Starting phenix.real_space_refine on Mon May 12 22:51:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t13_40953/05_2025/8t13_40953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t13_40953/05_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_40953/05_2025/8t13_40953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t13_40953/05_2025/8t13_40953.map" model { file = "/net/cci-nas-00/data/ceres_data/8t13_40953/05_2025/8t13_40953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t13_40953/05_2025/8t13_40953.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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, 'ASN:plan1': 1, 'TRP:plan': 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: 6.33, per 1000 atoms: 0.68 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: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.05 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: 2.86 Time building geometry restraints manager: 2.89 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: 8.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 26.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP B 859 HIS 0.003 0.001 HIS B 247 PHE 0.006 0.001 PHE B 483 TYR 0.012 0.001 TYR B 758 ARG 0.004 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.19336 ( 402) hydrogen bonds : angle 5.79707 ( 1155) metal coordination : bond 0.24476 ( 7) metal coordination : angle 2.86514 ( 2) covalent geometry : bond 0.00209 ( 9494) covalent geometry : angle 0.52641 (12830) *********************** 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 : 1.195 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: 0.2459 time to fit residues: 42.9191 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 : 1.098 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.171381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.127818 restraints weight = 13540.462| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.90 r_work: 0.3330 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9501 Z= 0.167 Angle : 0.572 8.079 12832 Z= 0.299 Chirality : 0.041 0.216 1408 Planarity : 0.004 0.032 1640 Dihedral : 4.264 22.453 1263 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.60 % Allowed : 26.93 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1157 helix: 2.01 (0.24), residues: 489 sheet: 0.07 (0.46), residues: 138 loop : -1.92 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 859 HIS 0.004 0.001 HIS B 768 PHE 0.011 0.002 PHE B 674 TYR 0.020 0.002 TYR B 758 ARG 0.005 0.000 ARG B 871 Details of bonding type rmsd hydrogen bonds : bond 0.05732 ( 402) hydrogen bonds : angle 4.42553 ( 1155) metal coordination : bond 0.00899 ( 7) metal coordination : angle 3.27835 ( 2) covalent geometry : bond 0.00386 ( 9494) covalent geometry : angle 0.57049 (12830) *********************** 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 133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 1.128 Fit side-chains REVERT: A 151 ASP cc_start: 0.7447 (p0) cc_final: 0.6881 (m-30) REVERT: A 195 GLU cc_start: 0.4543 (pp20) cc_final: 0.3813 (tt0) REVERT: B 467 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7140 (mttm) REVERT: B 472 ARG cc_start: 0.7888 (ptp-170) cc_final: 0.7355 (ptp90) REVERT: B 693 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: B 733 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6878 (mp0) outliers start: 36 outliers final: 18 residues processed: 124 average time/residue: 0.2203 time to fit residues: 38.2463 Evaluate side-chains 113 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 446 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 325 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 447 CYS Chi-restraints excluded: chain B residue 474 ILE 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 758 TYR Chi-restraints excluded: chain B residue 761 MET 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 0 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 869 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 = 0.4079 r_free = 0.4079 target = 0.168611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125400 restraints weight = 13754.142| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.26 r_work: 0.3289 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9501 Z= 0.201 Angle : 0.600 6.732 12832 Z= 0.316 Chirality : 0.042 0.257 1408 Planarity : 0.004 0.037 1640 Dihedral : 4.623 28.927 1261 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.30 % Allowed : 26.73 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1157 helix: 1.67 (0.24), residues: 492 sheet: -0.19 (0.46), residues: 146 loop : -2.03 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 859 HIS 0.006 0.001 HIS B 768 PHE 0.011 0.002 PHE B 491 TYR 0.032 0.002 TYR B 758 ARG 0.003 0.000 ARG B 871 Details of bonding type rmsd hydrogen bonds : bond 0.06200 ( 402) hydrogen bonds : angle 4.38807 ( 1155) metal coordination : bond 0.01050 ( 7) metal coordination : angle 4.68410 ( 2) covalent geometry : bond 0.00482 ( 9494) covalent geometry : angle 0.59747 (12830) *********************** 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 139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7435 (p0) cc_final: 0.6899 (m-30) REVERT: A 156 MET cc_start: 0.4883 (OUTLIER) cc_final: 0.4592 (ttt) REVERT: A 195 GLU cc_start: 0.4862 (pp20) cc_final: 0.4109 (tp30) REVERT: B 472 ARG cc_start: 0.7904 (ptp-170) cc_final: 0.7377 (ptp90) REVERT: B 693 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: B 733 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: B 826 ASP cc_start: 0.7839 (t0) cc_final: 0.7569 (t0) outliers start: 43 outliers final: 26 residues