Starting phenix.real_space_refine on Sat Aug 23 03:30:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t13_40953/08_2025/8t13_40953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t13_40953/08_2025/8t13_40953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t13_40953/08_2025/8t13_40953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t13_40953/08_2025/8t13_40953.map" model { file = "/net/cci-nas-00/data/ceres_data/8t13_40953/08_2025/8t13_40953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t13_40953/08_2025/8t13_40953.cif" } resolution = 3.45 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= 0.025 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 Zn 2 6.06 5 S 48 5.16 5 C 5870 2.51 5 N 1652 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 9304 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2311 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 6991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 877, 6991 Classifications: {'peptide': 877} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 846} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8053 SG CYS B 728 55.134 63.043 104.459 1.00118.78 S ATOM 9035 SG CYS B 847 57.686 63.062 101.545 1.00140.61 S ATOM 5810 SG CYS B 447 23.364 35.012 124.916 1.00116.02 S ATOM 5832 SG CYS B 450 22.384 37.761 121.962 1.00119.26 S Time building chain proxies: 2.31, per 1000 atoms: 0.25 Number of scatterers: 9304 At special positions: 0 Unit cell: (81.03, 96.57, 149.85, 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) Zn 2 29.99 S 48 16.00 O 1732 8.00 N 1652 7.00 C 5870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 363.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 712 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 714 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 728 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 847 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" NE2 HIS B 442 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 450 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 447 " Number of angles added : 2 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 49.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 140 through 184 removed outlier: 4.054A pdb=" N LYS A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 244 removed outlier: 3.777A pdb=" N LEU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Proline residue: A 233 - end of helix removed outlier: 3.579A pdb=" N ALA A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 284 Processing helix chain 'A' and resid 292 through 315 removed outlier: 5.130A pdb=" N ASP A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.908A pdb=" N GLY A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.515A pdb=" N GLY B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.879A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 68 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.604A pdb=" N GLY B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.574A pdb=" N PHE B 134 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 169 removed outlier: 3.711A pdb=" N GLU B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 5.099A pdb=" N LYS B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 243 removed outlier: 3.748A pdb=" N SER B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.646A pdb=" N ILE B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LYS B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ARG B 280 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 removed outlier: 3.638A pdb=" N TRP B 292 " --> pdb=" O GLU B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 367 through 386 Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.952A pdb=" N PHE B 399 " --> pdb=" O THR B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.879A pdb=" N GLU B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 511 through 513 No H-bonds generated for 'chain 'B' and resid 511 through 513' Processing helix chain 'B' and resid 514 through 523 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 543 through 551 Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.683A pdb=" N ASN B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 572 Processing helix chain 'B' and resid 602 through 626 Processing helix chain 'B' and resid 639 through 655 removed outlier: 5.839A pdb=" N ARG B 652 " --> pdb=" O VAL B 648 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU B 653 " --> pdb=" O ARG B 649 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 675 removed outlier: 3.665A pdb=" N ALA B 675 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 685 removed outlier: 3.669A pdb=" N ASN B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 739 removed outlier: 3.558A pdb=" N LEU B 734 " --> pdb=" O ASN B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 759 Processing helix chain 'B' and resid 759 through 765 removed outlier: 4.026A