Starting phenix.real_space_refine on Sat Feb 7 03:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rve_54287/02_2026/9rve_54287.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rve_54287/02_2026/9rve_54287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rve_54287/02_2026/9rve_54287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rve_54287/02_2026/9rve_54287.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rve_54287/02_2026/9rve_54287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rve_54287/02_2026/9rve_54287.map" } resolution = 2.53 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 106 5.16 5 C 9226 2.51 5 N 2524 2.21 5 O 2751 1.98 5 H 14582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s 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: 29189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11529 Classifications: {'peptide': 716} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 10797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 10797 Classifications: {'peptide': 678} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 647} Chain breaks: 5 Chain: "C" Number of atoms: 4942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4942 Classifications: {'peptide': 302} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Chain: "D" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1921 Classifications: {'peptide': 115} Link IDs: {'TRANS': 114} Time building chain proxies: 4.43, per 1000 atoms: 0.15 Number of scatterers: 29189 At special positions: 0 Unit cell: (134.212, 132.969, 101.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 O 2751 8.00 N 2524 7.00 C 9226 6.00 H 14582 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: 2.19 Conformation dependent library (CDL) restraints added in 583.6 milliseconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 52.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.507A pdb=" N GLN A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 31 through 49 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.715A pdb=" N ARG A 192 " --> pdb=" O ASP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 217 removed outlier: 3.538A 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 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 330 through 348 removed outlier: 3.894A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 449 Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.723A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 582 through 602 removed outlier: 3.871A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.767A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.552A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 19 through 22 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.942A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.668A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.558A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.914A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.564A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.636A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.517A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.515A pdb=" N LEU B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.760A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.510A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 688 through 700 removed outlier: 3.725A pdb=" N CYS B 692 " --> pdb=" O MET B 688 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 693 " --> pdb=" O TYR B 689 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASN B 694 " --> pdb=" O GLN B 690 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 755 Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.602A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 removed outlier: 3.634A pdb=" N GLU C 18 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.955A pdb=" N ILE C 31 " --> pdb=" O HIS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.555A pdb=" N MET C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.757A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.936A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 701 through 705 removed outlier: 3.802A pdb=" N GLY C 705 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 716 removed outlier: 3.702A pdb=" N SER C 714 " --> pdb=" O ASN C 711 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 716 " --> pdb=" O LEU C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 752 removed outlier: 3.929A pdb=" N THR C 749 " --> pdb=" O THR C 745 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 752 " --> pdb=" O GLN C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.511A