrogen bonds : angle 3.93460 ( 1229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7175.73 seconds wall clock time: 121 minutes 58.00 seconds (7318.00 seconds total)