pdb=" N SER B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.679A pdb=" N LEU B 774 " --> pdb=" O ARG B 770 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 776 " --> pdb=" O LEU B 772 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 777 " --> pdb=" O ARG B 773 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 778 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.923A pdb=" N MET B 804 " --> pdb=" O HIS B 801 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR B 805 " --> pdb=" O GLU B 802 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 801 through 805' Processing helix chain 'B' and resid 808 through 818 removed outlier: 3.664A pdb=" N VAL B 812 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 848 Processing helix chain 'B' and resid 854 through 859 removed outlier: 3.884A pdb=" N THR B 858 " --> pdb=" O THR B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 873 Processing sheet with id=AA1, first strand: chain 'A' and resid 316 through 323 removed outlier: 5.030A pdb=" N VAL A 318 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG A 345 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 343 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR A 341 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 342 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY A 401 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N THR A 344 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASP A 399 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N LEU A 346 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 397 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.137A pdb=" N LEU A 334 " --> pdb=" O ILE A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.618A pdb=" N LYS A 384 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 359 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 357 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR A 358 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 436 " --> pdb=" O THR A 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 36 removed outlier: 6.729A pdb=" N GLU B 35 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 127 removed outlier: 9.019A pdb=" N ARG B 125 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 100 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLN B 127 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B 102 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY B 75 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS B 101 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 77 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU B 103 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP B 79 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 204 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 310 removed outlier: 3.659A pdb=" N ARG B 595 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 579 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 454 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN B 581 " --> pdb=" O MET B 454 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N GLY B 456 " --> pdb=" O GLN B 581 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 455 " --> pdb=" O ILE B 474 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 474 " --> pdb=" O MET B 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 658 through 660 Processing sheet with id=AA8, first strand: chain 'B' and resid 714 through 717 removed outlier: 3.741A pdb=" N VAL B 726 " --> pdb=" O HIS B 714 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1155 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: 1.31 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: 3086 1.34 - 1.46: 2133 1.46 - 1.58: 4196 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 9494 Sorted by residual: bond pdb=" CB ARG B 737 " pdb=" CG ARG B 737 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.44e-01 bond pdb=" CB ILE B 33 " pdb=" CG1 ILE B 33 " ideal model delta sigma weight residual 1.530 1.549 -0.019 2.00e-02 2.50e+03 8.64e-01 bond pdb=" CB MET B 455 " pdb=" CG MET B 455 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.51e-01 bond pdb=" C VAL A 286 " pdb=" O VAL A 286 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.96e-01 bond pdb=" CA TRP B 859 " pdb=" CB TRP B 859 " ideal model delta sigma weight residual 1.524 1.534 -0.010 1.31e-02 5.83e+03 6.31e-01 ... (remaining 9489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12739 2.29 - 4.58: 72 4.58 - 6.88: 11 6.88 - 9.17: 6 9.17 - 11.46: 2 Bond angle restraints: 12830 Sorted by residual: angle pdb=" N TRP B 859 " pdb=" CA TRP B 859 " pdb=" C TRP B 859 " ideal model delta sigma weight residual 111.81 106.23 5.58 1.44e+00 4.82e-01 1.50e+01 angle pdb=" CB MET B 455 " pdb=" CG MET B 455 " pdb=" SD MET B 455 " ideal model delta sigma weight residual 112.70 124.16 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA TYR B 758 " pdb=" CB TYR B 