Starting phenix.real_space_refine on Sun Jul 5 03:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p98_71402/07_2026/9p98_71402_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p98_71402/07_2026/9p98_71402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p98_71402/07_2026/9p98_71402_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p98_71402/07_2026/9p98_71402_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p98_71402/07_2026/9p98_71402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p98_71402/07_2026/9p98_71402.map" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 S 58 5.16 5 C 7724 2.51 5 N 2120 2.21 5 O 2388 1.98 5 H 11908 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 11652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 11652 Classifications: {'peptide': 768} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 731} Chain breaks: 1 Chain: "B" Number of atoms: 5818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5818 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 21, 'TRANS': 357} Chain: "H" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3296 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Chain: "L" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3284 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.21, per 1000 atoms: 0.17 Number of scatterers: 24204 At special positions: 0 Unit cell: (102.102, 145.86, 167.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 58 16.00 O 2388 8.00 N 2120 7.00 C 7724 6.00 H 11908 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 221 " distance=2.04 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 96 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1201 " - " ASN A 303 " " NAG A1202 " - " ASN A 253 " " NAG B2004 " - " ASN B 260 " " NAG C 1 " - " ASN A 31 " " NAG D 1 " - " ASN A 426 " " NAG E 1 " - " ASN A 708 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 779.8 milliseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 16.9% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 697 through 701 Processing helix chain 'A' and resid 757 through 761 removed outlier: 4.200A pdb=" N ASP A 760 " --> pdb=" O CYS A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.648A pdb=" N GLU B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.964A pdb=" N PHE B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 252 removed outlier: 3.851A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 300 through 306 removed outlier: 4.348A pdb=" N THR B 304 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.792A pdb=" N LYS B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.580A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 141 removed outlier: 3.614A pdb=" N GLN H 139 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR H 140 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN H 141 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 130 through 136 removed outlier: 3.513A pdb=" N THR L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 197 removed outlier: 4.062A pdb=" N HIS L 197 " --> pdb=" O ALA L 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 4.581A pdb=" N ARG A 657 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA A 6 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 10.929A pdb=" N VAL A 655 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N ALA A 653 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 26 removed outlier: 3.827A pdb=" N SER A 21 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR A 33 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 54 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 82 removed outlier: 3.616A pdb=" N THR A 105 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLY A 106 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN A 122 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N CYS A 108 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN A 120 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 110 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 236 removed outlier: 6.789A pdb=" N LEU A 225 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 183 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA A 224 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 185 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 226 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 187 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA6, first strand: chain 'A' and