Starting phenix.real_space_refine on Sat Aug 23 02:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpw_60365/08_2025/8zpw_60365_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpw_60365/08_2025/8zpw_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zpw_60365/08_2025/8zpw_60365_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpw_60365/08_2025/8zpw_60365_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zpw_60365/08_2025/8zpw_60365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpw_60365/08_2025/8zpw_60365.map" } 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-2.0-5787/lib/python3.9/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, 16 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 2.25, per 1000 atoms: 0.24 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 328.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.36 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: 1.68 Time building geometry restraints manager: 1.14 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.400 Find NCS groups from input model: 0.040 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 aren 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 covalent geometry : bond 0.00281 ( 9486) covalent geometry : angle 0.52612 (12875) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.00723 ( 8) hydrogen bonds : bond 0.14497 ( 389) hydrogen bonds : angle 6.57824 ( 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 : 0.291 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: 0.4947 time to fit residues: 54.0561 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 : 0.223 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 747 HIS B 82 ASN B 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.123222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.094845 restraints weight = 14556.742| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.47 r_work: 0.3117 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9490 Z= 0.115 Angle : 0.505 6.814 12883 Z= 0.266 Chirality : 0.041 0.150 1410 Planarity : 0.004 0.035 1664 Dihedral : 5.044 53.230 1316 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.79 % Allowed : 15.67 % Favored : 82.54 % 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 aren not related in a simple way. whole: 1.27 (0.25), residues: 1129 helix: 2.16 (0.25), residues: 461 sheet: 0.37 (0.48), residues: 126 loop : -0.16 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 443 TYR 0.016 0.001 TYR A 698 PHE 0.017 0.001 PHE A 425 TRP 0.010 0.001 TRP B 60 HIS 0.005 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9486) covalent geometry : angle 0.50409 (12875) SS BOND : bond 0.00412 ( 4) SS BOND : angle 1.24630 ( 8) hydrogen bonds : bond 0.03861 ( 389) hydrogen bonds : angle 5.26623 ( 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: 18 poor density : 115 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8680 (tpp) cc_final: 0.8293 (mmt) REVERT: A 293 ASP cc_start: 0.8365 (t0) cc_final: 0.8151 (t0) REVERT: A 669 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6914 (tpp) REVERT: A 702 LEU cc_start: 0.8607 (tt) cc_final: 0.8152 (tm) REVERT: A 742 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8528 (mmt-90) REVERT: A 780 HIS cc_start: 0.7257 (m-70) cc_final: 0.6653 (m90) REVERT: B 76 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: B 79 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8444 (m) REVERT: B 198 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7236 (p0) outliers start: 18 outliers final: 7 residues processed: 125 average time/residue: 0.5059 time to fit residues: 68.6088 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 : 0.356 ------------------------------------------------------------------------------- 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: 0.6980 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 34 optimal weight: 0.0040 chunk 95 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.4710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 HIS A 747 HIS B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094762 restraints weight = 14771.660| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.56 r_work: 0.3126 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9490 Z= 0.104 Angle : 0.486 7.691 12883 Z= 0.253 Chirality : 0.041 0.147 1410 Planarity : 0.003 0.034 1664 Dihedral : 4.454 53.633 1303 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.38 % Allowed : 16.87 % 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 aren not related in a simple way. whole: 1.31 (0.25), residues: 1129 helix: 2.16 (0.25), residues: 459 sheet: 0.55 (0.47), residues: 122 loop : -0.13 (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 0.015 0.001 PHE A 425 TRP 0.008 0.001 TRP B 60 HIS 0.007 0.001 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9486) covalent geometry : angle 0.48458 (12875) SS BOND : bond 0.00485 ( 4) SS BOND : angle 1.37804 ( 8) hydrogen bonds : bond 0.03329 ( 389) hydrogen bonds : angle 4.93475 ( 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 126 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8637 (tpp) cc_final: 0.8278 (mmt) REVERT: A 702 LEU cc_start: 0.8646 (tt) cc_final: 0.8195 (tm) REVERT: A 751 GLN cc_start: 0.7793 (mt0) cc_final: 0.7548 (mt0) REVERT: A 780 HIS cc_start: 0.7259 (m-70) cc_final: 0.6662 (m90) REVERT: B 76 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: B 79 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8392 (m) REVERT: B 198 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7194 (p0) REVERT: B 271 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7806 (tm-30) REVERT: B 395 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8511 (mtpm) outliers start: 24 outliers final: 5 residues processed: 116 average time/residue: 0.4760 time to fit residues: 59.9660 Evaluate side-chains 97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 377 SER 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: 0.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS B 43 ASN B 174 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094315 restraints weight = 14770.644| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.58 r_work: 0.3120 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9490 Z= 0.110 Angle : 0.490 7.582 12883 Z= 0.250 Chirality : 0.041 0.138 1410 Planarity : 0.003 0.034 1664 Dihedral : 3.809 19.534 1299 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.18 % Allowed : 17.86 % Favored : 79.96 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1129 helix: 2.20 (0.25), residues: 455 sheet: 0.64 (0.48), residues: 122 loop : -0.11 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.022 0.001 TYR A 698 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 covalent geometry : bond 0.00252 ( 9486) covalent geometry : angle 0.48889 (12875) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.25294 ( 8) hydrogen bonds : bond 0.03228 ( 389) hydrogen bonds : angle 4.81137 ( 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: 22 poor density : 98 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8468 (tpp) cc_final: 0.8103 (mmt) REVERT: A 702 LEU cc_start: 0.8685 (tt) cc_final: 0.8278 (tm) REVERT: A 742 ARG cc_start: 0.8856 (mtt90) cc_final: 0.8424 (mmt-90) REVERT: A 751 GLN cc_start: 0.7744 (mt0) cc_final: 0.7514 (mt0) REVERT: A 780 HIS cc_start: 0.7165 (m-70) cc_final: 0.6633 (m90) REVERT: B 76 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: B 79 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8405 (m) REVERT: B 198 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7220 (p0) REVERT: B 271 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7785 (tm-30) REVERT: B 395 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8479 (mtpm) outliers start: 22 outliers final: 5 residues processed: 111 average time/residue: 0.5109 time to fit residues: 61.6141 Evaluate side-chains 98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.092680 restraints weight = 14866.878| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.58 r_work: 0.3093 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9490 Z= 0.133 Angle : 0.501 7.047 12883 Z= 0.259 Chirality : 0.041 0.149 1410 Planarity : 0.003 0.034 1664 Dihedral : 3.838 19.106 1299 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.28 % Allowed : 17.86 % 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 aren not related in a simple way. whole: 1.31 (0.25), residues: 1129 helix: 2.13 (0.25), residues: 455 sheet: 0.62 (0.48), residues: 122 loop : -0.10 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 443 TYR 0.023 0.001 TYR A 732 PHE 0.017 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 covalent geometry : bond 0.00309 ( 9486) covalent geometry : angle 0.50042 (12875) SS BOND : bond 0.00581 ( 4) SS BOND : angle 1.38249 ( 8) hydrogen bonds : bond 0.03368 ( 389) hydrogen bonds : angle 4.82256 ( 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 117 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8655 (tpp) cc_final: 0.8287 (mmt) REVERT: A 293 ASP cc_start: 0.8356 (t0) cc_final: 0.8153 (t0) REVERT: A 322 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7788 (mmm) REVERT: A 702 LEU cc_start: 0.8691 (tt) cc_final: 0.8275 (tm) REVERT: A 751 GLN cc_start: 