758 " pdb=" CG TYR B 758 " ideal model delta sigma weight residual 113.90 119.84 -5.94 1.80e+00 3.09e-01 1.09e+01 angle pdb=" C LYS B 689 " pdb=" N ASP B 690 " pdb=" CA ASP B 690 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" CA ARG B 737 " pdb=" CB ARG B 737 " pdb=" CG ARG B 737 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.43e+00 ... (remaining 12825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4817 17.95 - 35.90: 660 35.90 - 53.86: 181 53.86 - 71.81: 39 71.81 - 89.76: 16 Dihedral angle restraints: 5713 sinusoidal: 2357 harmonic: 3356 Sorted by residual: dihedral pdb=" CA TYR B 758 " pdb=" C TYR B 758 " pdb=" N ALA B 759 " pdb=" CA ALA B 759 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP B 664 " pdb=" CB ASP B 664 " pdb=" CG ASP B 664 " pdb=" OD1 ASP B 664 " ideal model delta sinusoidal sigma weight residual -30.00 -87.86 57.86 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CG ARG B 579 " pdb=" CD ARG B 579 " pdb=" NE ARG B 579 " pdb=" CZ ARG B 579 " ideal model delta sinusoidal sigma weight residual -90.00 -134.52 44.52 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 5710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1044 0.037 - 0.073: 269 0.073 - 0.110: 81 0.110 - 0.146: 12 0.146 - 0.183: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA TYR B 758 " pdb=" N TYR B 758 " pdb=" C TYR B 758 " pdb=" CB TYR B 758 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA ASP B 690 " pdb=" N ASP B 690 " pdb=" C ASP B 690 " pdb=" CB ASP B 690 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CB THR B 790 " pdb=" CA THR B 790 " pdb=" OG1 THR B 790 " pdb=" CG2 THR B 790 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1405 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 347 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO B 348 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 348 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 348 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 168 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" CG ASP A 168 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 168 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 168 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 584 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 585 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 585 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 585 " 0.017 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 776 2.74 - 3.28: 8870 3.28 - 3.82: 14616 3.82 - 4.36: 15587 4.36 - 4.90: 28359 Nonbonded interactions: 68208 Sorted by model distance: nonbonded pdb=" O ASN B 241 " pdb=" OG1 THR B 244 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN B 322 " pdb=" OG1 THR B 751 " model vdw 2.236 3.040 nonbonded pdb=" O ASN B 227 " pdb=" OG SER B 231 " model vdw 2.252 3.040 nonbonded pdb=" O VAL B 637 " pdb=" OG1 THR B 638 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 222 " pdb=" OD1 ASN B 223 " model vdw 2.269 3.040 ... (remaining 68203 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: 5.840 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 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: 0.6480 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 : 0.007 0.481 9501 Z= 0.243 Angle : 0.528 11.458 12832 Z= 0.268 Chirality : 0.037 0.183 1408 Planarity : 0.003 0.031 1640 Dihedral : 18.193 89.761 3547 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.10 % Allowed : 28.33 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1157 helix: 2.22 (0.25), residues: 483 sheet: 0.46 (0.45), residues: 141 loop : -1.90 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.012 0.001 TYR B 758 PHE 0.006 0.001 PHE B 483 TRP 0.012 0.001 TRP B 859 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9494) covalent geometry : angle 0.52641 (12830) hydrogen bonds : bond 0.19336 ( 402) hydrogen bonds : angle 5.79707 ( 1155) metal coordination : bond 0.24476 ( 7) metal coordination : angle 2.86514 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.368 Fit side-chains REVERT: A 151 ASP cc_start: 0.7349 (p0) cc_final: 0.6873 (m-30) REVERT: A 195 GLU cc_start: 0.4828 (pp20) cc_final: 0.3761 (tt0) REVERT: B 79 ASP cc_start: 0.7625 (m-30) cc_final: 0.7394 (m-30) REVERT: B 101 LYS cc_start: 0.7924 (tttt) cc_final: 0.7517 (tttp) REVERT: B 125 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7943 (ttt90) REVERT: B 169 GLU cc_start: 0.8406 (pp20) cc_final: 0.8139 (pt0) REVERT: B 194 MET cc_start: 0.6266 (tpp) cc_final: 0.6053 (tpp) REVERT: B 472 ARG cc_start: 0.6652 (ptp-170) cc_final: 0.6003 (ptp90) REVERT: B 533 ASP cc_start: 0.8174 (m-30) cc_final: 0.7965 (m-30) REVERT: B 549 ASN cc_start: 0.7552 (m-40) cc_final: 0.7313 (t0) REVERT: B 820 GLU cc_start: 0.7762 (mp0) cc_final: 0.7512 (mp0) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.1048 time to fit residues: 18.2474 Evaluate side-chains 99 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128334 