resid 447 through 451 removed outlier: 5.326A pdb=" N TYR A 458 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 471 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.200A pdb=" N VAL A 530 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 547 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 532 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565 Processing sheet with id=AA9, first strand: chain 'A' and resid 661 through 662 Processing sheet with id=AB1, first strand: chain 'A' and resid 664 through 671 Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 735 removed outlier: 3.583A pdb=" N LEU A 706 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 708 " --> pdb=" O GLN A 772 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.884A pdb=" N HIS B 434 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 103 through 104 removed outlier: 4.142A pdb=" N GLN B 103 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 211 through 217 removed outlier: 7.241A pdb=" N VAL B 213 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N SER B 176 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER B 215 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N PHE B 174 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR B 137 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP B 134 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 266 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR B 136 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR B 268 " --> pdb=" O TYR B 136 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 138 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG B 263 " --> pdb=" O GLN B 324 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE B 326 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 265 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA B 328 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE B 267 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.643A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.589A pdb=" N THR H 115 " --> pdb=" O TRP H 95 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 94 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE H 34 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG H 51 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP H 36 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG H 38 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.589A pdb=" N THR H 115 " --> pdb=" O TRP H 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR H 110 " --> pdb=" O TRP H 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.007A pdb=" N TYR H 183 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 128 through 131 removed outlier: 6.007A pdb=" N TYR H 183 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC3, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.661A pdb=" N TRP L 42 " --> pdb=" O LEU L 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AC5, first strand: chain 'L' and resid 69 through 70 Processing sheet with id=AC6, first strand: chain 'L' and resid 123 through 127 removed outlier: 3.886A pdb=" N VAL L 142 " --> pdb=" O PHE L 127 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N TYR L 181 " --> pdb=" O ASP L 147 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER L 174 " --> pdb=" O MET L 182 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 138 through 140 Processing sheet with id=AC8, first strand: chain 'L' and resid 162 through 163 removed outlier: 3.649A pdb=" N THR L 154 " --> pdb=" O THR L 205 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1101 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: 5.79 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11891 1.04 - 1.23: 885 1.23 - 1.43: 4498 1.43 - 1.63: 7113 1.63 - 1.83: 83 Bond restraints: 24470 Sorted by residual: bond pdb=" CG1 ILE B 363 " pdb=" CD1 ILE B 363 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.23e+00 bond pdb=" CG LEU B 159 " pdb=" CD2 LEU B 159 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" N PHE A 1 " pdb=" CA PHE A 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.26e+00 bond pdb=" N PHE A 1 " pdb=" H PHE A 1 " ideal model delta sigma weight residual 0.860 0.886 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 ... (remaining 24465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 43841 2.32 - 4.64: 220 4.64 - 6.96: 9 6.96 - 9.29: 1 9.29 - 11.61: 1 Bond angle restraints: 44072 Sorted by residual: angle pdb=" C ARG A 703 " pdb=" CA ARG A 703 " pdb=" CB ARG A 703 " ideal model delta sigma weight residual 116.63 110.76 5.87 1.16e+00 7.43e-01 2.56e+01 angle pdb=" C ASP A 589 " pdb=" CA ASP A 589 " pdb=" CB ASP A 589 " ideal model delta sigma weight residual 116.34 110.81 5.53 1.40e+00 5.10e-01 1.56e+01 angle pdb=" CB MET A 313 " pdb=" CG MET A 313 " pdb=" SD MET A 313 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA ARG A 703 " pdb=" C ARG A 703 " pdb=" N GLU A 704 " ideal model delta sigma weight residual 119.63 117.19 2.44 8.10e-01 1.52e+00 9.10e+00 angle pdb=" CA GLU A 699 " pdb=" CB GLU A 699 " pdb=" CG GLU A 699 " ideal model delta sigma weight residual 114.10 119.76 -5.66 2.00e+00 2.50e-01 8.02e+00 ... (remaining 44067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 10538 17.75 - 35.51: 852 35.51 - 53.26: 297 53.26 - 71.02: 90 71.02 - 88.77: 33 Dihedral angle restraints: 11810 sinusoidal: 6516 harmonic: 5294 Sorted by residual: dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 221 " pdb=" CB CYS A 221 " ideal model delta sinusoidal sigma weight residual 93.00 45.55 47.45 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA VAL B 182 " pdb=" C VAL B 182 " pdb=" N LEU B 183 " pdb=" CA LEU B 183 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PHE A 123 " pdb=" C PHE A 123 " pdb=" N PHE A 124 " pdb=" CA PHE A 124 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 11807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1533 0.047 - 0.094: 285 0.094 - 0.141: 124 0.141 - 0.188: 4 0.188 - 0.235: 1 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CG LEU B 159 " pdb=" CB LEU B 159 " pdb=" CD1 LEU B 159 " pdb=" CD2 LEU B 159 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C1 NAG A1202 " pdb=" ND2 ASN A 253 " pdb=" C2 NAG A1202 " pdb=" O5 NAG A1202 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE L 145 " pdb=" N ILE L 145 " pdb=" C ILE L 145 " pdb=" CB ILE L 145 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1944 not shown) Planarity restraints: 3709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 213 " -0.009 2.00e-02 2.50e+03 1.77e-02 4.72e+00 pdb=" CG ASN A 213 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 213 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 213 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 213 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN A 213 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP H 196 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO H 197 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 197 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 197 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 47 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 48 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " 0.026 5.00e-02 4.00e+02 ... (remaining 3706 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 5761 2.31 - 2.88: 54134 2.88 - 3.45: 59904 3.45 - 4.03: 85978 4.03 - 4.60: 126739 Nonbonded interactions: 332516 Sorted by model distance: nonbonded pdb=" HG SER A 638 " pdb="CA CA A1203 " model vdw 1.733 2.780 nonbonded pdb="HD22 ASN B 235 " pdb="CA CA B2002 " model vdw 1.743 2.780 nonbonded pdb=" HD2 PHE H 35 " pdb=" HE1 TRP H 48 " model vdw 1.791 2.100 nonbonded pdb=" HE2 TYR H 33 " pdb="HH11 ARG H 51 " model vdw 1.818 2.100 nonbonded pdb=" HE2 PHE H 35 " pdb="HH21 ARG L 102 " model vdw 1.864 2.100 ... (remaining 332511 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 'C' selection = chain 'D' } 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: 2.560 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: 0.170 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.690 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.004 0.070 12581 Z= 0.191 Angle : 0.622 11.608 17113 Z= 0.331 Chirality : 0.044 0.235 1947 Planarity : 0.005 0.059 2209 Dihedral : 14.907 87.971 4733 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.28 % Allowed : 15.55 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1572 helix: 0.11 (0.37), residues: 188 sheet: -0.49 (0.22), residues: 546 loop : -0.67 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.019 0.001 TYR A 354 PHE 0.024 0.002 PHE A 586 TRP 0.011 0.001 TRP A 34 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (12562) covalent geometry : angle 0.61231 / 0.33 (17064) SS BOND : bond 0.00371 / 0.18 ( 8) SS BOND : angle 1.38822 / 0.98 ( 16) hydrogen bonds : bond 0.21880 / 15.28 ( 415) hydrogen bonds : angle 8.97182 / 6.38 ( 1101) link_BETA1-4 : bond 0.00609 / 0.32 ( 5) link_BETA1-4 : angle 3.22801 / 1.85 ( 15) link_NAG-ASN : bond 0.00275 / 0.13 ( 6) link_NAG-ASN : angle 1.31583 / 0.