0.7849 (mt0) cc_final: 0.7561 (mt0) REVERT: A 780 HIS cc_start: 0.7175 (m-70) cc_final: 0.6657 (m90) REVERT: B 76 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: B 79 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8423 (m) REVERT: B 198 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7113 (p0) REVERT: B 231 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8165 (ttmm) REVERT: B 271 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7855 (tm-30) REVERT: B 395 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8728 (mtpm) outliers start: 23 outliers final: 5 residues processed: 111 average time/residue: 0.5025 time to fit residues: 60.3845 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 322 MET 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 231 LYS 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: 6.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 0.0050 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092060 restraints weight = 14740.059| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.62 r_work: 0.3084 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9490 Z= 0.134 Angle : 0.502 7.230 12883 Z= 0.257 Chirality : 0.042 0.153 1410 Planarity : 0.003 0.035 1664 Dihedral : 3.865 19.464 1299 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.48 % Allowed : 17.56 % Favored : 79.96 % 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 aren not related in a simple way. whole: 1.31 (0.25), residues: 1129 helix: 2.11 (0.25), residues: 455 sheet: 0.63 (0.47), residues: 122 loop : -0.08 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.025 0.001 TYR A 698 PHE 0.017 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 covalent geometry : bond 0.00314 ( 9486) covalent geometry : angle 0.50098 (12875) SS BOND : bond 0.00446 ( 4) SS BOND : angle 1.35847 ( 8) hydrogen bonds : bond 0.03356 ( 389) hydrogen bonds : angle 4.80891 ( 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: 25 poor density : 94 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8496 (tpp) cc_final: 0.8091 (mmt) REVERT: A 702 LEU cc_start: 0.8687 (tt) cc_final: 0.8281 (tm) REVERT: A 742 ARG cc_start: 0.8858 (mtt90) cc_final: 0.8347 (mmt-90) REVERT: A 780 HIS cc_start: 0.7100 (m-70) cc_final: 0.6625 (m90) REVERT: B 76 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: B 79 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8427 (m) REVERT: B 198 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7138 (p0) REVERT: B 231 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7964 (ttmm) REVERT: B 271 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7831 (tm-30) REVERT: B 395 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8634 (mtpm) outliers start: 25 outliers final: 6 residues processed: 113 average time/residue: 0.5123 time to fit residues: 62.8185 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 : 0.288 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 64 optimal weight: 20.0000 chunk 53 optimal weight: 0.0050 chunk 87 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.094231 restraints weight = 14741.939| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.57 r_work: 0.3118 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9490 Z= 0.107 Angle : 0.495 8.964 12883 Z= 0.253 Chirality : 0.041 0.156 1410 Planarity : 0.003 0.037 1664 Dihedral : 3.752 20.049 1299 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.79 % Allowed : 19.44 % Favored : 78.77 % 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 aren not related in a simple way. whole: 1.35 (0.25), residues: 1129 helix: 2.11 (0.25), residues: 453 sheet: 0.72 (0.48), residues: 122 loop : -0.04 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 443 TYR 0.022 0.001 TYR A 698 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 covalent geometry : bond 0.00246 ( 9486) covalent geometry : angle 0.49436 (12875) SS BOND : bond 0.00353 ( 4) SS BOND : angle 1.12104 ( 8) hydrogen bonds : bond 0.03082 ( 389) hydrogen bonds : angle 4.72804 ( 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 116 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8590 (tpp) cc_final: 0.8219 (mmt) REVERT: A 702 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8235 (tm) REVERT: A 732 TYR cc_start: 0.7755 (p90) cc_final: 0.7453 (p90) REVERT: A 742 ARG cc_start: 0.8933 (mtt90) cc_final: 0.8473 (mmt-90) REVERT: A 751 GLN cc_start: 0.7823 (mt0) cc_final: 0.7619 (mt0) REVERT: A 780 HIS cc_start: 0.7096 (m-70) cc_final: 0.6599 (m90) REVERT: B 76 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: B 79 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8431 (m) REVERT: B 198 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7055 (p0) REVERT: B 271 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7848 (tm-30) REVERT: B 320 THR cc_start: 0.8744 (m) cc_final: 0.8541 (p) REVERT: B 395 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8668 (mtpm) outliers start: 18 outliers final: 8 residues processed: 108 average time/residue: 0.4720 time to fit residues: 55.4585 Evaluate side-chains 100 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 398 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.121141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091881 restraints weight = 14732.303| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.59 r_work: 0.3083 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9490 Z= 0.142 Angle : 0.522 8.042 12883 Z= 0.266 Chirality : 0.042 0.156 1410 Planarity : 0.003 0.037 1664 Dihedral : 3.877 19.215 1299 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.08 % Allowed : 19.35 % Favored : 78.57 % 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 aren not related in a simple way. whole: 1.35 (0.25), residues: 1129 helix: 2.10 (0.25), residues: 453 sheet: 0.69 (0.47), residues: 122 loop : -0.03 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 443 TYR 0.021 0.001 TYR A 698 PHE 0.017 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 covalent geometry : bond 0.00336 ( 9486) covalent geometry : angle 0.52139 (12875) SS BOND : bond 0.00469 ( 4) SS BOND : angle 1.32375 ( 8) hydrogen bonds : bond 0.03400 ( 389) hydrogen bonds : angle 4.81011 ( 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 110 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8624 (tpp) cc_final: 0.8214 (mmt) REVERT: A 462 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8157 (ttt) REVERT: A 702 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8205 (tm) REVERT: A 732 TYR cc_start: 0.7866 (p90) cc_final: 0.7597 (p90) REVERT: A 742 ARG cc_start: 0.8930 (mtt90) cc_final: 0.8470 (mmt-90) REVERT: A 780 HIS cc_start: 0.7042 (m-70) cc_final: 0.6609 (m90) REVERT: B 76 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: B 79 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8458 (m) REVERT: B 198 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7076 (p0) REVERT: B 212 GLU cc_start: 0.8281 (tp30) cc_final: 0.7892 (pt0) REVERT: B 271 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7870 (tm-30) REVERT: B 395 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8673 (mtpm) outliers start: 21 outliers final: 9 residues processed: 104 average time/residue: 0.4845 time to fit residues: 54.7472 Evaluate side-chains 104 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 462 MET 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 188 TYR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 382 VAL 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: 0.9990 chunk 95 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3682 r_free = 0.3682 target = 0.122513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093549 restraints weight = 14603.301| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.53 r_work: 0.3112 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9490 Z= 0.112 Angle : 0.501 8.034 12883 Z= 0.256 Chirality : 0.041 0.152 1410 Planarity : 0.003 0.037 1664 Dihedral : 3.804 19.627 1299 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 aren not related in a simple way. whole: 1.34 (0.25), residues: 1129 helix: 2.03 (0.25), residues: 459 sheet: 0.70 (0.46), residues: 128 loop : -0.00 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 443 TYR 0.020 0.001 TYR A 698 PHE 0.017 0.001 PHE A 465 TRP 0.004 0.001 TRP A 301 HIS 0.007 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9486) covalent geometry : angle 0.50041 (12875) SS BOND : bond 0.00398 ( 4) SS BOND : angle 1.14144 ( 8) hydrogen bonds : bond 0.03139 ( 389) hydrogen bonds : angle 4.75585 ( 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 108 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 189 MET cc_start: 0.8578 (tpp) cc_final: 0.8172 (mmt) REVERT: A 462 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8087 (ttt) REVERT: A 669 MET cc_start: 0.7644 (mmt) cc_final: 0.7228 (mmm) REVERT: A 702 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8233 (tm) REVERT: A 732 TYR cc_start: 0.7892 (p90) cc_final: 0.7643 (p90) REVERT: A 742 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8506 (mmt-90) REVERT: A 751 GLN cc_start: 0.7867 (mt0) cc_final: 0.7655 (mt0) REVERT: A 780 HIS cc_start: 0.7021 (m-70) cc_final: 0.6544 (m90) REVERT: B 76 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 