Starting phenix.real_space_refine on Sat Jul 4 20:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sun_40768/07_2026/8sun_40768_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sun_40768/07_2026/8sun_40768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sun_40768/07_2026/8sun_40768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sun_40768/07_2026/8sun_40768.map" model { file = "/net/cci-nas-00/data/ceres_data/8sun_40768/07_2026/8sun_40768_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sun_40768/07_2026/8sun_40768_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.081 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7802 2.51 5 N 1898 2.21 5 O 2099 1.98 5 F 3 1.80 5 H 11544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23420 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 11125 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12188 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 62 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'JRF': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.49, per 1000 atoms: 0.15 Number of scatterers: 23420 At special positions: 0 Unit cell: (130.884, 87.256, 121.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 71 16.00 F 3 9.00 O 2099 8.00 N 1898 7.00 C 7802 6.00 H 11544 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.05 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.04 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM23353 O5 NAG A 903 .*. O " rejected from bonding due to valence issues. Atom "HETATM23368 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG A 903 " - " ASN A 778 " " NAG B 901 " - " ASN B 362 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 643.0 milliseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 63.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 4.165A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.798A pdb=" N ILE A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 326 removed outlier: 3.750A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.671A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.644A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 540 removed outlier: 4.065A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.612A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 Processing helix chain 'A' and resid 625 through 634 removed outlier: 4.556A pdb=" N TRP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.957A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.006A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 746 removed outlier: 3.944A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 removed outlier: 3.599A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 861 through 871 removed outlier: 4.009A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 removed outlier: 3.578A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.527A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.740A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 327 removed outlier: 7.191A pdb=" N GLU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N LYS B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 365 through 376 removed outlier: 3.604A pdb=" N LYS B 369 " --> pdb=" O CYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.684A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 488 Processing helix chain 'B' and resid 504 through 539 removed outlier: 4.075A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.208A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.988A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.102A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.934A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 116 removed outlier: 4.246A pdb=" N PHE A 73 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.737A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 76 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 78 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR B 242 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 4.380A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET B 225 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.984A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 784 through 785 689 hydrogen bonds defined for protein. 2031 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: 4.64 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11532 1.02 - 1.22: 26 1.22 - 1.42: 5277 1.42 - 1.62: 6801 1.62 - 1.82: 112 Bond restraints: 23748 Sorted by residual: bond pdb=" ND2 ASN A 778 " pdb="HD22 ASN A 778 " ideal model delta sigma weight residual 0.860 1.006 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C LEU B 371 " pdb=" O LEU B 371 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.19e-02 7.06e+03 4.99e+01 bond pdb=" ND2 ASN B 562 " pdb="HD22 ASN B 562 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 562 " pdb="HD21 ASN B 562 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN B 785 " pdb="HD22 ASN B 785 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.53e+01 ... (remaining 23743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.21: 