Starting phenix.real_space_refine on Sat Jul 4 10:38:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lck_66772/07_2026/9lck_66772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lck_66772/07_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_66772/07_2026/9lck_66772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lck_66772/07_2026/9lck_66772.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lck_66772/07_2026/9lck_66772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lck_66772/07_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-dev-6108/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: 3.16, per 1000 atoms: 0.16 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: 1.85 Conformation dependent library (CDL) restraints added in 381.5 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: 3.04 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: 4.59 Time building geometry restraints manager: 2.45 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: 1.270 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 20.950 Find NCS groups from input model: 0.050 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:7.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- 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= 0.202 Angle : 0.734 6.876 13883 Z= 0.412 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/Z covalent geometry : bond 0.00429 / 0.20 (10192) covalent geometry : angle 0.73354 / 0.41 (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 : 0.519 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: 1.4487 time to fit residues: 307.7814 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 : 0.523 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.164422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126617 restraints weight = 33026.256| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.97 r_work: 0.3253 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10192 Z= 0.137 Angle : 0.579 5.793 13883 Z= 0.305 Chirality : 0.039 0.141 1538 Planarity : 0.004 0.046 1688 Dihedral : 11.909 93.620 1665 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.74 % Allowed : 10.82 % Favored : 87.44 % 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: -0.75 (0.24), residues: 1158 helix: 0.65 (0.23), residues: 510 sheet: -0.72 (0.47), residues: 105 loop : -1.59 (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 0.00300 / 0.14 (10192) covalent geometry : angle 0.57928 / 0.31 (13883) hydrogen bonds : bond 0.05723 / 4.03 ( 444) hydrogen bonds : angle 4.99492 / 3.52 ( 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 167 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: B 227 MET cc_start: 0.8459 (ptt) cc_final: 0.8028 (ptt) REVERT: C 71 ASN cc_start: 0.6388 (p0) cc_final: 0.6122 (p0) outliers start: 18 outliers final: 10 residues processed: 158 average time/residue: 1.1892 time to fit residues: 202.5864 Evaluate side-chains 148 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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: 2.9990 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.162949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125290 restraints weight = 32917.275| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.87 r_work: 0.3216 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 10192 Z= 0.157 Angle : 0.558 8.161 13883 Z= 0.294 Chirality : 0.039 0.138 1538 Planarity : 0.005 0.060 1688 Dihedral : 11.875 93.177 1665 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 2.61 % Allowed : 11.30 % Favored : 86.09 % 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: -0.67 (0.24), residues: 1158 helix: 0.78 (0.23), residues: 509 sheet: -0.83 (0.46), residues: 107 loop : -1.57 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 204 TYR 0.012 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 B 562 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10192) covalent geometry : angle 0.55804 / 0.29 (13883) hydrogen bonds : bond 0.04948 / 3.45 ( 444) hydrogen bonds : angle 4.67545 / 3.27 ( 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 169 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: B 227 MET cc_start: 0.8503 (ptt) cc_final: 0.8051 (ptt) REVERT: B 348 MET cc_start: 0.8536 (mtp) cc_final: 0.8196 (mtp) REVERT: B 529 VAL cc_start: 0.7927 (p) cc_final: 0.7594 (m) REVERT: B 577 LYS cc_start: 0.6969 (tmmt) cc_final: 0.6768 (tmmt) REVERT: C 67 ILE cc_start: 0.7214 (mt) cc_final: 0.6937 (tt) REVERT: C 71 ASN cc_start: 0.6410 (p0) cc_final: 0.6170 (p0) outliers start: 27 outliers final: 13 residues processed: 152 average time/residue: 1.2701 time to fit residues: 207.3535 Evaluate side-chains 155 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 490 ARG Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 697 ASP 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 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: 0.0040 