Starting phenix.real_space_refine on Sun Aug 24 22:33:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sun_40768/08_2025/8sun_40768_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sun_40768/08_2025/8sun_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sun_40768/08_2025/8sun_40768_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sun_40768/08_2025/8sun_40768_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sun_40768/08_2025/8sun_40768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sun_40768/08_2025/8sun_40768.map" } 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-2.0-5787/lib/python3.9/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, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 64 Unusual residues: {' CA': 2, 'JRF': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.82, per 1000 atoms: 0.16 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: 2.18 Conformation dependent library (CDL) restraints added in 691.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.63 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: 4.94 Time building geometry restraints manager: 2.75 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 2.390 nonbonded pdb=" CD GLU A 667 " pdb="CA CA A 904 " model vdw 1.234 2.690 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 2.390 ... (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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.000 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 aren 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 covalent geometry : bond 0.00430 (12204) covalent geometry : angle 0.64138 (16571) SS BOND : bond 0.00846 ( 10) SS BOND : angle 2.40520 ( 20) hydrogen bonds : bond 0.12087 ( 689) hydrogen bonds : angle 5.35811 ( 2031) Misc. bond : bond 0.49999 ( 2) link_NAG-ASN : bond 0.33123 ( 3) link_NAG-ASN : angle 22.53893 ( 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 : 0.417 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: 0.2009 time to fit residues: 48.9778 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 : 0.607 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4387 r_free = 0.4387 target = 0.191189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.132810 restraints weight = 42584.328| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.59 r_work: 0.3583 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12219 Z= 0.143 Angle : 0.559 15.647 16600 Z= 0.296 Chirality : 0.046 0.485 1816 Planarity : 0.005 0.053 2057 Dihedral : 6.146 78.882 1727 Min Nonbonded Distance : 2.087 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 aren not related in a simple way. whole: 0.80 (0.22), residues: 1420 helix: 1.80 (0.18), residues: 832 sheet: -0.28 (0.72), residues: 51 loop : -1.48 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 289 TYR 0.014 0.001 TYR A 305 PHE 0.025 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 covalent geometry : bond 0.00312 (12204) covalent geometry : angle 0.55022 (16571) SS BOND : bond 0.00324 ( 10) SS BOND : angle 0.95702 ( 20) hydrogen bonds : bond 0.04910 ( 689) hydrogen bonds : angle 4.61376 ( 2031) Misc. bond : bond 0.00377 ( 2) link_NAG-ASN : bond 0.00396 ( 3) link_NAG-ASN : angle 4.03976 ( 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 147 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.664 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 351 GLN cc_start: 0.7702 (pp30) cc_final: 0.7446 (pp30) REVERT: A 525 ASN cc_start: 0.7576 (t0) cc_final: 0.7016 (t0) REVERT: A 529 GLU cc_start: 0.8097 (pt0) cc_final: 0.7875 (pt0) outliers start: 7 outliers final: 7 residues processed: 146 average time/residue: 0.2030 time to fit residues: 44.2586 Evaluate side-chains 135 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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: 4.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 50.0000 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.130059 restraints weight = 42714.041| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.57 r_work: 0.3552 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12219 Z= 0.180 Angle : 0.555 15.751 16600 Z= 0.298 Chirality : 0.046 0.493 1816 Planarity : 0.005 0.056 2057 Dihedral : 5.746 66.953 1723 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.72 % Allowed : 7.57 % Favored : 91.71 % 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 aren not related in a simple way. whole: 0.69 (0.22), residues: 1420 helix: 1.73 (0.18), residues: 834 sheet: -0.55 (0.71), residues: 50 loop : -1.57 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 289 TYR 0.013 0.001 TYR B 580 PHE 0.018 0.001 PHE B 253 TRP 0.013 0.001 TRP B 359 HIS 0.004 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00409 (12204) covalent geometry : angle 0.55035 (16571) SS BOND : bond 0.00320 ( 10) SS BOND : angle 0.82685 ( 20) hydrogen bonds : bond 0.04948 ( 689) hydrogen bonds : angle 4.45079 ( 