42738 7.21 - 14.41: 8 14.41 - 21.62: 0 21.62 - 28.82: 0 28.82 - 36.03: 24 Bond angle restraints: 42770 Sorted by residual: angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 73.97 36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.15 35.85 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.66 35.34 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.71 35.29 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 109.00 73.76 35.24 3.00e+00 1.11e-01 1.38e+02 ... (remaining 42765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10215 17.66 - 35.32: 860 35.32 - 52.97: 229 52.97 - 70.63: 57 70.63 - 88.29: 21 Dihedral angle restraints: 11382 sinusoidal: 5999 harmonic: 5383 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -168.22 82.22 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CA VAL A 625 " pdb=" C VAL A 625 " pdb=" N LEU A 626 " pdb=" CA LEU A 626 " ideal model delta harmonic sigma weight residual 180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual -86.00 -39.85 -46.15 1 1.00e+01 1.00e-02 2.95e+01 ... (remaining 11379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1805 0.197 - 0.395: 7 0.395 - 0.592: 2 0.592 - 0.789: 1 0.789 - 0.986: 1 Chirality restraints: 1816 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 778 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -3.39 0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -1.80 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 1813 not shown) Planarity restraints: 3425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 785 " 0.006 2.00e-02 2.50e+03 1.89e-01 4.45e+02 pdb=" CG ASN B 785 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 785 " -0.122 2.00e-02 2.50e+03 pdb=" ND2 ASN B 785 " 0.310 2.00e-02 2.50e+03 pdb="HD22 ASN B 785 " -0.252 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 778 " 0.143 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" CG ASN A 778 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 778 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 778 " -0.277 2.00e-02 2.50e+03 pdb=" C1 NAG A 903 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 559 " -0.036 2.00e-02 2.50e+03 3.74e-02 2.09e+01 pdb=" CD GLN B 559 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN B 559 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 GLN B 559 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 559 " 0.053 2.00e-02 2.50e+03 pdb="HE22 GLN B 559 " -0.056 2.00e-02 2.50e+03 ... (remaining 3422 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 61 1.82 - 2.52: 18167 2.52 - 3.21: 71097 3.21 - 3.91: 89926 3.91 - 4.60: 139869 Nonbonded interactions: 319120 Sorted by model distance: nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A 904 " model vdw 1.130 3.130 nonbonded pdb=" CD GLU A 667 " pdb="CA CA A 904 " model vdw 1.234 3.430 nonbonded pdb=" OD1 ASN B 785 " pdb=" O5 NAG B 903 " model vdw 1.281 2.800 nonbonded pdb=" HZ1 LYS B 370 " pdb=" C17 JRF B 906 " model vdw 1.316 2.200 nonbonded pdb=" OE2 GLU A 667 " pdb="CA CA A 904 " model vdw 1.415 3.130 ... (remaining 319115 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 361 or (resid 362 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 363 through 777 or (resid 778 and (name N or \ name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or na \ me H or name HA or name HB2 or name HB3)) or resid 779 through 868 or resid 901) \ ) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 634 or resid 647 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 784 or ( \ resid 785 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 786 t \ hrough 857 or (resid 858 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 859 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or resid 860 through 868 or res \ id 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.100 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.620 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.009 0.682 12219 Z= 0.738 Angle : 0.832 54.134 16600 Z= 0.413 Chirality : 0.056 0.986 1816 Planarity : 0.005 0.075 2057 Dihedral : 14.215 88.290 4488 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 0.40 % Allowed : 0.48 % Favored : 99.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1420 helix: 1.74 (0.18), residues: 827 sheet: -0.01 (0.69), residues: 54 loop : -1.42 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 289 TYR 0.021 0.001 TYR B 101 PHE 0.013 0.001 PHE A 393 TRP 0.023 0.001 TRP B 359 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.26 (12204) covalent geometry : angle 0.64138 / 0.37 (16571) SS BOND : bond 0.00846 / 0.52 ( 10) SS BOND : angle 2.40520 / 1.68 ( 20) hydrogen bonds : bond 0.12087 / 7.85 ( 689) hydrogen bonds : angle 5.35811 / 3.84 ( 2031) Misc. bond : bond 0.49999 / 33.50 ( 2) link_NAG-ASN : bond 0.33123 / 23.48 ( 3) link_NAG-ASN : angle 22.53893 / 8.