Starting phenix.real_space_refine on Thu Jul 2 16:06:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpw_60365/07_2026/8zpw_60365_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpw_60365/07_2026/8zpw_60365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpw_60365/07_2026/8zpw_60365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpw_60365/07_2026/8zpw_60365.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpw_60365/07_2026/8zpw_60365_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpw_60365/07_2026/8zpw_60365_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 38 5.16 5 C 5961 2.51 5 N 1480 2.21 5 O 1772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9252 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5431 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 629} Chain breaks: 6 Chain: "B" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3775 Classifications: {'peptide': 477} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 454} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.21 Number of scatterers: 9252 At special positions: 0 Unit cell: (104.775, 102.3, 102.3, 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) Ca 1 19.99 S 38 16.00 O 1772 8.00 N 1480 7.00 C 5961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 579 " - pdb=" SG CYS B 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS B 61 " distance=2.04 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 330.0 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 46.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 88 through 101 removed outlier: 4.278A pdb=" N THR A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.564A pdb=" N ILE A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 164 through 178 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 219 through 231 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 278 through 292 removed outlier: 3.755A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 311 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 349 through 368 removed outlier: 3.675A pdb=" N MET A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 423 through 441 removed outlier: 3.761A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 479 removed outlier: 4.110A pdb=" N LEU A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.777A pdb=" N SER A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.734A pdb=" N ALA A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 4.600A pdb=" N ASN B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.828A pdb=" N LYS B 65 " --> pdb=" O CYS B 61 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 4.048A pdb=" N GLU B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 127 through 140 Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.556A pdb=" N GLU B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.887A pdb=" N ILE B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 245 through 256 removed outlier: 4.353A pdb=" N ALA B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLN B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 256 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 Proline residue: B 275 - end of helix Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.785A pdb=" N GLY B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 382 through 391 removed outlier: 4.742A pdb=" N ASP B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 425 removed outlier: 3.672A pdb=" N LYS B 410 " --> pdb=" O CYS B 406 " (cutoff:3.500A) Proline residue: B 414 - end of helix removed outlier: 3.600A pdb=" N ASN B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.545A pdb=" N LEU B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.838A pdb=" N GLU A 59 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 66 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 334 Processing sheet with id=AA6, first strand: chain 'A' and resid 450 through 452 removed outlier: 6.773A pdb=" N GLU A 457 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA8, first strand: chain 'A' and resid 652 through 663 removed outlier: 3.609A pdb=" N LEU A 659 " --> pdb=" O GLY A 682 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLY A 661 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE A 680 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 685 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE A 739 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 687 " --> pdb=" O VAL A 737 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 668 through 669 removed outlier: 6.212A pdb=" N ILE A 675 " --> pdb=" O GLN A 751 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LYS A 753 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A 677 " --> pdb=" O LYS A 753 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 750 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 796 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE A 752 " --> pdb=" O VAL A 796 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 775 through 777 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.409A pdb=" N VAL B 35 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP B 89 