pdb=" N SER D 23 " --> pdb=" O MET D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 52 Processing helix chain 'D' and resid 54 through 90 removed outlier: 3.665A pdb=" N LEU D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN D 60 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.545A pdb=" N GLU A 77 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 110 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 116 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.689A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 292 removed outlier: 7.234A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 292 removed outlier: 5.692A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 removed outlier: 5.779A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 366 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 4.565A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.675A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 4.846A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.547A pdb=" N LYS C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 694 through 699 removed outlier: 6.388A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 3.08 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: 14555 1.03 - 1.23: 37 1.23 - 1.42: 6136 1.42 - 1.62: 8558 1.62 - 1.81: 185 Bond restraints: 29471 Sorted by residual: bond pdb=" CG GLU D 75 " pdb=" CD GLU D 75 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.26e+00 bond pdb=" CA PRO A 274 " pdb=" C PRO A 274 " ideal model delta sigma weight residual 1.514 1.521 -0.007 5.50e-03 3.31e+04 1.61e+00 bond pdb=" C TRP D 65 " pdb=" O TRP D 65 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.25e-02 6.40e+03 1.07e+00 bond pdb=" CB LYS C 41 " pdb=" CG LYS C 41 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.77e-01 bond pdb=" CB LYS A 635 " pdb=" CG LYS A 635 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.22e-01 ... (remaining 29466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 51271 1.24 - 2.49: 1848 2.49 - 3.73: 116 3.73 - 4.97: 21 4.97 - 6.22: 5 Bond angle restraints: 53261 Sorted by residual: angle pdb=" C GLU D 74 " pdb=" N GLU D 75 " pdb=" CA GLU D 75 " ideal model delta sigma weight residual 120.72 114.50 6.22 1.67e+00 3.59e-01 1.39e+01 angle pdb=" N GLU D 75 " pdb=" CA GLU D 75 " pdb=" CB GLU D 75 " ideal model delta sigma weight residual 110.39 116.19 -5.80 1.66e+00 3.63e-01 1.22e+01 angle pdb=" N ALA B 374 " pdb=" CA ALA B 374 " pdb=" C ALA B 374 " ideal model delta sigma weight residual 114.75 110.45 4.30 1.26e+00 6.30e-01 1.17e+01 angle pdb=" N ASP D 27 " pdb=" CA ASP D 27 " pdb=" C ASP D 27 " ideal model delta sigma weight residual 113.28 108.92 4.36 1.57e+00 4.06e-01 7.70e+00 angle pdb=" N GLU D 36 " pdb=" CA GLU D 36 " pdb=" CB GLU D 36 " ideal model delta sigma weight residual 110.28 114.19 -3.91 1.55e+00 4.16e-01 6.37e+00 ... (remaining 53256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 12524 17.52 - 35.04: 937 35.04 - 52.57: 244 52.57 - 70.09: 70 70.09 - 87.61: 18 Dihedral angle restraints: 13793 sinusoidal: 7642 harmonic: 6151 Sorted by residual: dihedral pdb=" CA ILE C 710 " pdb=" C ILE C 710 " pdb=" N ASN C 711 " pdb=" CA ASN C 711 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TYR A 540 " pdb=" C TYR A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LYS A 289 " pdb=" C LYS A 289 " pdb=" N LEU A 290 " pdb=" CA LEU A 290 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 13790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1379 0.029 - 0.058: 597 0.058 - 0.087: 118 0.087 - 0.117: 78 0.117 - 0.146: 19 Chirality restraints: 2191 Sorted by residual: chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 517 " pdb=" N ILE B 517 " pdb=" C ILE B 517 " pdb=" CB ILE B 517 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CB THR D 115 " pdb=" CA THR D 115 " pdb=" OG1 THR D 115 " pdb=" CG2 THR D 115 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 2188 not shown) Planarity restraints: 4308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 309 " 0.016 2.00e-02 2.50e+03 1.01e-02 4.08e+00 pdb=" CG TRP B 309 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 309 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 309 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 309 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 309 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 309 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 309 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 309 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 309 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP B 309 