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7945 (mtm) cc_final: 0.7557 (mtm) REVERT: A 525 ASN cc_start: 0.7305 (t0) cc_final: 0.6480 (t0) REVERT: A 529 GLU cc_start: 0.7678 (pt0) cc_final: 0.7439 (mt-10) REVERT: B 616 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7650 (tttp) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.1872 time to fit residues: 45.8587 Evaluate side-chains 130 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 616 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 559 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.191052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133100 restraints weight = 42543.639| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.57 r_work: 0.3584 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12219 Z= 0.145 Angle : 0.562 15.653 16600 Z= 0.298 Chirality : 0.046 0.485 1816 Planarity : 0.005 0.053 2057 Dihedral : 6.146 77.612 1727 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.56 % Allowed : 4.78 % Favored : 94.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1420 helix: 1.78 (0.18), residues: 831 sheet: -0.27 (0.72), residues: 51 loop : -1.48 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 289 TYR 0.013 0.001 TYR A 305 PHE 0.026 0.001 PHE A 461 TRP 0.011 0.001 TRP B 359 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (12204) covalent geometry : angle 0.55333 / 0.30 (16571) SS BOND : bond 0.00338 / 0.22 ( 10) SS BOND : angle 1.00451 / 0.64 ( 20) hydrogen bonds : bond 0.04877 / 3.38 ( 689) hydrogen bonds : angle 4.63131 / 3.34 ( 2031) Misc. bond : bond 0.00290 / 0.19 ( 2) link_NAG-ASN : bond 0.00615 / 0.44 ( 3) link_NAG-ASN : angle 4.10253 / 1.91 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7718 (pp30) cc_final: 0.7452 (pp30) REVERT: A 525 ASN cc_start: 0.7558 (t0) cc_final: 0.6999 (t0) REVERT: A 529 GLU cc_start: 0.8099 (pt0) cc_final: 0.7877 (pt0) outliers start: 7 outliers final: 7 residues processed: 143 average time/residue: 0.1874 time to fit residues: 40.3616 Evaluate side-chains 132 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.189797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136914 restraints weight = 42441.231| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.78 r_work: 0.3568 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12219 Z= 0.142 Angle : 0.530 15.884 16600 Z= 0.281 Chirality : 0.045 0.495 1816 Planarity : 0.005 0.055 2057 Dihedral : 5.628 66.945 1723 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.56 % Allowed : 7.33 % Favored : 92.11 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1420 helix: 1.88 (0.18), residues: 833 sheet: -0.54 (0.70), residues: 50 loop : -1.55 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 289 TYR 0.011 0.001 TYR B 580 PHE 0.025 0.001 PHE B 253 TRP 0.012 0.001 TRP B 359 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (12204) covalent geometry : angle 0.52562 / 0.28 (16571) SS BOND : bond 0.00288 / 0.19 ( 10) SS BOND : angle 0.78169 / 0.50 ( 20) hydrogen bonds : bond 0.04659 / 3.24 ( 689) hydrogen bonds : angle 4.38995 / 3.16 ( 2031) Misc. bond : bond 0.00153 / 0.10 ( 2) link_NAG-ASN : bond 0.00217 / 0.14 ( 3) link_NAG-ASN : angle 2.74095 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8094 (pt0) cc_final: 0.7630 (mt-10) outliers start: 7 outliers final: 7 residues processed: 141 average time/residue: 0.1746 time to fit residues: 37.8182 Evaluate side-chains 136 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 788 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 621 ASN B 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.186928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128793 restraints weight = 42851.648| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.58 r_work: 0.3530 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12219 Z= 0.200 Angle : 0.566 16.064 16600 Z= 0.304 Chirality : 0.046 0.500 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.818 70.817 1723 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.88 % Allowed : 8.84 % Favored : 90.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1420 helix: 1.68 (0.18), residues: 834 sheet: -0.64 (0.69), residues: 50 loop : -1.55 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 289 TYR 0.014 0.001 TYR B 580 PHE 0.018 0.001 PHE B 556 TRP 0.011 0.001 TRP B 359 HIS 0.004 0.001 HIS B 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (12204) covalent geometry : angle 0.56211 / 0.30 (16571) SS BOND : bond 0.00298 / 0.19 ( 10) SS BOND : angle 0.69561 / 0.44 ( 20) hydrogen bonds : bond 0.04883 / 3.42 ( 689) hydrogen bonds : angle 4.40464 / 3.17 ( 2031) Misc. bond : bond 0.00272 / 0.19 ( 2) link_NAG-ASN : bond 0.00217 / 0.12 ( 3) link_NAG-ASN : angle 2.96522 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.5572 (mttt) cc_final: 0.5306 (mmtp) REVERT: A 529 GLU cc_start: 0.8112 (pt0) cc_final: 0.7584 (mt-10) outliers start: 11 outliers final: 9 residues processed: 145 average time/residue: 0.1954 time to fit residues: 42.6712 Evaluate side-chains 144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 517 SER Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 70 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 621 ASN B 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.187118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133192 