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 53 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE B 88 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLU B 55 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 143 through 145 removed outlier: 6.219A pdb=" N ALA B 144 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 206 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 212 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 289 through 294 Processing sheet with id=AB5, first strand: chain 'B' and resid 379 through 381 removed outlier: 4.215A pdb=" N ASP B 436 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ASP B 396 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA B 433 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU B 398 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 435 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 400 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 397 " --> pdb=" O TYR B 456 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1092 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: 1.50 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2964 1.34 - 1.46: 2177 1.46 - 1.58: 4282 1.58 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 9486 Sorted by residual: bond pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLN B 24 " pdb=" CA GLN B 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" C5 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 9481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12369 1.14 - 2.28: 388 2.28 - 3.42: 79 3.42 - 4.56: 35 4.56 - 5.70: 4 Bond angle restraints: 12875 Sorted by residual: angle pdb=" C ASP A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.54 126.90 -5.36 1.91e+00 2.74e-01 7.86e+00 angle pdb=" CA GLU A 480 " pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " ideal model delta sigma weight residual 114.10 118.46 -4.36 2.00e+00 2.50e-01 4.75e+00 angle pdb=" CA CYS B 61 " pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " ideal model delta sigma weight residual 114.40 119.18 -4.78 2.30e+00 1.89e-01 4.32e+00 angle pdb=" CB GLU A 480 " pdb=" CG GLU A 480 " pdb=" CD GLU A 480 " ideal model delta sigma weight residual 112.60 116.07 -3.47 1.70e+00 3.46e-01 4.16e+00 angle pdb=" N ALA B 26 " pdb=" CA ALA B 26 " pdb=" CB ALA B 26 " ideal model delta sigma weight residual 113.65 110.73 2.92 1.47e+00 4.63e-01 3.94e+00 ... (remaining 12870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 5085 17.49 - 34.97: 469 34.97 - 52.46: 106 52.46 - 69.95: 28 69.95 - 87.44: 13 Dihedral angle restraints: 5701 sinusoidal: 2334 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS A 644 " pdb=" SG CYS A 644 " pdb=" SG CYS B 61 " pdb=" CB CYS B 61 " ideal model delta sinusoidal sigma weight residual -86.00 -120.28 34.28 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA CYS B 61 " pdb=" C CYS B 61 " pdb=" N GLY B 62 " pdb=" CA GLY B 62 " ideal model delta harmonic sigma weight residual -180.00 -162.67 -17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU B 25 " pdb=" CG GLU B 25 " pdb=" CD GLU B 25 " pdb=" OE1 GLU B 25 " ideal model delta sinusoidal sigma weight residual 0.00 -87.44 87.44 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 839 0.027 - 0.054: 366 0.054 - 0.081: 101 0.081 - 0.108: 62 0.108 - 0.135: 42 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA ILE A 795 " pdb=" N ILE A 795 " pdb=" C ILE A 795 " pdb=" CB ILE A 795 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE A 777 " pdb=" N ILE A 777 " pdb=" C ILE A 777 " pdb=" CB ILE A 777 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 587 " pdb=" N ILE A 587 " pdb=" C ILE A 587 " pdb=" CB ILE A 587 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1407 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 443 " 0.157 9.50e-02 1.11e+02 7.06e-02 3.36e+00 pdb=" NE ARG B 443 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 443 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 443 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 443 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 74 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO A 75 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 437 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LEU A 437 " -0.025 2.00e-02 2.50e+03 pdb=" O LEU A 437 " 0.009 2.00e-02 2.50e+03 pdb=" N LYS A 438 " 0.008 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 141 2.61 - 3.19: 8641 3.19 - 3.76: 14847 3.76 - 4.33: 21416 4.33 - 4.90: 34958 Nonbonded interactions: 80003 Sorted by model distance: nonbonded pdb=" O ALA A 338 " pdb=" OG SER A 413 " model vdw 2.043 3.040 nonbonded pdb=" O ARG A 137 " pdb=" OG SER A 141 " model vdw 2.044 3.040 nonbonded pdb=" NH1 ARG A 635 " pdb=" O LYS B 297 " model vdw 2.071 3.120 nonbonded pdb=" OE1 GLU A 236 " pdb=" OH TYR A 510 " model vdw 2.102 3.040 nonbonded pdb=" OD1 ASP A 74 " pdb=" OG1 THR A 76 " model vdw 2.116 3.040 ... (remaining 79998 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: 1.540 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.350 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 0.033 9490 Z= 0.129 Angle : 