2031) Misc. bond : bond 0.00307 ( 2) link_NAG-ASN : bond 0.00275 ( 3) link_NAG-ASN : angle 2.96369 ( 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: 9 poor density : 133 time to evaluate : 0.709 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 525 ASN cc_start: 0.7512 (t0) cc_final: 0.6827 (t0) REVERT: A 529 GLU cc_start: 0.8146 (pt0) cc_final: 0.7635 (mt-10) outliers start: 9 outliers final: 8 residues processed: 140 average time/residue: 0.2228 time to fit residues: 47.1198 Evaluate side-chains 138 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.187724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129651 restraints weight = 42751.253| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.58 r_work: 0.3553 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12219 Z= 0.163 Angle : 0.540 16.406 16600 Z= 0.288 Chirality : 0.046 0.504 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.729 68.064 1723 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.96 % Allowed : 8.45 % Favored : 90.60 % 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 aren not related in a simple way. whole: 0.74 (0.22), residues: 1420 helix: 1.78 (0.18), residues: 833 sheet: -0.61 (0.69), residues: 50 loop : -1.54 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 289 TYR 0.012 0.001 TYR B 477 PHE 0.016 0.001 PHE B 556 TRP 0.013 0.001 TRP B 359 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00368 (12204) covalent geometry : angle 0.53643 (16571) SS BOND : bond 0.00261 ( 10) SS BOND : angle 0.63321 ( 20) hydrogen bonds : bond 0.04682 ( 689) hydrogen bonds : angle 4.34301 ( 2031) Misc. bond : bond 0.00246 ( 2) link_NAG-ASN : bond 0.00140 ( 3) link_NAG-ASN : angle 2.72182 ( 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: 12 poor density : 137 time to evaluate : 0.640 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: 0.8094 (pt0) cc_final: 0.7572 (mt-10) REVERT: B 63 PHE cc_start: 0.8402 (m-80) cc_final: 0.8152 (m-80) REVERT: B 742 MET cc_start: 0.8049 (mmm) cc_final: 0.7767 (mmm) outliers start: 12 outliers final: 11 residues processed: 144 average time/residue: 0.2249 time to fit residues: 48.7449 Evaluate side-chains 146 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 464 ILE 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 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 Chi-restraints excluded: chain B residue 788 ASP 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: 6.9990 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 70 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN ** 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 = 0.4357 r_free = 0.4357 target = 0.187812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129668 restraints weight = 42588.493| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.59 r_work: 0.3543 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1706 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= 0.146 Angle : 0.525 16.417 16600 Z= 0.279 Chirality : 0.045 0.504 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.642 68.891 1723 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.96 % Allowed : 9.40 % Favored : 89.64 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1420 helix: 1.85 (0.18), residues: 834 sheet: -0.60 (0.69), residues: 50 loop : -1.50 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 289 TYR 0.011 0.001 TYR B 580 PHE 0.015 0.001 PHE B 556 TRP 0.011 0.001 TRP A 397 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00330 (12204) covalent geometry : angle 0.52228 (16571) SS BOND : bond 0.00226 ( 10) SS BOND : angle 0.59129 ( 20) hydrogen bonds : bond 0.04559 ( 689) hydrogen bonds : angle 4.25753 ( 2031) Misc. bond : bond 0.00112 ( 2) link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 2.37801 ( 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 152 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.654 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: 0.8086 (pt0) cc_final: 0.7599 (mt-10) REVERT: B 742 MET cc_start: 0.8112 (mmm) cc_final: 0.7572 (mmm) outliers start: 12 outliers final: 10 residues processed: 146 average time/residue: 0.2433 time to fit residues: 52.3057 Evaluate side-chains 146 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 517 SER 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: 4.9990 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: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4327 r_free = 0.4327 target = 0.185054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127103 restraints weight = 42974.534| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.56 r_work: 0.3517 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12219 Z= 0.217 Angle : 0.577 16.496 16600 Z= 0.312 Chirality : 0.047 0.510 1816 Planarity : 0.005 0.059 2057 Dihedral : 5.915 74.138 1723 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.35 % Allowed : 10.20 % Favored : 88.45 % 