79 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8439 (m) REVERT: B 198 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 212 GLU cc_start: 0.8269 (tp30) cc_final: 0.7928 (pt0) REVERT: B 271 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7869 (tm-30) REVERT: B 395 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8658 (mtpm) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.5072 time to fit residues: 56.4084 Evaluate side-chains 99 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 ILE 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 188 TYR Chi-restraints excluded: chain B residue 198 ASP 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: 1.9990 chunk 49 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 29 optimal weight: 0.0170 chunk 75 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094692 restraints weight = 14738.529| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.57 r_work: 0.3131 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9490 Z= 0.104 Angle : 0.510 7.996 12883 Z= 0.259 Chirality : 0.041 0.154 1410 Planarity : 0.003 0.036 1664 Dihedral : 3.725 19.978 1299 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.49 % Allowed : 19.94 % Favored : 78.57 % 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 aren not related in a simple way. whole: 1.36 (0.25), residues: 1129 helix: 2.03 (0.25), residues: 460 sheet: 0.71 (0.46), residues: 128 loop : 0.02 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 443 TYR 0.019 0.001 TYR A 698 PHE 0.016 0.001 PHE A 465 TRP 0.005 0.001 TRP A 364 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9486) covalent geometry : angle 0.50889 (12875) SS BOND : bond 0.00288 ( 4) SS BOND : angle 1.13833 ( 8) hydrogen bonds : bond 0.03046 ( 389) hydrogen bonds : angle 4.75973 ( 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 108 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 78 GLN cc_start: 0.7421 (mt0) cc_final: 0.7091 (mt0) REVERT: A 189 MET cc_start: 0.8392 (tpp) cc_final: 0.8029 (mmt) REVERT: A 462 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8251 (ttt) REVERT: A 669 MET cc_start: 0.7645 (mmt) cc_final: 0.7239 (mmm) REVERT: A 702 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8269 (tm) REVERT: A 732 TYR cc_start: 0.7888 (p90) cc_final: 0.7653 (p90) REVERT: A 742 ARG cc_start: 0.8827 (mtt90) cc_final: 0.8406 (mmt-90) REVERT: A 780 HIS cc_start: 0.6967 (m-70) cc_final: 0.6542 (m90) REVERT: B 76 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: B 79 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8433 (m) REVERT: B 198 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7115 (p0) REVERT: B 212 GLU cc_start: 0.8068 (tp30) cc_final: 0.7818 (pt0) REVERT: B 271 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7812 (tm-30) REVERT: B 395 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8659 (mtpm) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.5018 time to fit residues: 55.4832 Evaluate side-chains 100 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 398 ILE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 581 ILE 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 188 TYR Chi-restraints excluded: chain B residue 198 ASP 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: 0.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 77 optimal weight: 0.0570 chunk 96 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 747 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094790 restraints weight = 14558.511| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.54 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: 0.8484 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9490 Z= 0.106 Angle : 0.502 7.968 12883 Z= 0.256 Chirality : 0.041 0.157 1410 Planarity : 0.003 0.036 1664 Dihedral : 3.723 19.949 1299 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.79 % Allowed : 20.14 % Favored : 78.08 % 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 aren not related in a simple way. whole: 1.38 (0.25), residues: 1129 helix: 2.02 (0.25), residues: 460 sheet: 0.75 (0.46), residues: 128 loop : 0.05 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 443 TYR 0.019 0.001 TYR A 698 PHE 0.016 0.001 PHE A 465 TRP 0.006 0.001 TRP B 60 HIS 0.006 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9486) covalent geometry : angle 0.50103 (12875) SS BOND : bond 0.00347 ( 4) SS BOND : angle 1.14058 ( 8) hydrogen bonds : bond 0.03082 ( 389) hydrogen bonds : angle 4.75071 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2868.24 seconds wall clock time: 49 minutes 39.47 seconds (2979.47 seconds total)