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7281 (mt0) REVERT: A 69 ILE cc_start: 0.8216 (mt) cc_final: 0.7854 (pp) REVERT: A 217 LYS cc_start: 0.7474 (mttp) cc_final: 0.7192 (mttp) REVERT: A 480 GLU cc_start: 0.7608 (pm20) cc_final: 0.7367 (pm20) REVERT: A 499 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 690 GLU cc_start: 0.7025 (tt0) cc_final: 0.6689 (tt0) REVERT: A 772 GLN cc_start: 0.8237 (mt0) cc_final: 0.7742 (mt0) REVERT: B 202 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7427 (mt-10) REVERT: B 224 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7282 (mp0) REVERT: L 54 LEU cc_start: 0.8510 (mt) cc_final: 0.8138 (mt) REVERT: L 82 THR cc_start: 0.6928 (m) cc_final: 0.6682 (m) REVERT: L 104 PRO cc_start: 0.7814 (Cg_exo) cc_final: 0.7610 (Cg_endo) outliers start: 17 outliers final: 10 residues processed: 211 average time/residue: 1.1539 time to fit residues: 266.3146 Evaluate side-chains 209 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 399 ARG Chi-restraints excluded: chain L residue 97 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN B 154 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.202257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142118 restraints weight = 52056.653| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.48 r_work: 0.3466 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 12581 Z= 0.302 Angle : 0.633 6.489 17113 Z= 0.332 Chirality : 0.047 0.171 1947 Planarity : 0.005 0.067 2209 Dihedral : 7.402 61.294 1967 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.33 % Allowed : 13.90 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1572 helix: -0.29 (0.35), residues: 208 sheet: -0.21 (0.22), residues: 548 loop : -0.87 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.022 0.002 TYR A 354 PHE 0.021 0.002 PHE A 559 TRP 0.014 0.002 TRP B 258 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.30 (12562) covalent geometry : angle 0.62840 / 0.33 (17064) SS BOND : bond 0.00418 / 0.20 ( 8) SS BOND : angle 0.99457 / 0.63 ( 16) hydrogen bonds : bond 0.04984 / 3.46 ( 415) hydrogen bonds : angle 6.47494 / 4.59 ( 1101) link_BETA1-4 : bond 0.00373 / 0.20 ( 5) link_BETA1-4 : angle 2.33929 / 1.43 ( 15) link_NAG-ASN : bond 0.00410 / 0.20 ( 6) link_NAG-ASN : angle 1.31286 / 0.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: A 69 ILE cc_start: 0.8230 (mt) cc_final: 0.7839 (pp) REVERT: A 217 LYS cc_start: 0.7570 (mttp) cc_final: 0.7255 (mttp) REVERT: A 480 GLU cc_start: 0.7600 (pm20) cc_final: 0.7351 (pm20) REVERT: A 690 GLU cc_start: 0.6924 (tt0) cc_final: 0.6617 (tt0) REVERT: A 772 GLN cc_start: 0.8124 (mt0) cc_final: 0.7699 (mt0) REVERT: B 202 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7421 (mt-10) REVERT: B 225 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: L 54 LEU cc_start: 0.8586 (mt) cc_final: 0.8239 (mt) REVERT: L 82 THR cc_start: 0.6868 (m) cc_final: 0.6651 (m) outliers start: 31 outliers final: 18 residues processed: 221 average time/residue: 1.1903 time to fit residues: 287.6223 Evaluate side-chains 228 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 97 ARG Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 0.0570 chunk 151 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN B 154 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.203209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144238 restraints weight = 52224.664| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.44 r_work: 0.3472 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12581 Z= 0.181 Angle : 0.564 7.026 17113 Z= 0.292 Chirality : 0.044 0.153 1947 Planarity : 0.005 0.061 2209 Dihedral : 6.847 57.599 1957 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.18 % Allowed : 14.43 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1572 helix: 0.03 (0.37), residues: 209 sheet: -0.15 (0.22), residues: 544 loop : -0.86 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 135 TYR 0.018 0.001 TYR A 354 PHE 0.017 0.002 PHE A 236 TRP 0.008 0.001 TRP H 111 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (12562) covalent geometry : angle 0.55761 / 0.29 (17064) SS BOND : bond 0.00821 / 0.39 ( 8) SS BOND : angle 1.76230 / 1.06 ( 16) hydrogen bonds : bond 0.04292 / 3.02 ( 415) hydrogen bonds : angle 