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.160544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124027 restraints weight = 32763.135| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.84 r_work: 0.3148 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1978 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= 0.159 Angle : 0.544 5.832 13883 Z= 0.287 Chirality : 0.038 0.137 1538 Planarity : 0.005 0.060 1688 Dihedral : 11.864 93.560 1665 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 2.90 % Allowed : 12.46 % Favored : 84.64 % 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: -0.57 (0.25), residues: 1158 helix: 0.89 (0.23), residues: 510 sheet: -0.68 (0.45), residues: 118 loop : -1.60 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 204 TYR 0.014 0.001 TYR B 620 PHE 0.011 0.001 PHE A 611 TRP 0.008 0.001 TRP C 98 HIS 0.003 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10192) covalent geometry : angle 0.54420 / 0.29 (13883) hydrogen bonds : bond 0.04560 / 3.17 ( 444) hydrogen bonds : angle 4.45092 / 3.12 ( 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 177 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7284 (pm20) REVERT: B 146 THR cc_start: 0.8789 (t) cc_final: 0.8432 (m) REVERT: B 227 MET cc_start: 0.8458 (ptt) cc_final: 0.8056 (ptt) REVERT: B 317 MET cc_start: 0.8089 (ptt) cc_final: 0.7725 (mmp) REVERT: B 331 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8196 (tp30) REVERT: C 67 ILE cc_start: 0.7204 (mt) cc_final: 0.6974 (tt) outliers start: 30 outliers final: 19 residues processed: 158 average time/residue: 1.1735 time to fit residues: 199.5255 Evaluate side-chains 164 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 490 ARG 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 174 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 537 ASN 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: 0.6980 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 64 optimal weight: 0.0570 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.161931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.125044 restraints weight = 32761.498| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.82 r_work: 0.3229 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10192 Z= 0.103 Angle : 0.513 6.228 13883 Z= 0.270 Chirality : 0.037 0.139 1538 Planarity : 0.004 0.063 1688 Dihedral : 11.795 93.000 1665 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.42 % Allowed : 13.72 % Favored : 83.86 % 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: -0.42 (0.25), residues: 1158 helix: 1.09 (0.24), residues: 512 sheet: -0.53 (0.50), residues: 97 loop : -1.61 (0.26), residues: 549 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 0.009 0.001 PHE B 490 TRP 0.008 0.001 TRP C 98 HIS 0.002 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (10192) covalent geometry : angle 0.51267 / 0.27 (13883) hydrogen bonds : bond 0.03996 / 2.78 ( 444) hydrogen bonds : angle 4.27977 / 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 172 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.7182 (mtp-110) cc_final: 0.6830 (ptm160) REVERT: A 427 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: A 674 ASP cc_start: 0.8001 (t0) cc_final: 0.7638 (t0) REVERT: B 146 THR cc_start: 0.8872 (t) cc_final: 0.8532 (m) REVERT: B 227 MET cc_start: 0.8520 (ptt) cc_final: 0.8119 (ptt) REVERT: B 317 MET cc_start: 0.7993 (ptt) cc_final: 0.7782 (mmp) REVERT: C 61 LYS cc_start: 0.3729 (pttt) cc_final: 0.3496 (pptt) REVERT: C 67 ILE cc_start: 0.7203 (mt) cc_final: 0.6985 (tt) outliers start: 25 outliers final: 13 residues processed: 160 average time/residue: 1.1871 time to fit residues: 204.2786 Evaluate side-chains 158 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 B residue 1 MET Chi-restraints excluded: chain B residue 108 LEU 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: 0.9980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 587 GLN A 591 GLN B 536 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.161962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124118 restraints weight = 32858.115| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.97 r_work: 0.3264 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10192 Z= 0.120 Angle : 0.516 6.192 13883 Z= 0.274 Chirality : 0.037 0.138 1538 Planarity : 0.004 0.038 1688 Dihedral : 11.762 93.088 1665 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 1.93 % Allowed : 14.69 % Favored : 83.38 % 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: -0.30 (0.25), residues: 1158 helix: 1.22 (0.24), residues: 509 sheet: -0.35 (0.49), residues: 107 loop : -1.61 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 204 TYR 0.014 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 0.00280 / 0.12 (10192) covalent geometry : angle 0.51638 / 0.27 (13883) hydrogen bonds : bond 0.03964 / 2.75 ( 444) hydrogen bonds : angle 4.17437 / 