processed: 126 average time/residue: 0.2375 time to fit residues: 41.6815 Evaluate side-chains 124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 239 LEU Chi-restraints excluded: chain B residue 284 ILE 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 584 THR Chi-restraints excluded: chain B residue 623 MET 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 788 VAL Chi-restraints excluded: chain B residue 806 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 86 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 114 optimal weight: 0.0010 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.172914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128677 restraints weight = 13676.108| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.40 r_work: 0.3331 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9501 Z= 0.110 Angle : 0.497 8.341 12832 Z= 0.260 Chirality : 0.039 0.221 1408 Planarity : 0.003 0.036 1640 Dihedral : 4.150 25.900 1261 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.10 % Allowed : 27.93 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1157 helix: 2.09 (0.24), residues: 485 sheet: 0.13 (0.46), residues: 146 loop : -1.95 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 PHE 0.011 0.001 PHE B 243 TYR 0.022 0.001 TYR B 758 ARG 0.004 0.000 ARG B 871 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 402) hydrogen bonds : angle 4.06606 ( 1155) metal coordination : bond 0.00791 ( 7) metal coordination : angle 4.20505 ( 2) covalent geometry : bond 0.00246 ( 9494) covalent geometry : angle 0.49441 (12830) *********************** 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 134 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7415 (p0) cc_final: 0.6878 (m-30) REVERT: A 195 GLU cc_start: 0.4882 (pp20) cc_final: 0.3621 (tp30) REVERT: A 199 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4329 (mp) REVERT: A 324 MET cc_start: 0.2153 (pmm) cc_final: 0.1805 (pmm) REVERT: A 360 GLU cc_start: 0.5416 (OUTLIER) cc_final: 0.5181 (pm20) REVERT: B 328 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 472 ARG cc_start: 0.7868 (ptp-170) cc_final: 0.7327 (ptp90) outliers start: 31 outliers final: 19 residues processed: 130 average time/residue: 0.2199 time to fit residues: 40.3538 Evaluate side-chains 120 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 282 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 360 GLU 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 584 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 761 MET 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 806 THR Chi-restraints excluded: chain B residue 883 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 114 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 869 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.171702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128767 restraints weight = 13573.968| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.23 r_work: 0.3350 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2124 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= 0.125 Angle : 0.524 11.364 12832 Z= 0.270 Chirality : 0.039 0.221 1408 Planarity : 0.003 0.034 1640 Dihedral : 4.159 26.210 1261 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.20 % Allowed : 27.03 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1157 helix: 2.04 (0.24), residues: 487 sheet: 0.14 (0.46), residues: 146 loop : -1.92 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 859 HIS 0.003 0.001 HIS B 712 PHE 0.010 0.001 PHE B 629 TYR 0.025 0.001 TYR B 758 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 402) hydrogen bonds : angle 4.03346 ( 1155) metal coordination : bond 0.00832 ( 7) metal coordination : angle 3.94111 ( 2) covalent geometry : bond 0.00285 ( 9494) covalent geometry : angle 0.52168 (12830) *********************** 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 139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7483 (p0) cc_final: 0.6860 (m-30) REVERT: A 156 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4675 (ttt) REVERT: A 195 GLU cc_start: 0.4878 (pp20) cc_final: 0.3576 (tp30) REVERT: A 199 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4213 (mp) REVERT: A 324 MET cc_start: 0.2249 (pmm) cc_final: 0.1968 (pmm) REVERT: A 346 LEU cc_start: 0.6725 (tp) cc_final: 0.6340 (tp) REVERT: A 360 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.5038 (pm20) REVERT: B 328 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7698 (mt) REVERT: B 472 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7305 (ptp90) outliers start: 42 outliers final: 28 residues processed: 129 average time/residue: 0.2222 time to fit residues: 40.2406 Evaluate side-chains 127 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 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 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 210 LEU Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 313 GLN 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 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 783 VAL 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 84 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 111 optimal weight: 0.0060 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 845 GLN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.171152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128040 restraints weight = 13487.571| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.76 r_work: 0.3340 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9501 Z= 0.133 Angle : 0.539 9.984 12832 Z= 0.278 Chirality : 0.040 0.226 1408 Planarity : 0.003 0.034 1640 Dihedral : 4.194 26.913 1261 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.00 % Allowed : 27.23 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1157 helix: 1.93 (0.24), residues: 494 sheet: 0.10 (0.46), residues: 146 loop : -1.96 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 PHE 0.011 0.001 PHE B 243 TYR 0.025 0.001 TYR B 758 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 402) hydrogen bonds : angle 4.04542 ( 1155) metal coordination : bond 0.00678 ( 7) metal coordination : angle 3.75848 ( 2) covalent geometry : bond 0.00308 ( 9494) covalent geometry : angle 0.53694 (12830) *********************** 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 136 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7376 (p0) cc_final: 0.6786 (m-30) REVERT: A 156 MET cc_start: 0.4966 (OUTLIER) cc_final: 0.4722 (ttt) REVERT: A 195 GLU cc_start: 0.4919 (pp20) cc_final: 0.3587 (tp30) REVERT: A 199 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4107 (mp) REVERT: A 324 MET cc_start: 0.2367 (pmm) cc_final: 0.2101 (pmm) REVERT: A 346 LEU cc_start: 0.6748 (tp) cc_final: 0.6363 (tp) REVERT: A 360 GLU cc_start: 0.5235 (OUTLIER) cc_final: 0.4972 (pm20) REVERT: B 198 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: B 328 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7704 (mt) REVERT: B 472 ARG cc_start: 0.7871 (ptp-170) cc_final: 0.7311 (ptp90) outliers start: 40 outliers final: 31 residues processed: 126 average time/residue: 0.2147 time to fit residues: 37.8844 Evaluate side-chains 129 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 1.430 ------------------------------------------------------------------------------- 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 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 198 GLN 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 474 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 81 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.171655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128102 restraints weight = 13641.362| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.84 r_work: 0.3341 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2297 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= 0.120 Angle : 0.525 10.075 12832 Z= 0.270 Chirality : 0.039 0.222 1408 Planarity : 0.003 0.034 1640 Dihedral : 4.124 26.737 1261 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.90 % Allowed : 27.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1157 helix: 2.03 (0.24), residues: 491 sheet: 0.12 (0.46), residues: 146 loop : -1.95 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 PHE 0.011 0.001 PHE B 243 TYR 0.023 0.001 TYR B 758 ARG 0.012 0.000 ARG B 842 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 402) hydrogen bonds : angle 3.99577 ( 1155) metal coordination : bond 0.00657 ( 7) metal coordination : angle 4.00879 ( 2) covalent geometry : bond 0.00272 ( 9494) covalent geometry : angle 0.52236 (12830) *********************** 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 136 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7364 (p0) cc_final: 0.6821 (m-30) REVERT: A 156 MET cc_start: 0.4924 (OUTLIER) cc_final: 0.4684 (ttt) REVERT: A 195 GLU cc_start: 0.4986 (pp20) cc_final: 0.3538 (tp30) REVERT: A 199 LEU cc_start: 0.4340 (OUTLIER) cc_final: 0.4058 (mp) REVERT: A 324 MET cc_start: 0.2318 (pmm) cc_final: 0.2071 (pmm) REVERT: A 333 ILE cc_start: 0.3093 (tp) cc_final: 0.2735 (tp) REVERT: A 346 LEU cc_start: 0.6763 (tp) cc_final: 0.6369 (tp) REVERT: B 328 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7678 (mt) REVERT: B 472 ARG cc_start: 0.7867 (ptp-170) cc_final: 0.7302 (ptp90) REVERT: B 693 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7348 (tt0) outliers start: 39 outliers final: 29 residues processed: 126 average time/residue: 0.2132 time to fit residues: 37.8896 Evaluate side-chains 126 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 313 GLN 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 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 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 71 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124708 restraints weight = 13804.010| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.24 r_work: 0.3306 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2400 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= 0.138 Angle : 0.553 10.124 12832 Z= 0.287 Chirality : 0.040 0.228 1408 Planarity : 0.004 0.053 1640 Dihedral : 4.214 27.638 1261 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.30 % Allowed : 27.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1157 helix: 1.94 (0.24), residues: 492 sheet: 0.10 (0.46), residues: 146 loop : -1.99 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 PHE 0.012 0.001 PHE B 629 TYR 0.027 0.001 TYR B 758 ARG 0.017 0.000 ARG B 842 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 402) hydrogen bonds : angle 4.04795 ( 1155) metal coordination : bond 0.00845 ( 7) metal coordination : angle 3.76651 ( 2) covalent geometry : bond 0.00319 ( 9494) covalent geometry : angle 0.55140 (12830) *********************** 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 138 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7249 (p0) cc_final: 0.6876 (m-30) REVERT: A 156 MET cc_start: 0.4943 (OUTLIER) cc_final: 0.4711 (ttt) REVERT: A 195 GLU cc_start: 0.5076 (pp20) cc_final: 0.3543 (tp30) REVERT: A 199 LEU cc_start: 0.4359 (OUTLIER) cc_final: 0.4067 (mp) REVERT: A 324 MET cc_start: 0.2904 (pmm) cc_final: 0.2618 (pmm) REVERT: A 333 ILE cc_start: 0.3556 (tp) cc_final: 0.3218 (tp) REVERT: A 346 LEU cc_start: 0.6723 (tp) cc_final: 0.6359 (tp) REVERT: B 328 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 472 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7316 (ptp90) REVERT: B 693 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7414 (tt0) outliers start: 43 outliers final: 31 residues processed: 130 average time/residue: 0.2272 time to fit residues: 40.6568 Evaluate side-chains 124 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 693 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 0.0000 chunk 71 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.171505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128644 restraints weight = 13615.643| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.96 r_work: 0.3338 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2433 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= 0.126 Angle : 0.546 9.767 12832 Z= 0.281 Chirality : 0.039 0.225 1408 Planarity : 0.003 0.034 1640 Dihedral : 4.162 27.302 1261 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.70 % Allowed : 28.23 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1157 helix: 2.01 (0.24), residues: 492 sheet: 0.14 (0.46), residues: 146 loop : -1.99 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 PHE 0.012 0.001 PHE B 243 TYR 0.024 0.001 TYR B 758 ARG 0.007 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 402) hydrogen bonds : angle 3.98905 ( 1155) metal coordination : bond 0.00897 ( 7) metal coordination : angle 2.66686 ( 2) covalent geometry : bond 0.00289 ( 9494) covalent geometry : angle 0.54488 (12830) *********************** 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: 37 poor density : 94 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7246 (p0) cc_final: 0.6863 (m-30) REVERT: A 156 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4702 (ttt) REVERT: A 195 GLU cc_start: 0.5049 (pp20) cc_final: 0.3541 (tp30) REVERT: A 199 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.4052 (mp) REVERT: A 324 MET cc_start: 0.2720 (pmm) cc_final: 0.2447 (pmm) REVERT: A 333 ILE cc_start: 0.3568 (tp) cc_final: 0.3176 (tp) REVERT: A 346 LEU cc_start: 0.6769 (tp) cc_final: 0.6385 (tp) REVERT: B 328 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7697 (mt) REVERT: B 472 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7297 (ptp90) outliers start: 37 outliers final: 33 residues processed: 123 average time/residue: 0.2233 time to fit residues: 38.5751 Evaluate side-chains 126 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 112 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.171700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128094 restraints weight = 14005.840| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.10 r_work: 0.3331 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9501 Z= 0.127 Angle : 0.549 9.564 12832 Z= 0.283 Chirality : 0.039 0.225 1408 Planarity : 0.004 0.038 1640 Dihedral : 4.146 27.245 1261 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.90 % Allowed : 28.03 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1157 helix: 2.02 (0.24), residues: 491 sheet: 0.15 (0.46), residues: 146 loop : -1.98 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 859 HIS 0.003 0.001 HIS B 714 PHE 0.013 0.001 PHE B 243 TYR 0.024 0.001 TYR B 758 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 402) hydrogen bonds : angle 3.99915 ( 1155) metal coordination : bond 0.00858 ( 7) metal coordination : angle 2.70999 ( 2) covalent geometry : bond 0.00292 ( 9494) covalent geometry : angle 0.54825 (12830) ********************** 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 128 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.7514 (p0) cc_final: 0.7146 (m-30) REVERT: A 195 GLU cc_start: 0.5059 (pp20) cc_final: 0.3532 (tp30) REVERT: A 199 LEU cc_start: 0.4275 (OUTLIER) cc_final: 0.3988 (mp) REVERT: A 324 MET cc_start: 0.2831 (pmm) cc_final: 0.2554 (pmm) REVERT: A 333 ILE cc_start: 0.3552 (tp) cc_final: 0.3136 (tp) REVERT: A 346 LEU cc_start: 0.6819 (tp) cc_final: 0.6444 (tp) REVERT: B 187 MET cc_start: 0.5229 (mtm) cc_final: 0.4945 (mtt) REVERT: B 328 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7702 (mt) REVERT: B 472 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7286 (ptp90) outliers start: 39 outliers final: 34 residues processed: 119 average time/residue: 0.2179 time to fit residues: 36.6773 Evaluate side-chains 123 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 192 GLU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 20 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129022 restraints weight = 13602.381| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.71 r_work: 0.3351 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9501 Z= 0.111 Angle : 0.530 9.699 12832 Z= 0.272 Chirality : 0.039 0.218 1408 Planarity : 0.003 0.034 1640 Dihedral : 4.048 26.258 1261 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.20 % Allowed : 28.73 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1157 helix: 2.12 (0.24), residues: 491 sheet: 0.22 (0.46), residues: 146 loop : -1.97 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.003 0.001 HIS B 714 PHE 0.013 0.001 PHE B 243 TYR 0.022 0.001 TYR B 758 ARG 0.006 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 402) hydrogen bonds : angle 3.93398 ( 1155) metal coordination : bond 0.00817 ( 7) metal coordination : angle 2.84584 ( 2) covalent geometry : bond 0.00249 ( 9494) covalent geometry : angle 0.52853 (12830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.72 seconds wall clock time: 82 minutes 2.66 seconds (4922.66 seconds total)