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 aren not related in a simple way. whole: 0.52 (0.22), residues: 1420 helix: 1.60 (0.18), residues: 834 sheet: -0.64 (0.71), residues: 50 loop : -1.64 (0.26), residues: 536 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 0.024 0.002 PHE A 461 TRP 0.010 0.001 TRP B 132 HIS 0.005 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00502 (12204) covalent geometry : angle 0.57389 (16571) SS BOND : bond 0.00285 ( 10) SS BOND : angle 0.67404 ( 20) hydrogen bonds : bond 0.04983 ( 689) hydrogen bonds : angle 4.37527 ( 2031) Misc. bond : bond 0.00087 ( 2) link_NAG-ASN : bond 0.00133 ( 3) link_NAG-ASN : angle 2.65766 ( 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 163 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.693 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: 0.8071 (pt0) cc_final: 0.7550 (mt-10) REVERT: B 420 ARG cc_start: 0.5801 (mpt-90) cc_final: 0.5306 (mtt180) outliers start: 17 outliers final: 15 residues processed: 156 average time/residue: 0.2589 time to fit residues: 58.6656 Evaluate side-chains 155 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 537 ASN 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 517 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4321 r_free = 0.4321 target = 0.184383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.126747 restraints weight = 42859.374| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.55 r_work: 0.3508 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12219 Z= 0.224 Angle : 0.580 16.672 16600 Z= 0.314 Chirality : 0.047 0.512 1816 Planarity : 0.005 0.060 2057 Dihedral : 6.016 74.270 1723 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.12 % Allowed : 11.08 % Favored : 87.81 % 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 aren not related in a simple way. whole: 0.39 (0.22), residues: 1420 helix: 1.49 (0.18), residues: 835 sheet: -0.67 (0.72), residues: 50 loop : -1.69 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.014 0.002 TYR B 580 PHE 0.017 0.001 PHE B 556 TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00519 (12204) covalent geometry : angle 0.57680 (16571) SS BOND : bond 0.00281 ( 10) SS BOND : angle 0.69114 ( 20) hydrogen bonds : bond 0.05008 ( 689) hydrogen bonds : angle 4.38877 ( 2031) Misc. bond : bond 0.00082 ( 2) link_NAG-ASN : bond 0.00138 ( 3) link_NAG-ASN : angle 2.56226 ( 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 158 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.674 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: 0.8089 (pt0) cc_final: 0.7560 (mt-10) REVERT: B 420 ARG cc_start: 0.5911 (mpt-90) cc_final: 0.5311 (mtt180) outliers start: 14 outliers final: 14 residues processed: 153 average time/residue: 0.2601 time to fit residues: 57.4053 Evaluate side-chains 157 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 517 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 B 695 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.182737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.124043 restraints weight = 42856.008| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.54 r_work: 0.3391 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12219 Z= 0.167 Angle : 0.551 16.864 16600 Z= 0.296 Chirality : 0.046 0.513 1816 Planarity : 0.005 0.058 2057 Dihedral : 5.907 72.703 1723 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.27 % Allowed : 11.08 % Favored : 87.65 % 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 aren not related in a simple way. whole: 0.52 (0.22), residues: 1420 helix: 1.61 (0.18), residues: 835 sheet: -0.65 (0.73), residues: 50 loop : -1.66 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.013 0.001 TYR B 580 PHE 0.025 0.001 PHE A 711 TRP 0.013 0.001 TRP A 463 HIS 0.003 0.001 HIS B 768 Details of bonding type rmsd covalent geometry : bond 0.00379 (12204) covalent geometry : angle 0.54862 (16571) SS BOND : bond 0.00226 ( 10) SS BOND : angle 0.62372 ( 20) hydrogen bonds : bond 0.04767 ( 689) hydrogen bonds : angle 4.31192 ( 2031) Misc. bond : bond 0.00109 ( 2) link_NAG-ASN : bond 0.00166 ( 3) link_NAG-ASN : angle 2.35302 ( 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 163 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.699 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: 0.8100 (pt0) cc_final: 0.7559 (mt-10) REVERT: B 420 ARG cc_start: 0.5854 (mpt-90) cc_final: 0.5312 (mtt180) REVERT: B 742 MET cc_start: 0.8418 (mmm) cc_final: 0.7948 (mmm) outliers start: 16 outliers final: 15 residues processed: 155 average time/residue: 0.2620 time to fit residues: 58.6950 Evaluate side-chains 155 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 537 ASN 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 517 SER Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER 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: 0.0570 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 130 optimal