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 161 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6958 (m-30) REVERT: A 427 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7138 (pm20) REVERT: A 674 ASP cc_start: 0.8028 (t0) cc_final: 0.7697 (t0) REVERT: B 146 THR cc_start: 0.9008 (t) cc_final: 0.8667 (m) REVERT: B 227 MET cc_start: 0.8624 (ptt) cc_final: 0.8116 (ptt) REVERT: B 481 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8543 (mtmt) REVERT: C 61 LYS cc_start: 0.3976 (pttt) cc_final: 0.3481 (pptt) REVERT: C 67 ILE cc_start: 0.7222 (mt) cc_final: 0.7012 (tt) outliers start: 20 outliers final: 14 residues processed: 150 average time/residue: 1.1597 time to fit residues: 186.9424 Evaluate side-chains 153 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 692 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 108 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3867 r_free = 0.3867 target = 0.159162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121400 restraints weight = 33024.643| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.97 r_work: 0.3127 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10192 Z= 0.206 Angle : 0.565 6.369 13883 Z= 0.301 Chirality : 0.040 0.144 1538 Planarity : 0.005 0.082 1688 Dihedral : 11.838 94.699 1665 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 2.90 % Allowed : 14.69 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 512 sheet: -0.30 (0.50), residues: 107 loop : -1.73 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 204 TYR 0.018 0.002 TYR A 564 PHE 0.011 0.001 PHE B 412 TRP 0.012 0.002 TRP C 98 HIS 0.006 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (10192) covalent geometry : angle 0.56477 / 0.30 (13883) hydrogen bonds : bond 0.04521 / 3.12 ( 444) hydrogen bonds : angle 4.24791 / 2.97 ( 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 172 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.7249 (mtp-110) cc_final: 0.6877 (ptm160) REVERT: A 380 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6939 (m-30) REVERT: A 427 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7119 (pm20) REVERT: A 524 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8454 (mm-30) REVERT: A 590 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 112 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7257 (tp30) REVERT: B 146 THR cc_start: 0.8795 (t) cc_final: 0.8478 (m) REVERT: B 227 MET cc_start: 0.8530 (ptt) cc_final: 0.8113 (ptt) REVERT: B 481 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8599 (mtmt) REVERT: C 61 LYS cc_start: 0.3931 (pttt) cc_final: 0.3388 (pptt) outliers start: 30 outliers final: 16 residues processed: 155 average time/residue: 1.2013 time to fit residues: 200.3258 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 : 0.513 ------------------------------------------------------------------------------- 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 523 MET Chi-restraints excluded: chain A residue 524 GLU 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 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 112 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.159973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122994 restraints weight = 32702.549| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.91 r_work: 0.3154 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10192 Z= 0.112 Angle : 0.520 6.560 13883 Z= 0.275 Chirality : 0.037 0.140 1538 Planarity : 0.005 0.080 1688 Dihedral : 11.795 94.855 1665 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 1.93 % Allowed : 15.94 % 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: -0.30 (0.25), residues: 1158 helix: 1.25 (0.24), residues: 514 sheet: -0.31 (0.50), residues: 107 loop : -1.67 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 204 TYR 0.014 0.001 TYR B 620 PHE 0.009 0.001 PHE B 490 TRP 0.015 0.001 TRP B 613 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10192) covalent geometry : angle 0.52037 / 0.28 (13883) hydrogen bonds : bond 0.03913 / 2.70 ( 444) hydrogen bonds : angle 4.13035 / 2.90 ( 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 156 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: A 427 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: A 441 MET cc_start: 0.7556 (ttm) cc_final: 0.7218 (ttm) REVERT: A 590 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 146 THR cc_start: 0.8770 (t) cc_final: 0.8478 (m) REVERT: B 227 MET cc_start: 0.8539 (ptt) cc_final: 0.8119 (ptt) REVERT: B 481 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8567 (mtmt) REVERT: C 61 LYS cc_start: 0.3917 (pttt) cc_final: 0.3395 (pptt) outliers start: 20 outliers final: 11 residues processed: 145 average time/residue: 1.2038 time to fit residues: 187.6772 Evaluate side-chains 147 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 523 MET Chi-restraints excluded: chain A residue 559 ARG 