restraints weight = 42509.307| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.75 r_work: 0.3529 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12219 Z= 0.162 Angle : 0.537 16.501 16600 Z= 0.287 Chirality : 0.046 0.507 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.717 70.435 1723 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.80 % Allowed : 9.40 % Favored : 89.80 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1420 helix: 1.73 (0.18), residues: 834 sheet: -0.61 (0.70), residues: 50 loop : -1.57 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 289 TYR 0.018 0.001 TYR A 305 PHE 0.015 0.001 PHE B 556 TRP 0.010 0.001 TRP A 463 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12204) covalent geometry : angle 0.53441 / 0.29 (16571) SS BOND : bond 0.00231 / 0.15 ( 10) SS BOND : angle 0.61329 / 0.39 ( 20) hydrogen bonds : bond 0.04668 / 3.27 ( 689) hydrogen bonds : angle 4.31436 / 3.10 ( 2031) Misc. bond : bond 0.00105 / 0.07 ( 2) link_NAG-ASN : bond 0.00147 / 0.10 ( 3) link_NAG-ASN : angle 2.45915 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8095 (pt0) cc_final: 0.7551 (mt-10) outliers start: 10 outliers final: 9 residues processed: 146 average time/residue: 0.2067 time to fit residues: 45.2681 Evaluate side-chains 144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.187539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135299 restraints weight = 42845.875| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.87 r_work: 0.3540 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12219 Z= 0.147 Angle : 0.528 16.656 16600 Z= 0.281 Chirality : 0.045 0.509 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.661 70.678 1723 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.96 % Allowed : 9.88 % Favored : 89.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1420 helix: 1.81 (0.18), residues: 834 sheet: -0.54 (0.72), residues: 50 loop : -1.56 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.011 0.001 TYR B 580 PHE 0.022 0.001 PHE A 461 TRP 0.009 0.001 TRP A 397 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12204) covalent geometry : angle 0.52564 / 0.28 (16571) SS BOND : bond 0.00222 / 0.14 ( 10) SS BOND : angle 0.57319 / 0.36 ( 20) hydrogen bonds : bond 0.04538 / 3.18 ( 689) hydrogen bonds : angle 4.24595 / 3.04 ( 2031) Misc. bond : bond 0.00094 / 0.06 ( 2) link_NAG-ASN : bond 0.00157 / 0.11 ( 3) link_NAG-ASN : angle 2.31097 / 0.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8131 (pt0) cc_final: 0.7621 (mt-10) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.2052 time to fit residues: 45.6622 Evaluate side-chains 144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 621 ASN B 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.187052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129702 restraints weight = 42510.865| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.55 r_work: 0.3535 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12219 Z= 0.154 Angle : 0.534 16.864 16600 Z= 0.284 Chirality : 0.046 0.511 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.650 71.269 1723 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.96 % Allowed : 10.44 % Favored : 88.61 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1420 helix: 1.81 (0.18), residues: 835 sheet: -0.53 (0.73), residues: 50 loop : -1.53 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.011 0.001 TYR B 580 PHE 0.034 0.001 PHE A 711 TRP 0.009 0.001 TRP A 397 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12204) covalent geometry : angle 0.53099 / 0.28 (16571) SS BOND : bond 0.00220 / 0.14 ( 10) SS BOND : angle 0.58928 / 0.37 ( 20) hydrogen bonds : bond 0.04545 / 3.19 ( 689) hydrogen bonds : angle 4.21876 / 3.02 ( 2031) Misc. bond : bond 0.00086 / 0.06 ( 2) link_NAG-ASN : bond 0.00152 / 0.11 ( 3) link_NAG-ASN : angle 2.31435 / 0.99 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8133 (pt0) cc_final: 0.7630 (mt-10) outliers start: 12 outliers final: 10 residues processed: 144 average time/residue: 0.2059 time to fit residues: 44.1159 Evaluate side-chains 144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 795 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 621 ASN B 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.182121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123701 restraints weight = 42958.426| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.93 r_work: 0.3363 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12219 Z= 0.216 Angle : 0.574 16.786 16600 Z= 0.310 Chirality : 0.047 0.514 1816 Planarity : 0.005 0.059 2057 Dihedral : 5.879 74.145 1723 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.04 % Allowed : 11.08 % Favored : 87.