Starting phenix.real_space_refine on Thu May 22 22:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sun_40768/05_2025/8sun_40768_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sun_40768/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sun_40768/05_2025/8sun_40768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sun_40768/05_2025/8sun_40768.map" model { file = "/net/cci-nas-00/data/ceres_data/8sun_40768/05_2025/8sun_40768_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sun_40768/05_2025/8sun_40768_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'GLU:plan': 2, 'ARG:plan': 1} 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: 10.95, per 1000 atoms: 0.47 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: 6.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.73 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: 8.05 Time building geometry restraints manager: 7.45 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 48.230 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.950 ------------------------------------------------------------------------------- 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 : 8.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (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 TRP 0.023 0.001 TRP B 359 HIS 0.005 0.001 HIS A 108 PHE 0.013 0.001 PHE A 393 TYR 0.021 0.001 TYR B 101 ARG 0.014 0.001 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.33123 ( 3) link_NAG-ASN : angle 22.53893 ( 9) hydrogen bonds : bond 0.12087 ( 689) hydrogen bonds : angle 5.35811 ( 2031) SS BOND : bond 0.00846 ( 10) SS BOND : angle 2.40520 ( 20) covalent geometry : bond 0.00430 (12204) covalent geometry : angle 0.64138 (16571) Misc. bond : bond 0.49999 ( 2) *********************** 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 : 1.767 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: 0.7658 (tttp) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.4738 time to fit residues: 115.5693 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 : 1.981 ------------------------------------------------------------------------------- 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 120 optimal weight: 8.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.190115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.136322 restraints weight = 42426.145| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.98 r_work: 0.3558 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12219 Z= 0.170 Angle : 0.573 15.393 16600 Z= 0.305 Chirality : 0.046 0.483 1816 Planarity : 0.005 0.052 2057 Dihedral : 6.135 77.047 1727 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.56 % Allowed : 5.02 % Favored : 94.42 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1420 helix: 1.73 (0.18), residues: 832 sheet: -0.27 (0.72), residues: 51 loop : -1.55 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 359 HIS 0.002 0.001 HIS B 830 PHE 0.022 0.001 PHE A 461 TYR 0.016 0.001 TYR A 305 ARG 0.011 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 3) link_NAG-ASN : angle 4.37222 ( 9) hydrogen bonds : bond 0.05084 ( 689) hydrogen bonds : angle 4.68106 ( 2031) SS BOND : bond 0.00347 ( 10) SS BOND : angle 1.03752 ( 20) covalent geometry : bond 0.00379 (12204) covalent geometry : angle 0.56277 (16571) Misc. bond : bond 0.00163 ( 2) *********************** 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 145 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 GLN cc_start: 0.7770 (pp30) cc_final: 0.7505 (pp30) REVERT: A 525 ASN cc_start: 0.7598 (t0) cc_final: 0.7054 (t0) REVERT: A 529 GLU cc_start: 0.8115 (pt0) cc_final: 0.7893 (pt0) outliers start: 7 outliers final: 7 residues processed: 144 average time/residue: 0.4776 time to fit residues: 102.2928 Evaluate side-chains 136 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.690 ------------------------------------------------------------------------------- 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 7 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 ASN ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.187047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128701 restraints weight = 42568.687| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.57 r_work: 0.3531 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1450 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= 0.206 Angle : 0.576 15.763 16600 Z= 0.311 Chirality : 0.047 0.494 1816 Planarity : 0.005 0.058 2057 Dihedral : 5.876 63.892 1723 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.88 % Allowed : 7.81 % Favored : 91.31 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1420 helix: 1.59 (0.18), residues: 834 sheet: -0.56 (0.71), residues: 50 loop : -1.63 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 359 HIS 0.004 0.001 HIS B 768 PHE 0.018 0.001 PHE B 556 TYR 0.014 0.001 TYR B 580 ARG 0.013 0.001 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 3) link_NAG-ASN : angle 2.83367 ( 9) hydrogen bonds : bond 0.05115 ( 689) hydrogen bonds : angle 4.53674 ( 2031) SS BOND : bond 0.00332 ( 10) SS BOND : angle 0.83637 ( 20) covalent geometry : bond 0.00473 (12204) covalent geometry : angle 0.57185 (16571) Misc. bond : bond 0.00269 ( 2) *********************** 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 146 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.921 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 127 LYS cc_start: 0.5709 (mttt) cc_final: 0.5472 (mmtp) REVERT: A 525 ASN cc_start: 0.7601 (t0) cc_final: 0.6918 (t0) REVERT: A 529 GLU cc_start: 0.8141 (pt0) cc_final: 0.7629 (mt-10) outliers start: 11 outliers final: 9 residues processed: 142 average time/residue: 0.4738 time to fit residues: 101.2591 Evaluate side-chains 139 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.188186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130112 restraints weight = 42909.416| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.59 r_work: 0.3552 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1573 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= 0.147 Angle : 0.535 16.520 16600 Z= 0.284 Chirality : 0.045 0.505 1816 Planarity : 0.005 0.056 2057 Dihedral : 5.731 68.539 1723 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.96 % Allowed : 9.00 % Favored : 90.04 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1420 helix: 1.75 (0.18), residues: 833 sheet: -0.62 (0.69), residues: 50 loop : -1.55 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS B 768 PHE 0.015 0.001 PHE B 556 TYR 0.011 0.001 TYR B 477 ARG 0.007 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 3) link_NAG-ASN : angle 2.71347 ( 9) hydrogen bonds : bond 0.04630 ( 689) hydrogen bonds : angle 4.35225 ( 2031) SS BOND : bond 0.00244 ( 10) SS BOND : angle 0.60974 ( 20) covalent geometry : bond 0.00330 (12204) covalent geometry : angle 0.53164 (16571) Misc. bond : bond 0.00146 ( 2) *********************** 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 152 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.722 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: 0.8062 (pt0) cc_final: 0.7523 (mt-10) outliers start: 12 outliers final: 12 residues processed: 147 average time/residue: 0.4676 time to fit residues: 102.5685 Evaluate side-chains 146 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 535 ILE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER 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: 5.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.187312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129658 restraints weight = 43005.181| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.57 r_work: 0.3553 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12219 Z= 0.156 Angle : 0.535 16.436 16600 Z= 0.285 Chirality : 0.045 0.505 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.690 69.258 1723 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.04 % Allowed : 9.48 % Favored : 89.48 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1420 helix: 1.78 (0.18), residues: 834 sheet: -0.64 (0.70), residues: 50 loop : -1.56 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.003 0.001 HIS B 768 PHE 0.022 0.001 PHE B 253 TYR 0.012 0.001 TYR B 580 ARG 0.006 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 2.41899 ( 9) hydrogen bonds : bond 0.04633 ( 689) hydrogen bonds : angle 4.30134 ( 2031) SS BOND : bond 0.00241 ( 10) SS BOND : angle 0.59688 ( 20) covalent geometry : bond 0.00354 (12204) covalent geometry : angle 0.53223 (16571) Misc. bond : bond 0.00111 ( 2) *********************** 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 153 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.789 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: 0.7528 (mt-10) outliers start: 13 outliers final: 12 residues processed: 148 average time/residue: 0.5339 time to fit residues: 114.3798 Evaluate side-chains 148 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Chi-restraints excluded: chain B residue 795 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4354 r_free = 0.4354 target = 0.187645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.129640 restraints weight = 42513.509| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.57 r_work: 0.3543 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12219 Z= 0.146 Angle : 0.530 16.721 16600 Z= 0.282 Chirality : 0.045 0.509 1816 Planarity : 0.005 0.057 2057 Dihedral : 5.645 69.763 1723 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.12 % Allowed : 10.12 % Favored : 88.76 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1420 helix: 1.82 (0.18), residues: 834 sheet: -0.61 (0.71), residues: 50 loop : -1.53 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 768 PHE 0.015 0.001 PHE B 556 TYR 0.024 0.001 TYR A 305 ARG 0.002 0.000 ARG B 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 2.26873 ( 9) hydrogen bonds : bond 0.04524 ( 689) hydrogen bonds : angle 4.24519 ( 2031) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.56804 ( 20) covalent geometry : bond 0.00329 (12204) covalent geometry : angle 0.52738 (16571) Misc. bond : bond 0.00089 ( 2) *********************** 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 153 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.767 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: 0.8073 (pt0) cc_final: 0.7562 (mt-10) REVERT: A 569 TYR cc_start: 0.8220 (t80) cc_final: 0.7852 (t80) outliers start: 14 outliers final: 13 residues processed: 147 average time/residue: 0.4993 time to fit residues: 107.9108 Evaluate side-chains 145 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER 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 16 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.188596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135710 restraints weight = 42525.021| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.83 r_work: 0.3550 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1976 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= 0.115 Angle : 0.513 16.768 16600 Z= 0.270 Chirality : 0.045 0.508 1816 Planarity : 0.004 0.056 2057 Dihedral : 5.518 68.470 1723 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.04 % Allowed : 10.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1420 helix: 1.97 (0.18), residues: 835 sheet: -0.63 (0.70), residues: 53 loop : -1.49 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.000 HIS B 108 PHE 0.013 0.001 PHE B 556 TYR 0.013 0.001 TYR A 305 ARG 0.004 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 3) link_NAG-ASN : angle 2.07952 ( 9) hydrogen bonds : bond 0.04286 ( 689) hydrogen bonds : angle 4.14443 ( 2031) SS BOND : bond 0.00195 ( 10) SS BOND : angle 0.55350 ( 20) covalent geometry : bond 0.00251 (12204) covalent geometry : angle 0.51081 (16571) Misc. bond : bond 0.00100 ( 2) *********************** 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 151 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.857 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: 0.8141 (pt0) cc_final: 0.7626 (mt-10) REVERT: A 569 TYR cc_start: 0.8157 (t80) cc_final: 0.7806 (t80) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.4797 time to fit residues: 103.7539 Evaluate side-chains 145 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 76 VAL 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 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.186314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133749 restraints weight = 42867.107| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.80 r_work: 0.3523 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12219 Z= 0.176 Angle : 0.543 16.742 16600 Z= 0.290 Chirality : 0.046 0.510 1816 Planarity : 0.005 0.058 2057 Dihedral : 5.612 69.689 1723 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.04 % Allowed : 11.00 % Favored : 87.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1420 helix: 1.86 (0.18), residues: 835 sheet: -0.75 (0.71), residues: 53 loop : -1.54 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS B 768 PHE 0.017 0.001 PHE B 556 TYR 0.014 0.001 TYR B 580 ARG 0.005 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 2.33832 ( 9) hydrogen bonds : bond 0.04544 ( 689) hydrogen bonds : angle 4.21733 ( 2031) SS BOND : bond 0.00239 ( 10) SS BOND : angle 0.60520 ( 20) covalent geometry : bond 0.00408 (12204) covalent geometry : angle 0.54053 (16571) Misc. bond : bond 0.00080 ( 2) *********************** 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 153 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.874 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: 0.8114 (pt0) cc_final: 0.7604 (mt-10) REVERT: B 420 ARG cc_start: 0.5764 (mpt-90) cc_final: 0.5216 (mtt180) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.5099 time to fit residues: 107.5796 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 : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.187317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130006 restraints weight = 42685.420| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.56 r_work: 0.3552 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12219 Z= 0.134 Angle : 0.521 17.134 16600 Z= 0.277 Chirality : 0.045 0.516 1816 Planarity : 0.004 0.057 2057 Dihedral : 5.559 69.336 1723 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.12 % Allowed : 10.84 % Favored : 88.