0.527 5.703 12883 Z= 0.272 Chirality : 0.040 0.135 1410 Planarity : 0.004 0.071 1664 Dihedral : 15.061 87.435 3513 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.19 % Allowed : 18.06 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1129 helix: 2.00 (0.25), residues: 460 sheet: 0.42 (0.49), residues: 128 loop : -0.13 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 443 TYR 0.018 0.001 TYR A 732 PHE 0.014 0.001 PHE A 425 TRP 0.008 0.001 TRP A 374 HIS 0.009 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9486) covalent geometry : angle 0.52612 / 0.27 (12875) SS BOND : bond 0.00306 / 0.15 ( 4) SS BOND : angle 1.00723 / 0.47 ( 8) hydrogen bonds : bond 0.14497 / 9.13 ( 389) hydrogen bonds : angle 6.57824 / 4.70 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.351 Fit side-chains REVERT: A 189 MET cc_start: 0.8426 (tpp) cc_final: 0.8031 (mmt) REVERT: B 198 ASP cc_start: 0.7588 (m-30) cc_final: 0.7178 (p0) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 0.4505 time to fit residues: 49.3697 Evaluate side-chains 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 476 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0770 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS B 82 ASN B 289 ASN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.123401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095048 restraints weight = 14551.258| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.47 r_work: 0.3122 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9490 Z= 0.111 Angle : 0.507 6.854 12883 Z= 0.267 Chirality : 0.042 0.149 1410 Planarity : 0.004 0.034 1664 Dihedral : 5.079 53.561 1316 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.69 % Allowed : 15.87 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1129 helix: 2.12 (0.25), residues: 461 sheet: 0.36 (0.47), residues: 126 loop : -0.17 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 137 TYR 0.016 0.001 TYR A 698 PHE 0.017 0.001 PHE A 425 TRP 0.011 0.001 TRP B 60 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9486) covalent geometry : angle 0.50577 / 0.27 (12875) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 1.23392 / 0.60 ( 8) hydrogen bonds : bond 0.03655 / 2.26 ( 389) hydrogen bonds : angle 5.25379 / 3.80 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8673 (tpp) cc_final: 0.8286 (mmt) REVERT: A 293 ASP cc_start: 0.8357 (t0) cc_final: 0.8149 (t0) REVERT: A 669 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6932 (tpp) REVERT: A 702 LEU cc_start: 0.8629 (tt) cc_final: 0.8171 (tm) REVERT: A 742 ARG cc_start: 0.8863 (mtp85) cc_final: 0.8497 (mmt-90) REVERT: A 780 HIS cc_start: 0.7248 (m-70) cc_final: 0.6635 (m90) REVERT: B 76 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: B 79 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8442 (m) REVERT: B 198 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7244 (p0) outliers start: 17 outliers final: 7 residues processed: 125 average time/residue: 0.4116 time to fit residues: 55.8144 Evaluate side-chains 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 669 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 313 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 34 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 HIS A 747 HIS ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.124117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095103 restraints weight = 14763.966| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.56 r_work: 0.3133 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9490 Z= 0.101 Angle : 0.482 7.413 12883 Z= 0.251 Chirality : 0.041 0.143 1410 Planarity : 0.003 0.035 1664 Dihedral : 4.405 52.963 1303 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.18 % Allowed : 17.26 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1129 helix: 2.16 (0.25), residues: 459 sheet: 0.56 (0.48), residues: 122 loop : -0.11 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.020 0.001 TYR A 732 PHE 0.014 0.001 PHE A 425 TRP 0.008 0.001 TRP B 60 HIS 0.006 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9486) covalent geometry : angle 0.48132 / 0.25 (12875) SS BOND : bond 0.00653 / 0.33 ( 4) SS BOND : angle 1.24738 / 0.61 ( 8) hydrogen bonds : bond 0.03277 / 2.02 ( 389) hydrogen bonds : angle 4.92052 / 3.57 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8632 (tpp) cc_final: 0.8275 (mmt) REVERT: A 702 LEU cc_start: 0.8644 (tt) cc_final: 0.8188 (tm) REVERT: A 742 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8454 (mmt-90) REVERT: A 751 GLN cc_start: 0.7796 (mt0) cc_final: 0.7550 (mt0) REVERT: A 780 HIS cc_start: 0.7252 (m-70) cc_final: 0.6657 (m90) REVERT: B 76 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: B 79 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8383 (m) REVERT: B 198 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7192 (p0) REVERT: B 271 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7805 (tm-30) REVERT: B 395 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8498 (mtpm) outliers start: 22 outliers final: 4 residues processed: 115 average time/residue: 0.4718 time to fit residues: 59.0317 Evaluate