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1420 helix: 1.60 (0.18), residues: 835 sheet: -0.61 (0.74), residues: 50 loop : -1.63 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.015 0.002 TYR B 580 PHE 0.018 0.002 PHE B 556 TRP 0.011 0.001 TRP B 132 HIS 0.005 0.001 HIS B 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (12204) covalent geometry : angle 0.57078 / 0.31 (16571) SS BOND : bond 0.00272 / 0.17 ( 10) SS BOND : angle 0.66479 / 0.43 ( 20) hydrogen bonds : bond 0.04897 / 3.44 ( 689) hydrogen bonds : angle 4.33538 / 3.11 ( 2031) Misc. bond : bond 0.00233 / 0.17 ( 2) link_NAG-ASN : bond 0.00128 / 0.09 ( 3) link_NAG-ASN : angle 2.58372 / 1.09 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8171 (pt0) cc_final: 0.7659 (mt-10) outliers start: 13 outliers final: 12 residues processed: 154 average time/residue: 0.2089 time to fit residues: 47.6869 Evaluate side-chains 154 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 795 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 50.0000 chunk 70 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.184621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.126016 restraints weight = 42746.825| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.56 r_work: 0.3417 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12219 Z= 0.125 Angle : 0.529 17.511 16600 Z= 0.280 Chirality : 0.045 0.523 1816 Planarity : 0.004 0.057 2057 Dihedral : 5.667 70.458 1723 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.96 % Allowed : 11.47 % Favored : 87.57 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1420 helix: 1.84 (0.18), residues: 834 sheet: -0.59 (0.74), residues: 50 loop : -1.49 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 701 TYR 0.010 0.001 TYR B 477 PHE 0.019 0.001 PHE A 461 TRP 0.015 0.001 TRP A 463 HIS 0.003 0.000 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12204) covalent geometry : angle 0.52688 / 0.28 (16571) SS BOND : bond 0.00188 / 0.12 ( 10) SS BOND : angle 0.58329 / 0.36 ( 20) hydrogen bonds : bond 0.04420 / 3.09 ( 689) hydrogen bonds : angle 4.16717 / 2.99 ( 2031) Misc. bond : bond 0.00112 / 0.08 ( 2) link_NAG-ASN : bond 0.00176 / 0.13 ( 3) link_NAG-ASN : angle 2.09733 / 0.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8101 (pt0) cc_final: 0.7606 (mt-10) REVERT: B 420 ARG cc_start: 0.5796 (mpt-90) cc_final: 0.5255 (mtt180) outliers start: 12 outliers final: 11 residues processed: 145 average time/residue: 0.2004 time to fit residues: 43.2452 Evaluate side-chains 148 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 96 optimal weight: 0.9990 chunk 138 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.183658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.125258 restraints weight = 42838.571| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.55 r_work: 0.3403 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12219 Z= 0.163 Angle : 0.544 16.992 16600 Z= 0.290 Chirality : 0.046 0.515 1816 Planarity : 0.005 0.058 2057 Dihedral : 5.677 70.629 1723 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.80 % Allowed : 11.87 % Favored : 87.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1420 helix: 1.79 (0.18), residues: 836 sheet: -0.59 (0.75), residues: 50 loop : -1.52 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 701 TYR 0.013 0.001 TYR B 580 PHE 0.016 0.001 PHE A 461 TRP 0.018 0.001 TRP A 463 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (12204) covalent geometry : angle 0.54109 / 0.29 (16571) SS BOND : bond 0.00219 / 0.14 ( 10) SS BOND : angle 0.60561 / 0.38 ( 20) hydrogen bonds : bond 0.04536 / 3.18 ( 689) hydrogen bonds : angle 4.20924 / 3.03 ( 2031) Misc. bond : bond 0.00077 / 0.05 ( 2) link_NAG-ASN : bond 0.00155 / 0.11 ( 3) link_NAG-ASN : angle 2.27644 / 0.95 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8101 (pt0) cc_final: 0.7651 (mt-10) REVERT: B 420 ARG cc_start: 0.5811 (mpt-90) cc_final: 0.5240 (mtt180) outliers start: 10 outliers final: 10 residues processed: 145 average time/residue: 0.1885 time to fit residues: 40.2490 Evaluate side-chains 149 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 621 ASN B 674 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.183593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124910 restraints weight = 42786.188| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.56 r_work: 0.3402 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12219 Z= 0.154 Angle : 0.539 17.261 16600 Z= 0.287 Chirality : 0.046 0.521 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.642 71.100 1723 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.80 % Allowed : 11.87 % Favored : 87.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1420 helix: 1.79 (0.18), residues: 837 sheet: -0.61 (0.75), residues: 50 loop : -1.49 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 701 TYR 0.011 0.001 TYR B 580 PHE 0.016 0.001 PHE A 461 TRP 0.016 0.001 TRP A 463 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12204) covalent geometry : angle 0.53653 / 0.29 (16571) SS BOND : bond 0.00206 / 0.13 ( 10) SS BOND : angle 0.60368 / 0.38 ( 20) hydrogen bonds : bond 0.04509 / 3.16 ( 689) hydrogen bonds : angle 4.18404 / 3.01 ( 2031) Misc. bond : bond 0.00095 / 0.07 ( 2) link_NAG-ASN : bond 0.00165 / 0.12 ( 3) link_NAG-ASN : angle 2.22067 / 0.94 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6161.93 seconds wall clock time: 104 minutes 56.46 seconds (6296.46 seconds total)