restraints weight = 13567.364| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.10 r_work: 0.3341 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9501 Z= 0.153 Angle : 0.561 7.965 12832 Z= 0.293 Chirality : 0.041 0.210 1408 Planarity : 0.003 0.032 1640 Dihedral : 4.224 21.910 1263 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.60 % Allowed : 27.13 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.25), residues: 1157 helix: 2.03 (0.24), residues: 489 sheet: 0.08 (0.46), residues: 138 loop : -1.92 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 871 TYR 0.018 0.002 TYR B 758 PHE 0.011 0.001 PHE B 674 TRP 0.012 0.001 TRP B 859 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9494) covalent geometry : angle 0.56002 (12830) hydrogen bonds : bond 0.05438 ( 402) hydrogen bonds : angle 4.36891 ( 1155) metal coordination : bond 0.00831 ( 7) metal coordination : angle 3.26109 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.387 Fit side-chains REVERT: A 151 ASP cc_start: 0.7382 (p0) cc_final: 0.6880 (m-30) REVERT: A 195 GLU cc_start: 0.4517 (pp20) cc_final: 0.3777 (tt0) REVERT: B 328 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7869 (mt) REVERT: B 467 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7212 (mttm) REVERT: B 472 ARG cc_start: 0.7874 (ptp-170) cc_final: 0.7332 (ptp90) REVERT: B 693 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: B 733 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: B 859 TRP cc_start: 0.7289 (t60) cc_final: 0.6265 (t60) outliers start: 36 outliers final: 18 residues processed: 126 average time/residue: 0.1060 time to fit residues: 18.7162 Evaluate side-chains 115 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 693 GLN Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 883 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 113 optimal weight: 3.9990 chunk 64 optimal weight: 0.0020 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 869 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.175340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133366 restraints weight = 13524.173| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.30 r_work: 0.3379 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9501 Z= 0.100 Angle : 0.484 7.068 12832 Z= 0.252 Chirality : 0.038 0.187 1408 Planarity : 0.003 0.034 1640 Dihedral : 3.911 19.852 1263 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.40 % Allowed : 28.73 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.25), residues: 1157 helix: 2.21 (0.24), residues: 493 sheet: 0.19 (0.46), residues: 146 loop : -1.88 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 871 TYR 0.018 0.001 TYR B 758 PHE 0.010 0.001 PHE B 243 TRP 0.011 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9494) covalent geometry : angle 0.48157 (12830) hydrogen bonds : bond 0.04131 ( 402) hydrogen bonds : angle 4.03951 ( 1155) metal coordination : bond 0.00635 ( 7) metal coordination : angle 3.91168 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7419 (p0) cc_final: 0.6858 (m-30) REVERT: A 195 GLU cc_start: 0.4596 (pp20) cc_final: 0.3757 (tt0) REVERT: A 324 MET cc_start: 0.1398 (pmm) cc_final: 0.1165 (pmm) REVERT: A 346 LEU cc_start: 0.6587 (tp) cc_final: 0.6363 (tp) REVERT: B 330 LYS cc_start: 0.8755 (tppp) cc_final: 0.8504 (mttm) REVERT: B 472 ARG cc_start: 0.7879 (ptp-170) cc_final: 0.7328 (ptp90) REVERT: B 733 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: B 859 TRP cc_start: 0.7231 (t60) cc_final: 0.6986 (t60) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.1164 time to fit residues: 19.2497 Evaluate side-chains 109 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 883 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 3.9990 chunk 96 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.168160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125409 restraints weight = 13713.279| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.62 r_work: 0.3304 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9501 Z= 0.216 Angle : 0.624 7.980 12832 Z= 0.328 Chirality : 0.043 0.248 1408 Planarity : 0.004 0.036 1640 Dihedral : 4.671 29.415 1261 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.50 % Allowed : 26.63 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.25), residues: 1157 helix: 1.62 (0.23), residues: 492 sheet: -0.07 (0.46), residues: 146 loop : -2.03 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 842 TYR 0.032 0.002 TYR B 758 PHE 0.012 0.002 PHE B 674 TRP 0.020 0.002 TRP B 859 HIS 0.007 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 9494) covalent geometry : angle 0.62130 (12830) hydrogen bonds : bond 0.06456 ( 402) hydrogen bonds : angle 4.38697 ( 1155) metal coordination : bond 0.00873 ( 7) metal coordination : angle 4.77136 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.397 Fit side-chains REVERT: A 151 ASP cc_start: 0.7455 (p0) cc_final: 0.6911 (m-30) REVERT: A 156 MET cc_start: 0.5190 (OUTLIER) cc_final: 0.4794 (ttt) REVERT: A 195 GLU cc_start: 0.5103 (pp20) cc_final: 0.4148 (tp30) REVERT: A 346 LEU cc_start: 0.6773 (tp) cc_final: 0.6373 (tp) REVERT: B 241 ASN cc_start: 0.7454 (t0) cc_final: 0.7199 (t0) REVERT: B 374 MET cc_start: 0.8426 (mtm) cc_final: 0.8152 (ptp) REVERT: B 460 LYS cc_start: 0.5221 (OUTLIER) cc_final: 0.4989 (tttt) REVERT: B 472 ARG cc_start: 0.7969 (ptp-170) cc_final: 0.7474 (ptp90) REVERT: B 693 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: B 733 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: B 842 ARG cc_start: 0.8347 (tmt170) cc_final: 0.8015 (tpt90) outliers start: 45 outliers final: 29 residues processed: 128 average time/residue: 0.1072 time to fit residues: 19.1688 Evaluate side-chains 127 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 693 GLN Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 806 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0670 chunk 86 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.171116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128508 restraints weight = 13518.074| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.39 r_work: 0.3322 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9501 Z= 0.129 Angle : 0.525 9.592 12832 Z= 0.274 Chirality : 0.039 0.218 1408 Planarity : 0.003 0.035 1640 Dihedral : 4.270 27.137 1261 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.00 % Allowed : 26.93 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1157 helix: 1.89 (0.24), residues: 492 sheet: -0.10 (0.45), residues: 150 loop : -1.99 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 237 TYR 0.023 0.001 TYR B 758 PHE 0.010 0.001 PHE B 243 TRP 0.016 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9494) covalent geometry : angle 0.52312 (12830) hydrogen bonds : bond 0.04740 ( 402) hydrogen bonds : angle 4.10532 ( 1155) metal coordination : bond 0.00855 ( 7) metal coordination : angle 3.76803 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7483 (p0) cc_final: 0.6880 (m-30) REVERT: A 156 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.4655 (ttt) REVERT: A 195 GLU cc_start: 0.4958 (pp20) cc_final: 0.3606 (tp30) REVERT: A 199 LEU cc_start: 0.4559 (OUTLIER) cc_final: 0.4246 (mp) REVERT: A 324 MET cc_start: 0.1916 (pmm) cc_final: 0.1561 (pmm) REVERT: A 346 LEU cc_start: 0.6763 (tp) cc_final: 0.6388 (tp) REVERT: A 360 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.5196 (pm20) REVERT: B 241 ASN cc_start: 0.7408 (t0) cc_final: 0.7129 (t0) REVERT: B 328 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7743 (mt) REVERT: B 472 ARG cc_start: 0.7847 (ptp-170) cc_final: 0.7305 (ptp90) outliers start: 40 outliers final: 23 residues processed: 129 average time/residue: 0.1090 time to fit residues: 19.5896 Evaluate side-chains 123 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 883 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 45 optimal weight: 0.0030 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN B 869 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129350 restraints weight = 13511.058| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.93 r_work: 0.3348 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9501 Z= 0.118 Angle : 0.516 9.877 12832 Z= 0.268 Chirality : 0.039 0.214 1408 Planarity : 0.003 0.035 1640 Dihedral : 4.133 26.690 1261 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.00 % Allowed : 27.43 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.25), residues: 1157 helix: 1.95 (0.24), residues: 493 sheet: 0.19 (0.46), residues: 146 loop : -2.02 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 842 TYR 0.021 0.001 TYR B 758 PHE 0.011 0.001 PHE B 243 TRP 0.014 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9494) covalent geometry : angle 0.51328 (12830) hydrogen bonds : bond 0.04465 ( 402) hydrogen bonds : angle 4.01896 ( 1155) metal coordination : bond 0.00501 ( 7) metal coordination : angle 3.88216 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 100 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7480 (p0) cc_final: 0.6916 (m-30) REVERT: A 156 MET cc_start: 0.4781 (OUTLIER) cc_final: 0.4512 (ttt) REVERT: A 195 GLU cc_start: 0.4968 (pp20) cc_final: 0.3513 (tp30) REVERT: A 199 LEU cc_start: 0.4324 (OUTLIER) cc_final: 0.4042 (mp) REVERT: A 324 MET cc_start: 0.2130 (pmm) cc_final: 0.1804 (pmm) REVERT: A 346 LEU cc_start: 0.6782 (tp) cc_final: 0.6396 (tp) REVERT: B 187 MET cc_start: 0.5502 (mtm) cc_final: 0.5242 (mtt) REVERT: B 198 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: B 241 ASN cc_start: 0.7403 (t0) cc_final: 0.7138 (t0) REVERT: B 328 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7684 (mt) REVERT: B 472 ARG cc_start: 0.7856 (ptp-170) cc_final: 0.7289 (ptp90) outliers start: 40 outliers final: 31 residues processed: 131 average time/residue: 0.0833 time to fit residues: 