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 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: 0.7980 chunk 101 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3872 r_free = 0.3872 target = 0.159543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122727 restraints weight = 32594.432| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.85 r_work: 0.3262 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10192 Z= 0.129 Angle : 0.525 6.770 13883 Z= 0.278 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.090 1688 Dihedral : 11.773 95.431 1665 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 2.13 % Allowed : 16.43 % Favored : 81.45 % 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: -0.27 (0.25), residues: 1158 helix: 1.27 (0.24), residues: 513 sheet: -0.27 (0.50), residues: 107 loop : -1.66 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 204 TYR 0.015 0.001 TYR B 559 PHE 0.008 0.001 PHE A 520 TRP 0.014 0.001 TRP B 613 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (10192) covalent geometry : angle 0.52547 / 0.28 (13883) hydrogen bonds : bond 0.03925 / 2.70 ( 444) hydrogen bonds : angle 4.09900 / 2.88 ( 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 156 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.7055 (mtp-110) cc_final: 0.6691 (ptm160) REVERT: A 380 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: A 427 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: A 441 MET cc_start: 0.7762 (ttm) cc_final: 0.7444 (ttm) REVERT: B 146 THR cc_start: 0.9005 (t) cc_final: 0.8692 (m) REVERT: B 227 MET cc_start: 0.8669 (ptt) cc_final: 0.8241 (ptt) REVERT: B 481 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8553 (mtmt) REVERT: B 613 TRP cc_start: 0.6085 (t-100) cc_final: 0.5816 (t-100) REVERT: C 61 LYS cc_start: 0.4148 (pttt) cc_final: 0.3571 (pptt) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 1.2071 time to fit residues: 189.3043 Evaluate side-chains 151 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 533 ASN B 536 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.159108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120010 restraints weight = 32768.998| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.82 r_work: 0.3245 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10192 Z= 0.139 Angle : 0.527 6.828 13883 Z= 0.279 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.084 1688 Dihedral : 11.781 96.298 1665 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 2.22 % Allowed : 16.43 % Favored : 81.35 % 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: -0.27 (0.25), residues: 1158 helix: 1.27 (0.24), residues: 513 sheet: -0.28 (0.50), residues: 107 loop : -1.65 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 204 TYR 0.016 0.001 TYR B 559 PHE 0.009 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/Z covalent geometry : bond 0.00332 / 0.14 (10192) covalent geometry : angle 0.52712 / 0.28 (13883) hydrogen bonds : bond 0.03965 / 2.73 ( 444) hydrogen bonds : angle 4.09970 / 2.87 ( 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: 23 poor density : 136 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7050 (m-30) REVERT: A 427 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: A 441 MET cc_start: 0.7747 (ttm) cc_final: 0.7409 (ttm) REVERT: B 146 THR cc_start: 0.8913 (t) cc_final: 0.8620 (m) REVERT: B 227 MET cc_start: 0.8649 (ptt) cc_final: 0.8220 (ptt) REVERT: B 481 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8600 (mtmt) REVERT: B 613 TRP cc_start: 0.6216 (t-100) cc_final: 0.5916 (t-100) REVERT: C 61 LYS cc_start: 0.4097 (pttt) cc_final: 0.3516 (pptt) outliers start: 23 outliers final: 16 residues processed: 148 average time/residue: 1.1799 time to fit residues: 187.5669 Evaluate side-chains 153 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.160464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.122514 restraints weight = 32847.433| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.98 r_work: 0.3175 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10192 Z= 0.120 Angle : 0.523 6.809 13883 Z= 0.276 Chirality : 0.037 0.138 1538 Planarity : 0.005 0.090 1688 Dihedral : 11.763 97.033 1665 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.84 % Allowed : 17.10 % Favored : 81.06 % 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: -0.22 (0.25), residues: 1158 helix: 1.32 (0.24), residues: 514 sheet: -0.32 (0.50), residues: 107 loop : -1.62 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 204 TYR 0.015 0.001 TYR B 559 PHE 0.009 0.001 PHE B 490 TRP 0.010 0.001 TRP B 613 HIS 0.002 0.001 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10192) covalent geometry : angle 0.52337 / 0.28 (13883) hydrogen bonds : bond 0.03778 / 2.60 ( 444) hydrogen bonds : angle 4.05675 / 2.85 ( 1229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6714.21 seconds wall clock time: 114 minutes 15.36 seconds (6855.36 seconds total)