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 309 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 309 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 309 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 309 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP B 309 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 199 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO C 200 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 27 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C ASP D 27 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP D 27 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU D 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 4305 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1370 2.18 - 2.79: 59674 2.79 - 3.39: 82680 3.39 - 4.00: 109549 4.00 - 4.60: 170730 Nonbonded interactions: 424003 Sorted by model distance: nonbonded pdb=" OD2 ASP B 522 " pdb=" HH TYR B 559 " model vdw 1.581 2.450 nonbonded pdb="HH11 ARG C 70 " pdb=" O GLY C 74 " model vdw 1.592 2.450 nonbonded pdb=" HD2 PHE B 574 " pdb="HD22 ASN C 71 " model vdw 1.594 2.100 nonbonded pdb="HD21 ASN B 310 " pdb=" O MET B 407 " model vdw 1.603 2.450 nonbonded pdb=" O THR B 583 " pdb=" HZ2 LYS B 586 " model vdw 1.611 2.450 ... (remaining 423998 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.090 Find NCS groups from input model: 0.090 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:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 0.003 0.045 14889 Z= 0.138 Angle : 0.523 6.218 20055 Z= 0.287 Chirality : 0.037 0.146 2191 Planarity : 0.004 0.050 2582 Dihedral : 13.735 87.611 5708 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % 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 (0.20), residues: 1789 helix: 1.21 (0.18), residues: 891 sheet: -0.01 (0.41), residues: 169 loop : -1.15 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 192 TYR 0.022 0.001 TYR D 41 PHE 0.016 0.001 PHE D 118 TRP 0.034 0.001 TRP B 309 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00313 (14889) covalent geometry : angle 0.52295 (20055) hydrogen bonds : bond 0.16819 ( 742) hydrogen bonds : angle 6.14776 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6546 (mm-30) REVERT: A 155 MET cc_start: 0.7522 (ptp) cc_final: 0.7225 (ptp) REVERT: A 182 MET cc_start: 0.7500 (mtt) cc_final: 0.7254 (mtt) REVERT: B 289 MET cc_start: 0.9048 (mmm) cc_final: 0.8447 (mmm) REVERT: B 343 MET cc_start: 0.8456 (mtp) cc_final: 0.8139 (mtm) REVERT: B 356 MET cc_start: 0.8195 (ttm) cc_final: 0.7863 (ttm) REVERT: C 146 ASP cc_start: 0.7964 (p0) cc_final: 0.7711 (p0) REVERT: C 699 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7546 (mmtm) REVERT: D 33 THR cc_start: 0.8779 (p) cc_final: 0.8391 (p) REVERT: D 43 ASP cc_start: 0.8235 (m-30) cc_final: 0.7909 (m-30) outliers start: 0 outliers final: 1 residues processed: 296 average time/residue: 1.8380 time to fit residues: 583.6204 Evaluate side-chains 243 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 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 41 HIS A 321 ASN A 513 ASN A 590 GLN B 153 ASN C 138 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.166522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106934 restraints weight = 44348.438| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.05 r_work: 0.3266 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14889 Z= 0.174 Angle : 0.563 6.953 20055 Z= 0.305 Chirality : 0.039 0.146 2191 Planarity : 0.004 0.048 2582 Dihedral : 4.267 24.740 1974 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.30 % Allowed : 8.11 % Favored : 90.59 % 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 (0.20), residues: 1789 helix: 1.33 (0.18), residues: 900 sheet: -0.15 (0.43), residues: 155 loop : -1.26 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.014 0.001 TYR D 41 PHE 0.014 0.002 PHE B 490 TRP 0.022 0.002 TRP B 309 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00402 (14889) covalent geometry : angle 0.56344 (20055) hydrogen bonds : bond 0.05732 ( 742) hydrogen bonds : angle 5.01589 ( 2106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 256 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6721 (mm-30) REVERT: A 155 MET cc_start: 0.7632 (ptp) cc_final: 0.7362 (ptp) REVERT: A 182 MET cc_start: 0.7327 (mtt) cc_final: 0.7096 (mtt) REVERT: A 576 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8199 (mttt) REVERT: B 104 GLU cc_start: 0.7249 (mp0) cc_final: 0.6857 (mp0) REVERT: B 151 ARG cc_start: 0.7849 (ttt90) cc_final: 0.7546 (ttt-90) REVERT: B 343 MET cc_start: 0.8637 (mtp) cc_final: 0.8415 (mtm) REVERT: B 356 MET cc_start: 0.8496 (ttm) cc_final: 