15.5683 Evaluate side-chains 133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 198 GLN Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 883 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 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 142 GLN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128235 restraints weight = 13639.017| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.76 r_work: 0.3333 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9501 Z= 0.142 Angle : 0.546 10.105 12832 Z= 0.284 Chirality : 0.040 0.224 1408 Planarity : 0.003 0.034 1640 Dihedral : 4.251 27.912 1261 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.20 % Allowed : 26.73 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 1157 helix: 1.88 (0.24), residues: 492 sheet: 0.12 (0.46), residues: 146 loop : -2.00 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 842 TYR 0.025 0.002 TYR B 758 PHE 0.012 0.001 PHE B 674 TRP 0.012 0.001 TRP B 859 HIS 0.004 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9494) covalent geometry : angle 0.54380 (12830) hydrogen bonds : bond 0.04881 ( 402) hydrogen bonds : angle 4.07114 ( 1155) metal coordination : bond 0.00900 ( 7) metal coordination : angle 3.79098 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 99 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7301 (p0) cc_final: 0.6932 (m-30) REVERT: A 156 MET cc_start: 0.4876 (OUTLIER) cc_final: 0.4618 (ttt) REVERT: A 195 GLU cc_start: 0.4950 (pp20) cc_final: 0.3609 (tp30) REVERT: A 199 LEU cc_start: 0.4386 (OUTLIER) cc_final: 0.4103 (mp) REVERT: A 324 MET cc_start: 0.2238 (pmm) cc_final: 0.1902 (pmm) REVERT: A 333 ILE cc_start: 0.3133 (tp) cc_final: 0.2732 (tp) REVERT: A 346 LEU cc_start: 0.6798 (tp) cc_final: 0.6395 (tp) REVERT: B 241 ASN cc_start: 0.7459 (t0) cc_final: 0.7214 (t0) REVERT: B 328 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7748 (mt) REVERT: B 472 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7302 (ptp90) outliers start: 42 outliers final: 33 residues processed: 132 average time/residue: 0.1054 time to fit residues: 19.3183 Evaluate side-chains 131 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 790 THR Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 883 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 94 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.173547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131486 restraints weight = 13434.180| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.51 r_work: 0.3384 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9501 Z= 0.100 Angle : 0.499 9.966 12832 Z= 0.260 Chirality : 0.038 0.205 1408 Planarity : 0.003 0.036 1640 Dihedral : 3.981 25.508 1261 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.10 % Allowed : 28.63 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.25), residues: 1157 helix: 2.08 (0.24), residues: 492 sheet: 0.20 (0.46), residues: 146 loop : -1.96 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 842 TYR 0.019 0.001 TYR B 758 PHE 0.010 0.001 PHE B 243 TRP 0.011 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9494) covalent geometry : angle 0.49764 (12830) hydrogen bonds : bond 0.03928 ( 402) hydrogen bonds : angle 3.92560 ( 1155) metal coordination : bond 0.00779 ( 7) metal coordination : angle 2.76731 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7264 (p0) cc_final: 0.6808 (m-30) REVERT: A 195 GLU cc_start: 0.5079 (pp20) cc_final: 0.3526 (tp30) REVERT: A 199 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4110 (mp) REVERT: A 324 MET cc_start: 0.2343 (pmm) cc_final: 0.1943 (pmm) REVERT: A 333 ILE cc_start: 0.3291 (tp) cc_final: 0.2852 (tp) REVERT: A 346 LEU cc_start: 0.6835 (tp) cc_final: 0.6488 (tp) REVERT: B 111 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6914 (pm20) REVERT: B 187 MET cc_start: 0.5251 (mtm) cc_final: 0.4967 (mtt) REVERT: B 241 ASN cc_start: 0.7465 (t0) cc_final: 0.7218 (t0) REVERT: B 328 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (mt) REVERT: B 472 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7382 (ptp90) outliers start: 31 outliers final: 23 residues processed: 124 average time/residue: 0.1065 time to fit residues: 18.6353 Evaluate side-chains 119 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 790 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 213 ASN B 561 HIS ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.167293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122938 restraints weight = 13759.710| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.04 r_work: 0.3268 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9501 Z= 0.235 Angle : 0.656 9.910 12832 Z= 0.343 Chirality : 0.043 0.253 1408 Planarity : 0.004 0.061 1640 Dihedral : 4.723 32.669 1261 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.50 % Allowed : 27.93 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.25 (0.25), residues: 1157 helix: 