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1420 helix: 1.91 (0.18), residues: 836 sheet: -0.72 (0.70), residues: 53 loop : -1.47 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 463 HIS 0.002 0.001 HIS B 768 PHE 0.014 0.001 PHE B 215 TYR 0.010 0.001 TYR A 305 ARG 0.004 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 3) link_NAG-ASN : angle 2.09643 ( 9) hydrogen bonds : bond 0.04382 ( 689) hydrogen bonds : angle 4.14894 ( 2031) SS BOND : bond 0.00198 ( 10) SS BOND : angle 0.58011 ( 20) covalent geometry : bond 0.00299 (12204) covalent geometry : angle 0.51898 (16571) Misc. bond : bond 0.00072 ( 2) *********************** 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 147 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.782 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: 0.8102 (pt0) cc_final: 0.7598 (mt-10) outliers start: 14 outliers final: 12 residues processed: 142 average time/residue: 0.5092 time to fit residues: 107.1579 Evaluate side-chains 146 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 0.0870 chunk 66 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 621 ASN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.187279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129339 restraints weight = 42599.749| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.54 r_work: 0.3459 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12219 Z= 0.101 Angle : 0.497 17.318 16600 Z= 0.261 Chirality : 0.045 0.516 1816 Planarity : 0.004 0.054 2057 Dihedral : 5.379 70.428 1723 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.88 % Allowed : 11.24 % Favored : 87.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1420 helix: 2.11 (0.18), residues: 841 sheet: -0.67 (0.70), residues: 53 loop : -1.38 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 463 HIS 0.002 0.000 HIS B 108 PHE 0.015 0.001 PHE B 215 TYR 0.009 0.001 TYR A 305 ARG 0.007 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 3) link_NAG-ASN : angle 1.82244 ( 9) hydrogen bonds : bond 0.04003 ( 689) hydrogen bonds : angle 4.04558 ( 2031) SS BOND : bond 0.00171 ( 10) SS BOND : angle 0.59102 ( 20) covalent geometry : bond 0.00215 (12204) covalent geometry : angle 0.49478 (16571) Misc. bond : bond 0.00125 ( 2) ********************** 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 148 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.967 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 113 GLU cc_start: 0.6286 (mt-10) cc_final: 0.5397 (mp0) REVERT: A 529 GLU cc_start: 0.8111 (pt0) cc_final: 0.7598 (mt-10) REVERT: A 569 TYR cc_start: 0.8150 (t80) cc_final: 0.7824 (t80) outliers start: 11 outliers final: 10 residues processed: 144 average time/residue: 0.4748 time to fit residues: 102.3570 Evaluate side-chains 144 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 347 LEU 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 481 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 759 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 128 optimal weight: 0.2980 chunk 9 optimal weight: 20.0000 chunk 139 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 621 ASN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.186409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128069 restraints weight = 42545.979| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.55 r_work: 0.3448 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12219 Z= 0.110 Angle : 0.505 16.953 16600 Z= 0.265 Chirality : 0.045 0.511 1816 Planarity : 0.004 0.055 2057 Dihedral : 5.341 70.122 1723 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.88 % Allowed : 11.39 % Favored : 87.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.23), residues: 1420 helix: 2.14 (0.18), residues: 843 sheet: -0.65 (0.70), residues: 53 loop : -1.33 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 463 HIS 0.002 0.000 HIS B 108 PHE 0.014 0.001 PHE B 215 TYR 0.012 0.001 TYR B 138 ARG 0.006 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 3) link_NAG-ASN : angle 1.91765 ( 9) hydrogen bonds : bond 0.04055 ( 689) hydrogen bonds : angle 4.04969 ( 2031) SS BOND : bond 0.00173 ( 10) SS BOND : angle 0.58080 ( 20) covalent geometry : bond 0.00239 (12204) covalent geometry : angle 0.50302 (16571) Misc. bond : bond 0.00088 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14085.57 seconds wall clock time: 241 minutes 22.80 seconds (14482.80 seconds total)