0.7805 (ttm) REVERT: B 409 MET cc_start: 0.7018 (mmp) cc_final: 0.6640 (tpt) REVERT: B 411 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6560 (mpt) REVERT: B 581 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: C 144 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.7358 (tpp80) REVERT: C 146 ASP cc_start: 0.8137 (p0) cc_final: 0.7854 (p0) REVERT: C 699 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7548 (mmtm) REVERT: C 703 ARG cc_start: 0.7992 (ttp-110) cc_final: 0.7723 (ttp-110) REVERT: D 43 ASP cc_start: 0.8542 (m-30) cc_final: 0.8155 (m-30) REVERT: D 111 GLN cc_start: 0.8034 (tp40) cc_final: 0.7383 (tp-100) REVERT: D 119 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8595 (tm-30) outliers start: 21 outliers final: 8 residues processed: 267 average time/residue: 1.6993 time to fit residues: 487.7028 Evaluate side-chains 259 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 249 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 321 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 10 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.166048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106506 restraints weight = 44479.230| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.06 r_work: 0.3259 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14889 Z= 0.178 Angle : 0.555 9.182 20055 Z= 0.297 Chirality : 0.039 0.156 2191 Planarity : 0.004 0.051 2582 Dihedral : 4.305 24.748 1974 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.36 % Allowed : 9.78 % Favored : 88.86 % 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: 0.26 (0.20), residues: 1789 helix: 1.38 (0.18), residues: 895 sheet: -0.26 (0.42), residues: 165 loop : -1.26 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 663 TYR 0.017 0.001 TYR D 41 PHE 0.014 0.002 PHE A 520 TRP 0.012 0.002 TRP B 309 HIS 0.006 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00419 (14889) covalent geometry : angle 0.55509 (20055) hydrogen bonds : bond 0.05188 ( 742) hydrogen bonds : angle 4.79943 ( 2106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.5891 (mtp85) cc_final: 0.5562 (mtp85) REVERT: A 153 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6717 (mm-30) REVERT: A 182 MET cc_start: 0.7399 (mtt) cc_final: 0.7178 (mtt) REVERT: A 576 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8181 (mttt) REVERT: B 104 GLU cc_start: 0.7148 (mp0) cc_final: 0.6806 (mp0) REVERT: B 151 ARG cc_start: 0.7842 (ttt90) cc_final: 0.7545 (ttt-90) REVERT: B 289 MET cc_start: 0.9034 (mmm) cc_final: 0.8457 (mmm) REVERT: B 581 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: C 144 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7308 (tpp80) REVERT: C 146 ASP cc_start: 0.7639 (p0) cc_final: 0.7340 (p0) REVERT: C 699 LYS cc_start: 0.7789 (mmtp) cc_final: 0.7518 (mmtm) REVERT: D 43 ASP cc_start: 0.8537 (m-30) cc_final: 0.8140 (m-30) REVERT: D 71 GLN cc_start: 0.8364 (pm20) cc_final: 0.8091 (pm20) REVERT: D 72 LYS cc_start: 0.8165 (mmpt) cc_final: 0.7896 (mmpt) REVERT: D 111 GLN cc_start: 0.7967 (tp40) cc_final: 0.7330 (tp-100) REVERT: D 119 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8689 (tm-30) outliers start: 22 outliers final: 10 residues processed: 265 average time/residue: 1.6074 time to fit residues: 460.0514 Evaluate side-chains 256 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 245 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 150 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106696 restraints weight = 44050.972| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.05 r_work: 0.3263 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14889 Z= 0.161 Angle : 0.536 6.763 20055 Z= 0.286 Chirality : 0.038 0.148 2191 Planarity : 0.004 0.061 2582 Dihedral : 4.277 24.784 1974 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.61 % Allowed : 10.33 % Favored : 88.06 % 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: 0.26 (0.20), residues: 1789 helix: 1.40 (0.17), residues: 905 sheet: -0.38 (0.41), residues: 165 loop : -1.31 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 42 TYR 0.022 0.001 TYR D 41 PHE 0.013 0.001 PHE A 658 TRP 0.010 0.001 TRP B 438 HIS 0.006 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00376 (14889) covalent geometry : angle 0.53610 (20055) hydrogen bonds : bond 0.04822 ( 742) hydrogen bonds : angle 4.68261 ( 2106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6732 (mm-30) REVERT: A 182 MET cc_start: 0.7436 (mtt) cc_final: 0.7218 (mtt) REVERT: A 262 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8193 (mmtm) REVERT: A 576 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8186 (mttt) REVERT: B 