1.59 (0.23), residues: 492 sheet: -0.01 (0.46), residues: 142 loop : -2.04 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 842 TYR 0.030 0.002 TYR B 758 PHE 0.015 0.002 PHE B 674 TRP 0.015 0.002 TRP B 475 HIS 0.007 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 9494) covalent geometry : angle 0.65533 (12830) hydrogen bonds : bond 0.06472 ( 402) hydrogen bonds : angle 4.33708 ( 1155) metal coordination : bond 0.00971 ( 7) metal coordination : angle 2.84731 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7269 (p0) cc_final: 0.6924 (m-30) REVERT: A 156 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.4482 (ttt) REVERT: A 195 GLU cc_start: 0.4936 (pp20) cc_final: 0.3584 (tp30) REVERT: A 199 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.4263 (mp) REVERT: A 324 MET cc_start: 0.2875 (pmm) cc_final: 0.2517 (pmm) REVERT: A 333 ILE cc_start: 0.3696 (tp) cc_final: 0.3320 (tp) REVERT: A 346 LEU cc_start: 0.6839 (tp) cc_final: 0.6435 (tp) REVERT: B 241 ASN cc_start: 0.7529 (t0) cc_final: 0.7321 (t0) REVERT: B 472 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7277 (ptp90) REVERT: B 733 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: B 826 ASP cc_start: 0.7892 (t0) cc_final: 0.7447 (t0) outliers start: 35 outliers final: 26 residues processed: 125 average time/residue: 0.0732 time to fit residues: 13.1345 Evaluate side-chains 122 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 786 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.170152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127340 restraints weight = 13580.944| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.83 r_work: 0.3318 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9501 Z= 0.140 Angle : 0.559 9.377 12832 Z= 0.291 Chirality : 0.040 0.228 1408 Planarity : 0.004 0.036 1640 Dihedral : 4.364 29.726 1261 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.10 % Allowed : 28.53 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.25), residues: 1157 helix: 1.81 (0.24), residues: 492 sheet: -0.10 (0.45), residues: 150 loop : -1.99 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 842 TYR 0.025 0.002 TYR B 758 PHE 0.013 0.001 PHE B 629 TRP 0.012 0.001 TRP B 859 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9494) covalent geometry : angle 0.55846 (12830) hydrogen bonds : bond 0.04901 ( 402) hydrogen bonds : angle 4.11368 ( 1155) metal coordination : bond 0.00892 ( 7) metal coordination : angle 2.26515 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2314 Ramachandran restraints generated. 1157 Oldfield, 0 Emsley, 1157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7547 (p0) cc_final: 0.7187 (m-30) REVERT: A 156 MET cc_start: 0.4962 (OUTLIER) cc_final: 0.4727 (ttt) REVERT: A 195 GLU cc_start: 0.5097 (pp20) cc_final: 0.3877 (tp30) REVERT: A 199 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.4273 (mp) REVERT: A 324 MET cc_start: 0.2812 (pmm) cc_final: 0.2581 (pmm) REVERT: A 333 ILE cc_start: 0.3669 (tp) cc_final: 0.3364 (pt) REVERT: A 346 LEU cc_start: 0.6882 (tp) cc_final: 0.6509 (tp) REVERT: B 187 MET cc_start: 0.5287 (mtm) cc_final: 0.4996 (mtt) REVERT: B 241 ASN cc_start: 0.7454 (t0) cc_final: 0.7244 (t0) REVERT: B 472 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7277 (ptp90) outliers start: 31 outliers final: 28 residues processed: 120 average time/residue: 0.0959 time to fit residues: 16.1673 Evaluate side-chains 124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 623 MET Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 733 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 758 TYR Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 788 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 731 GLN ** 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 = 0.4095 r_free = 0.4095 target = 0.170269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126650 restraints weight = 13522.693| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.03 r_work: 0.3320 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9501 Z= 0.131 Angle : 0.555 9.388 12832 Z= 0.288 Chirality : 0.039 0.226 1408 Planarity : 0.004 0.066 1640 Dihedral : 4.341 29.160 1261 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.10 % Allowed : 28.33 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1157 helix: 1.90 (0.24), residues: 490 sheet: -0.10 (0.45), residues: 150 loop : -2.00 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 842 TYR 0.025 0.001 TYR B 758 PHE 0.013 0.001 PHE B 629 TRP 0.011 0.001 TRP B 859 HIS 0.003 0.001 HIS B 712 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9494) covalent geometry : angle 0.55416 (12830) hydrogen bonds : bond 0.04772 ( 402) hydrogen bonds : angle 4.06686 ( 1155) metal coordination : bond 0.00869 ( 7) metal coordination : angle 2.38480 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.77 seconds wall clock time: 40 minutes 37.35 seconds (2437.35 seconds total)