side-chains 97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 75 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 104 optimal weight: 0.0370 chunk 86 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS B 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094793 restraints weight = 14783.913| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.59 r_work: 0.3122 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9490 Z= 0.106 Angle : 0.489 7.914 12883 Z= 0.250 Chirality : 0.041 0.138 1410 Planarity : 0.003 0.034 1664 Dihedral : 3.755 19.066 1299 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.98 % Allowed : 17.86 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1129 helix: 2.16 (0.25), residues: 459 sheet: 0.64 (0.48), residues: 122 loop : -0.08 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.021 0.001 TYR A 732 PHE 0.016 0.001 PHE A 465 TRP 0.008 0.001 TRP B 60 HIS 0.005 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9486) covalent geometry : angle 0.48796 / 0.25 (12875) SS BOND : bond 0.00334 / 0.17 ( 4) SS BOND : angle 1.22385 / 0.58 ( 8) hydrogen bonds : bond 0.03181 / 1.95 ( 389) hydrogen bonds : angle 4.77077 / 3.46 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8453 (tpp) cc_final: 0.8091 (mmt) REVERT: A 702 LEU cc_start: 0.8683 (tt) cc_final: 0.8269 (tm) REVERT: A 751 GLN cc_start: 0.7736 (mt0) cc_final: 0.7498 (mt0) REVERT: A 780 HIS cc_start: 0.7161 (m-70) cc_final: 0.6652 (m90) REVERT: B 76 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: B 79 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8405 (m) REVERT: B 198 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7219 (p0) REVERT: B 271 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7747 (tm-30) REVERT: B 395 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8486 (mtpm) outliers start: 20 outliers final: 6 residues processed: 111 average time/residue: 0.4251 time to fit residues: 51.4141 Evaluate side-chains 97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 8.9990 chunk 50 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 0.0070 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095715 restraints weight = 14812.518| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.58 r_work: 0.3138 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9490 Z= 0.098 Angle : 0.471 6.846 12883 Z= 0.243 Chirality : 0.041 0.135 1410 Planarity : 0.003 0.034 1664 Dihedral : 3.634 19.830 1299 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.88 % Allowed : 18.25 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1129 helix: 2.17 (0.25), residues: 454 sheet: 0.66 (0.47), residues: 128 loop : -0.05 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 742 TYR 0.022 0.001 TYR A 732 PHE 0.015 0.001 PHE A 465 TRP 0.008 0.001 TRP B 60 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9486) covalent geometry : angle 0.47048 / 0.24 (12875) SS BOND : bond 0.00457 / 0.23 ( 4) SS BOND : angle 1.16733 / 0.56 ( 8) hydrogen bonds : bond 0.02998 / 1.83 ( 389) hydrogen bonds : angle 4.68780 / 3.39 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8411 (tpp) cc_final: 0.8059 (mmt) REVERT: A 702 LEU cc_start: 0.8691 (tt) cc_final: 0.8297 (tm) REVERT: A 742 ARG cc_start: 0.8808 (mtt90) cc_final: 0.8269 (mpt180) REVERT: A 751 GLN cc_start: 0.7740 (mt0) cc_final: 0.7527 (mt0) REVERT: A 780 HIS cc_start: 0.7122 (m-70) cc_final: 0.6647 (m90) REVERT: B 76 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: B 79 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8389 (m) REVERT: B 198 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7266 (p0) REVERT: B 271 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7737 (tm-30) REVERT: B 395 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8548 (mtpm) outliers start: 19 outliers final: 4 residues processed: 111 average time/residue: 0.4414 time to fit residues: 53.2138 Evaluate side-chains 96 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095611 restraints weight = 14697.655| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.57 r_work: 0.3141 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9490 Z= 0.100 Angle : 0.478 7.085 12883 Z= 0.243 Chirality : 0.041 0.154 1410 Planarity : 0.003 0.033 1664 Dihedral : 3.607 20.196 1299 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.38 % Allowed : 18.55 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1129 helix: 2.20 (0.25), residues: 454 sheet: 0.70 (0.46), residues: 128 loop : -0.01 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.024 0.001 TYR A 698 PHE 0.015 0.001 PHE A 465 TRP 0.009 0.001 TRP B 60 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 9486) covalent geometry : angle 0.47692 / 0.24 (12875) SS BOND : bond 0.00350 / 0.18 ( 4) SS BOND : angle 1.07563 / 0.51 ( 8) hydrogen bonds : bond 0.02987 / 1.82 ( 389) hydrogen bonds : angle 4.62711 / 3.34 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8119 (tp) cc_final: 0.7904 (mt) REVERT: A 189 MET cc_start: 0.8401 (tpp) cc_final: 0.8050 (mmt) REVERT: A 698 TYR cc_start: 0.8319 (t80) cc_final: 0.8100 (t80) REVERT: A 702 LEU cc_start: 0.8636 (tt) cc_final: 0.8257 (tm) REVERT: A 742 ARG cc_start: 0.8836 (mtt90) cc_final: 0.8384 (mmt-90) REVERT: A 780 HIS cc_start: 0.7029 (m-70) cc_final: 0.6601 (m90) REVERT: B 76 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 79 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8423 (m) REVERT: B 135 MET cc_start: 0.9099 (mmt) cc_final: 0.8761 (mmt) REVERT: B 198 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7191 (p0) REVERT: B 231 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7819 (tptt) REVERT: B 271 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7766 (tm-30) REVERT: B 395 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8581 (mtpm) REVERT: B 428 SER cc_start: 0.8000 (t) cc_final: 0.7790 (p) outliers start: 24 outliers final: 6 residues processed: 111 average time/residue: 0.4583 time to fit residues: 55.3672 Evaluate side-chains 98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 40 optimal weight: 0.0010 chunk 25 optimal weight: 0.0070 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096820 restraints weight = 14764.779| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.57 r_work: 0.3161 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9490 Z= 0.094 Angle : 0.480 9.461 12883 Z= 0.242 Chirality : 0.040 0.145 1410 Planarity : 0.003 0.033 1664 Dihedral : 3.567 20.675 1299 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.69 % Allowed : 19.44 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1129 helix: 2.23 (0.25), residues: 455 sheet: 0.69 (0.47), residues: 128 loop : 0.01 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.021 0.001 TYR A 732 PHE 0.016 0.001 PHE A 465 TRP 0.008 0.001 TRP B 60 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.09 ( 9486) covalent geometry : angle 0.47928 / 0.24 (12875) SS BOND : bond 0.00415 / 0.21 ( 4) SS BOND : angle 1.07224 / 0.51 ( 8) hydrogen bonds : bond 0.02909 / 1.75 ( 389) hydrogen bonds : angle 4.58393 / 3.29 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7984 (tp) cc_final: 0.7745 (mt) REVERT: A 189 MET cc_start: 0.8368 (tpp) cc_final: 0.8027 (mmt) REVERT: A 668 LEU cc_start: 0.5379 (OUTLIER) cc_final: 0.5170 (tm) REVERT: A 702 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8256 (tm) REVERT: A 732 TYR cc_start: 0.7667 (p90) cc_final: 0.7384 (p90) REVERT: A 742 ARG cc_start: 0.8792 (mtt90) cc_final: 0.8305 (mpt180) REVERT: A 780 HIS cc_start: 0.6981 (m-70) cc_final: 0.6547 (m90) REVERT: B 76 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 79 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8408 (m) REVERT: B 140 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: B 198 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7187 (p0) REVERT: B 231 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7826 (tptt) REVERT: B 271 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7751 (tm-30) REVERT: B 395 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8499 (mtpm) outliers start: 17 outliers final: 3 residues processed: 107 average time/residue: 0.4895 time to fit residues: 56.9338 Evaluate side-chains 98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090484 restraints weight = 14770.600| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.54 r_work: 0.3056 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9490 Z= 0.193 Angle : 0.550 8.128 12883 Z= 0.282 Chirality : 0.044 0.174 1410 Planarity : 0.004 0.035 1664 Dihedral : 4.007 18.440 1299 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.38 % Allowed : 19.25 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1129 helix: 2.02 (0.25), residues: 453 sheet: 0.68 (0.48), residues: 122 loop : -0.05 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 443 TYR 0.020 0.002 TYR A 698 PHE 0.021 0.002 PHE A 367 TRP 0.011 0.001 TRP B 60 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 9486) covalent geometry : angle 0.54890 / 0.28 (12875) SS BOND : bond 0.00628 / 0.32 ( 4) SS BOND : angle 1.44383 / 0.67 ( 8) hydrogen bonds : bond 0.03807 / 2.35 ( 389) hydrogen bonds : angle 4.90295 / 3.54 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8649 (tpp) cc_final: 0.8231 (mmt) REVERT: A 669 MET cc_start: 0.7686 (mmt) cc_final: 0.7302 (mmm) REVERT: A 702 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8205 (tm) REVERT: A 732 TYR cc_start: 0.7887 (p90) cc_final: 0.7562 (p90) REVERT: A 780 HIS cc_start: 0.7116 (m-70) cc_final: 0.6604 (m90) REVERT: B 76 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: B 79 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8425 (m) REVERT: B 140 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: B 198 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7039 (p0) REVERT: B 271 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7893 (tm-30) REVERT: B 395 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8570 (mtpm) outliers start: 24 outliers final: 6 residues processed: 110 average time/residue: 0.4864 time to fit residues: 58.0270 Evaluate side-chains 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.122019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092914 restraints weight = 14642.142| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.55 r_work: 