104 GLU cc_start: 0.7174 (mp0) cc_final: 0.6821 (mp0) REVERT: B 151 ARG cc_start: 0.8012 (ttt90) cc_final: 0.7707 (ttt-90) REVERT: B 220 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7848 (mtm180) REVERT: B 289 MET cc_start: 0.9044 (mmm) cc_final: 0.8508 (mmm) REVERT: B 348 MET cc_start: 0.8480 (mtp) cc_final: 0.8040 (mmm) REVERT: B 491 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8182 (tm-30) REVERT: B 581 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: B 686 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7089 (mt-10) REVERT: C 144 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7262 (tpp80) REVERT: C 146 ASP cc_start: 0.7542 (p0) cc_final: 0.7247 (p0) REVERT: C 699 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7566 (mmtm) REVERT: D 32 ILE cc_start: 0.8664 (mt) cc_final: 0.8091 (mt) REVERT: D 36 GLU cc_start: 0.7963 (mp0) cc_final: 0.7629 (mp0) REVERT: D 43 ASP cc_start: 0.8544 (m-30) cc_final: 0.8162 (m-30) REVERT: D 77 ARG cc_start: 0.7532 (ttt-90) cc_final: 0.7099 (ttt-90) REVERT: D 111 GLN cc_start: 0.7972 (tp40) cc_final: 0.7347 (tp-100) REVERT: D 119 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8667 (tm-30) outliers start: 26 outliers final: 14 residues processed: 263 average time/residue: 1.6821 time to fit residues: 478.1494 Evaluate side-chains 263 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN B 153 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.165939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106547 restraints weight = 44416.030| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.06 r_work: 0.3260 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14889 Z= 0.165 Angle : 0.538 6.679 20055 Z= 0.285 Chirality : 0.038 0.143 2191 Planarity : 0.004 0.059 2582 Dihedral : 4.274 24.819 1974 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.73 % Allowed : 10.95 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1789 helix: 1.42 (0.17), residues: 906 sheet: -0.41 (0.41), residues: 165 loop : -1.31 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 703 TYR 0.018 0.001 TYR D 41 PHE 0.013 0.002 PHE B 490 TRP 0.010 0.002 TRP B 438 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00389 (14889) covalent geometry : angle 0.53816 (20055) hydrogen bonds : bond 0.04728 ( 742) hydrogen bonds : angle 4.61429 ( 2106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 247 time to evaluate : 0.844 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: A 124 ARG cc_start: 0.6192 (mtp85) cc_final: 0.5861 (mtp85) REVERT: A 153 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6818 (mm-30) REVERT: A 262 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8218 (mmtm) REVERT: A 675 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8288 (m110) REVERT: B 104 GLU cc_start: 0.7151 (mp0) cc_final: 0.6806 (mp0) REVERT: B 151 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7694 (ttt-90) REVERT: B 220 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7885 (mtm180) REVERT: B 289 MET cc_start: 0.9069 (mmm) cc_final: 0.8539 (mmm) REVERT: B 348 MET cc_start: 0.8533 (mtp) cc_final: 0.8097 (mmm) REVERT: B 411 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6225 (mpp) REVERT: B 491 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 581 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: B 618 GLU cc_start: 0.8017 (tt0) cc_final: 0.7736 (tt0) REVERT: B 686 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7092 (mt-10) REVERT: C 146 ASP cc_start: 0.7495 (p0) cc_final: 0.7206 (p0) REVERT: D 32 ILE cc_start: 0.8829 (mt) cc_final: 0.8476 (mt) REVERT: D 43 ASP cc_start: 0.8547 (m-30) cc_final: 0.8217 (m-30) REVERT: D 86 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7471 (mtp180) REVERT: D 111 GLN cc_start: 0.8010 (tp40) cc_final: 0.7401 (tp-100) REVERT: D 119 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8641 (tm-30) outliers start: 28 outliers final: 14 residues processed: 260 average time/residue: 1.8060 time to fit residues: 507.7271 Evaluate side-chains 264 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 245 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 154 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 10 GLN D 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.166240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.106947 restraints weight = 44264.770| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.05 r_work: 0.3262 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14889 Z= 0.150 Angle : 0.535 6.683 20055 Z= 0.283 Chirality : 0.038 0.156 2191 Planarity : 0.004 0.065 2582 Dihedral : 4.240 24.849 1974 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.79 % Allowed : 11.51 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1789 helix: 1.49 (0.18), residues: 906 sheet: -0.42 (0.41), residues: 165 loop : -1.30 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 703 TYR 0.024 0.001 TYR D 41 PHE 0.013 0.001 PHE A 658 TRP 0.010 0.001 TRP B 438 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00351 (14889) covalent geometry : angle 0.53499 (20055) hydrogen bonds : bond 0.04535 ( 742) hydrogen bonds : angle 4.57264 ( 2106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.836 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: symmetry clash REVERT: A 153 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6833 (mm-30) REVERT: A 262 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8179 (mmtm) REVERT: A 675 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8224 (m110) REVERT: B 104 GLU cc_start: 0.7090 (mp0) cc_final: 0.6745 (mp0) REVERT: B 151 ARG cc_start: 0.7968 (ttt90) cc_final: 0.7664 (ttt-90) REVERT: B 220 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7841 (mtm180) REVERT: B 289 MET cc_start: 0.9037 (mmm) cc_final: 0.8566 (mmm) REVERT: B 343 MET cc_start: 0.8684 (mtp) cc_final: 0.8467 (mtm) REVERT: B 348 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: B 491 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 581 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: B 618 GLU cc_start: 0.7968 (tt0) cc_final: 0.7676 (tt0) REVERT: B 686 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7034 (mt-10) REVERT: C 146 ASP cc_start: 0.7502 (p0) cc_final: 0.7218 (p0) REVERT: C 206 MET cc_start: 0.8319 (mmm) cc_final: 0.7454 (mmm) REVERT: D 32 ILE cc_start: 0.8812 (mt) cc_final: 0.8278 (mt) REVERT: D 36 GLU cc_start: 0.7907 (mp0) cc_final: 0.7691 (mp0) REVERT: D 75 GLU cc_start: 0.8046 (pm20) cc_final: 0.7572 (pm20) REVERT: D 111 GLN cc_start: 0.7955 (tp40) cc_final: 0.7460 (tp-100) outliers start: 29 outliers final: 14 residues processed: 266 average time/residue: 1.7903 time to fit residues: 514.5867 Evaluate side-chains 263 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 36 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 10 GLN D 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.166697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107597 restraints weight = 44513.731| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.06 r_work: 0.3274 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14889 Z= 0.128 Angle : 0.524 10.636 20055 Z= 0.275 Chirality : 0.037 0.155 2191 Planarity : 0.004 0.071 2582 Dihedral : 4.174 24.728 1974 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.55 % Allowed : 12.25 % Favored : 86.20 % 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: 0.47 (0.20), residues: 1789 helix: 1.67 (0.18), residues: 897 sheet: -0.42 (0.41), residues: 165 loop : -1.26 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 703 TYR 0.026 0.001 TYR D 41 PHE 0.012 0.001 PHE A 658 TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00298 (14889) covalent geometry : angle 0.52449 (20055) hydrogen bonds : bond 0.04299 ( 742) hydrogen bonds : angle 4.49785 ( 2106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.855 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: A 124 ARG cc_start: 0.6158 (mtp85) cc_final: 0.5794 (mtp85) REVERT: A 153 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6711 (mm-30) REVERT: A 262 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8153 (mmtm) REVERT: A 675 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8240 (m110) REVERT: B 104 GLU cc_start: 0.7120 (mp0) cc_final: 0.6790 (mp0) REVERT: B 151 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7646 (ttt-90) REVERT: B 220 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7850 (mtm180) REVERT: B 289 MET cc_start: 0.9024 (mmm) cc_final: 0.8580 (mmm) REVERT: B 343 MET cc_start: 0.8672 (mtp) cc_final: 0.8455 (mtm) REVERT: B 348 MET cc_start: 0.8506 (mtp) cc_final: 0.8146 (mmm) REVERT: B 491 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8442 (tm-30) REVERT: B 581 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 686 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7002 (mt-10) REVERT: C 146 ASP cc_start: 0.7468 (p0) cc_final: 0.7169 (p0) REVERT: C 206 MET cc_start: 0.8325 (mmm) cc_final: 0.7465 (mmm) REVERT: D 32 ILE cc_start: 0.8722 (mt) cc_final: 0.8462 (mt) REVERT: D 43 ASP cc_start: 0.8537 (m-30) cc_final: 0.8201 (m-30) REVERT: D 111 GLN cc_start: 0.7967 (tp40) cc_final: 0.7486 (tp-100) outliers start: 25 outliers final: 15 residues processed: 264 average time/residue: 1.6760 time to fit residues: 478.3984 Evaluate side-chains 259 