weight: 0.8980 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4255 r_free = 0.4255 target = 0.184550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127283 restraints weight = 42920.715| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.00 r_work: 0.3403 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12219 Z= 0.117 Angle : 0.525 17.060 16600 Z= 0.278 Chirality : 0.045 0.515 1816 Planarity : 0.005 0.055 2057 Dihedral : 5.668 70.947 1723 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.88 % Allowed : 11.87 % Favored : 87.25 % 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 aren not related in a simple way. whole: 0.82 (0.22), residues: 1420 helix: 1.84 (0.18), residues: 836 sheet: -0.69 (0.72), residues: 50 loop : -1.50 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 277 TYR 0.009 0.001 TYR A 305 PHE 0.017 0.001 PHE A 461 TRP 0.016 0.001 TRP A 397 HIS 0.003 0.000 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00254 (12204) covalent geometry : angle 0.52320 (16571) SS BOND : bond 0.00181 ( 10) SS BOND : angle 0.60291 ( 20) hydrogen bonds : bond 0.04319 ( 689) hydrogen bonds : angle 4.15616 ( 2031) Misc. bond : bond 0.00074 ( 2) link_NAG-ASN : bond 0.00181 ( 3) link_NAG-ASN : angle 2.03608 ( 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 153 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.643 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: 0.8050 (pt0) cc_final: 0.7499 (mt-10) REVERT: B 277 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7423 (ptm160) REVERT: B 420 ARG cc_start: 0.5870 (mpt-90) cc_final: 0.5325 (mtt180) REVERT: B 742 MET cc_start: 0.8221 (mmm) cc_final: 0.7748 (mmm) outliers start: 11 outliers final: 11 residues processed: 149 average time/residue: 0.2731 time to fit residues: 58.1150 Evaluate side-chains 152 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 96 optimal weight: 0.7980 chunk 138 optimal weight: 0.0770 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.183942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125525 restraints weight = 42768.979| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.54 r_work: 0.3411 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12219 Z= 0.140 Angle : 0.530 16.691 16600 Z= 0.281 Chirality : 0.045 0.509 1816 Planarity : 0.005 0.056 2057 Dihedral : 5.625 70.399 1723 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.88 % Allowed : 11.71 % Favored : 87.41 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1420 helix: 1.85 (0.18), residues: 837 sheet: -0.65 (0.73), residues: 50 loop : -1.51 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.011 0.001 TYR B 580 PHE 0.017 0.001 PHE A 461 TRP 0.017 0.001 TRP A 463 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00314 (12204) covalent geometry : angle 0.52805 (16571) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.60251 ( 20) hydrogen bonds : bond 0.04406 ( 689) hydrogen bonds : angle 4.16942 ( 2031) Misc. bond : bond 0.00105 ( 2) link_NAG-ASN : bond 0.00169 ( 3) link_NAG-ASN : angle 2.19830 ( 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 151 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLU cc_start: 0.8106 (pt0) cc_final: 0.7562 (mt-10) REVERT: B 420 ARG cc_start: 0.5835 (mpt-90) cc_final: 0.5280 (mtt180) REVERT: B 742 MET cc_start: 0.8358 (mmm) cc_final: 0.7923 (mmm) outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.2545 time to fit residues: 54.0215 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 : 0.533 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 138 optimal weight: 0.0570 chunk 123 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4249 r_free = 0.4249 target = 0.183932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125730 restraints weight = 42695.711| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.51 r_work: 0.3413 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12219 Z= 0.137 Angle : 0.529 16.937 16600 Z= 0.281 Chirality : 0.045 0.514 1816 Planarity : 0.005 0.056 2057 Dihedral : 5.570 71.232 1723 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.96 % Allowed : 11.87 % Favored : 87.17 % 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 aren not related in a simple way. whole: 0.85 (0.22), residues: 1420 helix: 1.83 (0.17), residues: 843 sheet: -0.66 (0.73), residues: 50 loop : -1.48 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 701 TYR 0.010 0.001 TYR B 477 PHE 0.018 0.001 PHE A 711 TRP 0.015 0.001 TRP A 463 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00307 (12204) covalent geometry : angle 0.52646 (16571) SS BOND : bond 0.00195 ( 10) SS BOND : angle 0.60759 ( 20) hydrogen bonds : bond 0.04373 ( 689) hydrogen bonds : angle 4.15126 ( 2031) Misc. bond : bond 0.00067 ( 2) link_NAG-ASN : bond 0.00175 ( 3) link_NAG-ASN : angle 2.15085 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7416.67 seconds wall clock time: 126 minutes 21.33 seconds (7581.33 seconds total)