0.3097 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9490 Z= 0.121 Angle : 0.513 8.242 12883 Z= 0.264 Chirality : 0.042 0.153 1410 Planarity : 0.003 0.036 1664 Dihedral : 3.856 19.293 1299 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.49 % Allowed : 20.24 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1129 helix: 2.01 (0.25), residues: 453 sheet: 0.65 (0.48), residues: 122 loop : -0.01 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 742 TYR 0.019 0.001 TYR A 732 PHE 0.018 0.001 PHE A 367 TRP 0.004 0.001 TRP A 364 HIS 0.007 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 9486) covalent geometry : angle 0.51177 / 0.26 (12875) SS BOND : bond 0.00299 / 0.15 ( 4) SS BOND : angle 1.24421 / 0.59 ( 8) hydrogen bonds : bond 0.03291 / 2.01 ( 389) hydrogen bonds : angle 4.83800 / 3.49 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8422 (tp) cc_final: 0.8062 (mt) REVERT: A 189 MET cc_start: 0.8566 (tpp) cc_final: 0.8162 (mmt) REVERT: A 669 MET cc_start: 0.7708 (mmt) cc_final: 0.7331 (mmm) REVERT: A 702 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8260 (tm) REVERT: A 732 TYR cc_start: 0.7838 (p90) cc_final: 0.7608 (p90) REVERT: A 742 ARG cc_start: 0.8908 (mtt90) cc_final: 0.8433 (mmt-90) REVERT: A 780 HIS cc_start: 0.7027 (m-70) cc_final: 0.6560 (m90) REVERT: B 76 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: B 79 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8419 (m) REVERT: B 140 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: B 198 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7054 (p0) REVERT: B 271 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7888 (tm-30) REVERT: B 395 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8564 (mtpm) outliers start: 15 outliers final: 5 residues processed: 101 average time/residue: 0.4331 time to fit residues: 47.6026 Evaluate side-chains 96 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092284 restraints weight = 14826.859| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.58 r_work: 0.3083 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9490 Z= 0.146 Angle : 0.537 8.215 12883 Z= 0.277 Chirality : 0.042 0.154 1410 Planarity : 0.003 0.036 1664 Dihedral : 3.921 19.117 1299 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.59 % Allowed : 20.63 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.25), residues: 1129 helix: 1.93 (0.25), residues: 453 sheet: 0.62 (0.47), residues: 122 loop : -0.01 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 443 TYR 0.019 0.001 TYR A 732 PHE 0.018 0.001 PHE A 132 TRP 0.004 0.001 TRP A 364 HIS 0.007 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 9486) covalent geometry : angle 0.53564 / 0.28 (12875) SS BOND : bond 0.00396 / 0.20 ( 4) SS BOND : angle 1.37880 / 0.66 ( 8) hydrogen bonds : bond 0.03438 / 2.11 ( 389) hydrogen bonds : angle 4.88343 / 3.52 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.8474 (tp) cc_final: 0.8111 (mt) REVERT: A 189 MET cc_start: 0.8566 (tpp) cc_final: 0.8158 (mmt) REVERT: A 669 MET cc_start: 0.7771 (mmt) cc_final: 0.7363 (mmm) REVERT: A 702 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8266 (tm) REVERT: A 732 TYR cc_start: 0.7869 (p90) cc_final: 0.7644 (p90) REVERT: A 742 ARG cc_start: 0.8909 (mtt90) cc_final: 0.8450 (mmt-90) REVERT: A 780 HIS cc_start: 0.7065 (m-70) cc_final: 0.6590 (m90) REVERT: B 76 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: B 79 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8417 (m) REVERT: B 140 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8379 (mt0) REVERT: B 198 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 212 GLU cc_start: 0.8245 (tp30) cc_final: 0.8038 (mt-10) REVERT: B 271 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7909 (tm-30) REVERT: B 395 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8559 (mtpm) outliers start: 16 outliers final: 5 residues processed: 100 average time/residue: 0.4497 time to fit residues: 48.9072 Evaluate side-chains 99 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 395 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093060 restraints weight = 14613.488| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.55 r_work: 0.3106 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9490 Z= 0.128 Angle : 0.524 8.050 12883 Z= 0.269 Chirality : 0.042 0.154 1410 Planarity : 0.003 0.036 1664 Dihedral : 3.848 19.434 1299 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.39 % Allowed : 20.73 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1129 helix: 1.95 (0.25), residues: 454 sheet: 0.63 (0.47), residues: 122 loop : 0.01 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 742 TYR 0.018 0.001 TYR A 732 PHE 0.017 0.001 PHE A 367 TRP 0.004 0.001 TRP A 301 HIS 0.007 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9486) covalent geometry : angle 0.52324 / 0.27 (12875) SS BOND : bond 0.00371 / 0.19 ( 4) SS BOND : angle 1.26065 / 0.60 ( 8) hydrogen bonds : bond 0.03300 / 2.02 ( 389) hydrogen bonds : angle 4.85057 / 3.49 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.53 seconds wall clock time: 45 minutes 16.89 seconds (2716.89 seconds total)