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 52 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 10 GLN D 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.165914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106578 restraints weight = 44412.020| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.06 r_work: 0.3275 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14889 Z= 0.162 Angle : 0.544 8.766 20055 Z= 0.287 Chirality : 0.038 0.160 2191 Planarity : 0.004 0.076 2582 Dihedral : 4.222 24.705 1974 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.55 % Allowed : 12.69 % Favored : 85.77 % 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: 0.34 (0.20), residues: 1789 helix: 1.48 (0.18), residues: 908 sheet: -0.39 (0.41), residues: 169 loop : -1.29 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 703 TYR 0.025 0.001 TYR D 41 PHE 0.013 0.001 PHE B 490 TRP 0.009 0.001 TRP B 438 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00384 (14889) covalent geometry : angle 0.54441 (20055) hydrogen bonds : bond 0.04518 ( 742) hydrogen bonds : angle 4.52356 ( 2106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.787 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.6120 (mtp85) cc_final: 0.5748 (mtp85) REVERT: A 153 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6612 (mm-30) REVERT: A 262 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8140 (mmtm) REVERT: A 675 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8206 (m110) REVERT: B 104 GLU cc_start: 0.7103 (mp0) cc_final: 0.6748 (mp0) REVERT: B 151 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7648 (ttt-90) REVERT: B 220 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7861 (mtm180) REVERT: B 343 MET cc_start: 0.8691 (mtp) cc_final: 0.8471 (mtm) REVERT: B 348 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: B 491 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 581 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: B 686 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7030 (mt-10) REVERT: C 206 MET cc_start: 0.8309 (mmm) cc_final: 0.7445 (mmm) REVERT: C 735 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7483 (ptm) REVERT: D 32 ILE cc_start: 0.8758 (mt) cc_final: 0.8261 (mt) REVERT: D 36 GLU cc_start: 0.7885 (mp0) cc_final: 0.7657 (mp0) REVERT: D 111 GLN cc_start: 0.7959 (tp40) cc_final: 0.7479 (tp-100) outliers start: 25 outliers final: 14 residues processed: 256 average time/residue: 1.6290 time to fit residues: 450.3468 Evaluate side-chains 267 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 247 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 133 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 163 optimal weight: 0.0570 chunk 33 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106300 restraints weight = 44288.275| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.05 r_work: 0.3271 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14889 Z= 0.174 Angle : 0.552 6.487 20055 Z= 0.292 Chirality : 0.039 0.157 2191 Planarity : 0.005 0.080 2582 Dihedral : 4.258 24.661 1974 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.49 % Allowed : 13.12 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1789 helix: 1.43 (0.18), residues: 908 sheet: -0.40 (0.41), residues: 169 loop : -1.29 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 703 TYR 0.042 0.002 TYR D 41 PHE 0.013 0.002 PHE B 490 TRP 0.010 0.002 TRP A 368 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00413 (14889) covalent geometry : angle 0.55211 (20055) hydrogen bonds : bond 0.04575 ( 742) hydrogen bonds : angle 4.54230 ( 2106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.828 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: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.6128 (mtt180) cc_final: 0.5762 (mtp85) REVERT: A 153 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6711 (mm-30) REVERT: A 204 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.6977 (tpm170) REVERT: A 262 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8181 (mmtm) REVERT: A 675 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8209 (m110) REVERT: B 104 GLU cc_start: 0.7116 (mp0) cc_final: 0.6768 (mp0) REVERT: B 151 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7654 (ttt-90) REVERT: B 220 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7866 (mtm180) REVERT: B 343 MET cc_start: 0.8715 (mtp) cc_final: 0.8495 (mtm) REVERT: B 348 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: B 491 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 581 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: B 686 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7056 (mt-10) REVERT: C 206 MET cc_start: 0.8306 (mmm) cc_final: 0.7443 (mmm) REVERT: C 703 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: C 735 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7485 (ptm) REVERT: D 32 ILE cc_start: 0.8680 (mt) cc_final: 0.7879 (mt) REVERT: D 36 GLU cc_start: 0.7815 (mp0) cc_final: 0.7493 (mp0) REVERT: D 111 GLN cc_start: 0.7941 (tp40) cc_final: 0.7446 (tp-100) outliers start: 24 outliers final: 14 residues processed: 263 average time/residue: 1.8237 time to fit residues: 517.2287 Evaluate side-chains 269 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 115 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 64 optimal weight: 0.1980 chunk 134 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 16 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 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 = 0.3996 r_free = 0.3996 target = 0.166987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107677 restraints weight = 44220.208| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.07 r_work: 0.3278 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14889 Z= 0.122 Angle : 0.526 6.929 20055 Z= 0.278 Chirality : 0.037 0.159 2191 Planarity : 0.004 0.072 2582 Dihedral : 4.163 24.607 1974 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.11 % Allowed : 13.61 % Favored : 85.27 % 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: 0.46 (0.20), residues: 1789 helix: 1.63 (0.18), residues: 905 sheet: -0.40 (0.41), residues: 163 loop : -1.26 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 703 TYR 0.031 0.001 TYR D 41 PHE 0.012 0.001 PHE A 658 TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00281 (14889) covalent geometry : angle 0.52575 (20055) hydrogen bonds : bond 0.04183 ( 742) hydrogen bonds : angle 4.44734 ( 2106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 0.872 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.6121 (mtt180) cc_final: 0.5753 (mtp85) REVERT: A 153 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6655 (mm-30) REVERT: A 204 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7015 (tpm170) REVERT: A 675 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8269 (m110) REVERT: B 104 GLU cc_start: 0.7164 (mp0) cc_final: 0.6852 (mp0) REVERT: B 151 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7656 (ttt-90) REVERT: B 220 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7935 (mtm180) REVERT: B 343 MET cc_start: 0.8735 (mtp) cc_final: 0.8521 (mtm) REVERT: B 348 MET cc_start: 0.8500 (mtp) cc_final: 0.8252 (mmm) REVERT: B 372 MET cc_start: 0.7779 (ptm) cc_final: 0.7394 (ppp) REVERT: B 491 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 581 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: B 686 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7120 (mt-10) REVERT: C 206 MET cc_start: 0.8392 (mmm) cc_final: 0.7537 (mmm) REVERT: C 703 ARG cc_start: 0.7997 (ttp-110) cc_final: 0.7780 (ttp-110) REVERT: D 32 ILE cc_start: 0.8655 (mt) cc_final: 0.8368 (mt) REVERT: D 111 GLN cc_start: 0.7972 (tp40) cc_final: 0.7512 (tp-100) outliers start: 18 outliers final: 13 residues processed: 262 average time/residue: 1.7975 time to fit residues: 507.2907 Evaluate side-chains 269 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 496 ARG Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 110 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 118 optimal weight: 0.9990 chunk 35 optimal weight: 0.0270 chunk 102 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A 590 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.167040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107945 restraints weight = 44591.182| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3277 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14889 Z= 0.125 Angle : 0.539 9.538 20055 Z= 0.284 Chirality : 0.037 0.147 2191 Planarity : 0.004 0.069 2582 Dihedral : 4.112 24.492 1972 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.11 % Allowed : 13.68 % Favored : 85.21 % 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: 0.47 (0.20), residues: 1789 helix: 1.63 (0.18), residues: 907 sheet: -0.39 (0.41), residues: 163 loop : -1.25 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 703 TYR 0.032 0.001 TYR D 41 PHE 0.012 0.001 PHE A 658 TRP 0.009 0.001 TRP A 368 HIS 0.004 0.001 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00291 (14889) covalent geometry : angle 0.53895 (20055) hydrogen bonds : bond 0.04155 ( 742) hydrogen bonds : angle 4.44605 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14247.21 seconds wall clock time: 240 minutes 59.10 seconds (14459.10 seconds total)