6.00078 / 4.22 ( 1101) link_BETA1-4 : bond 0.00329 / 0.18 ( 5) link_BETA1-4 : angle 2.10795 / 1.29 ( 15) link_NAG-ASN : bond 0.00158 / 0.08 ( 6) link_NAG-ASN : angle 1.15701 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: A 69 ILE cc_start: 0.8202 (mt) cc_final: 0.7803 (pp) REVERT: A 217 LYS cc_start: 0.7408 (mttp) cc_final: 0.7112 (mttp) REVERT: A 690 GLU cc_start: 0.6868 (tt0) cc_final: 0.6583 (tt0) REVERT: A 772 GLN cc_start: 0.8115 (mt0) cc_final: 0.7758 (mt0) REVERT: B 225 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7754 (ttp80) REVERT: L 54 LEU cc_start: 0.8573 (mt) cc_final: 0.8236 (mt) REVERT: L 82 THR cc_start: 0.6889 (m) cc_final: 0.6628 (m) outliers start: 29 outliers final: 18 residues processed: 215 average time/residue: 1.2488 time to fit residues: 293.2449 Evaluate side-chains 213 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.202500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142466 restraints weight = 51985.793| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.43 r_work: 0.3445 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12581 Z= 0.252 Angle : 0.593 6.694 17113 Z= 0.306 Chirality : 0.045 0.162 1947 Planarity : 0.005 0.060 2209 Dihedral : 6.742 57.848 1953 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.78 % Allowed : 14.43 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.21), residues: 1572 helix: -0.05 (0.36), residues: 207 sheet: -0.18 (0.22), residues: 556 loop : -0.97 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 200 TYR 0.020 0.002 TYR A 354 PHE 0.020 0.002 PHE A 236 TRP 0.009 0.001 TRP B 258 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.25 (12562) covalent geometry : angle 0.58750 / 0.31 (17064) SS BOND : bond 0.00612 / 0.29 ( 8) SS BOND : angle 1.44219 / 0.85 ( 16) hydrogen bonds : bond 0.04017 / 2.79 ( 415) hydrogen bonds : angle 5.72295 / 4.03 ( 1101) link_BETA1-4 : bond 0.00320 / 0.17 ( 5) link_BETA1-4 : angle 2.01603 / 1.28 ( 15) link_NAG-ASN : bond 0.00297 / 0.15 ( 6) link_NAG-ASN : angle 1.32071 / 0.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: A 69 ILE cc_start: 0.8216 (mt) cc_final: 0.7824 (pp) REVERT: A 217 LYS cc_start: 0.7386 (mttp) cc_final: 0.7098 (mttp) REVERT: A 317 GLU cc_start: 0.7388 (mp0) cc_final: 0.7172 (mp0) REVERT: A 690 GLU cc_start: 0.6913 (tt0) cc_final: 0.6634 (tt0) REVERT: A 772 GLN cc_start: 0.8119 (mt0) cc_final: 0.7742 (mt0) REVERT: B 225 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7765 (ttp80) REVERT: L 54 LEU cc_start: 0.8588 (mt) cc_final: 0.8260 (mt) REVERT: L 82 THR cc_start: 0.6876 (m) cc_final: 0.6650 (m) outliers start: 37 outliers final: 24 residues processed: 220 average time/residue: 1.3251 time to fit residues: 317.4509 Evaluate side-chains 229 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 97 ARG Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 154 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.203013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143382 restraints weight = 51621.353| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.40 r_work: 0.3469 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12581 Z= 0.221 Angle : 0.571 7.781 17113 Z= 0.296 Chirality : 0.044 0.156 1947 Planarity : 0.005 0.060 2209 Dihedral : 6.659 58.770 1953 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.55 % Allowed : 14.95 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1572 helix: 0.05 (0.37), residues: 207 sheet: -0.21 (0.22), residues: 567 loop : -0.99 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 40 TYR 0.018 0.001 TYR A 354 PHE 0.019 0.002 PHE A 236 TRP 0.009 0.001 TRP B 258 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (12562) covalent geometry : angle 0.56623 / 0.29 (17064) SS BOND : bond 0.00482 / 0.23 ( 8) SS BOND : angle 1.19776 / 0.71 ( 16) hydrogen bonds : bond 0.03825 / 2.66 ( 415) hydrogen bonds : angle 5.54453 / 3.88 ( 1101) link_BETA1-4 : bond 0.00313 / 0.17 ( 5) link_BETA1-4 : angle 1.92098 / 1.23 ( 15) link_NAG-ASN : bond 0.00233 / 0.12 ( 6) link_NAG-ASN : angle 1.26787 / 0.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: A 69 ILE cc_start: 0.8209 (mt) cc_final: 0.7802 (pp) REVERT: A 217 LYS cc_start: 0.7366 (mttp) cc_final: 0.7071 (mttp) REVERT: A 394 ASP cc_start: 0.8146 (p0) cc_final: 0.7940 (p0) REVERT: A 499 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: A 690 GLU cc_start: 0.6871 (tt0) cc_final: 0.6597 (tt0) REVERT: A 772 GLN cc_start: 0.8110 (mt0) cc_final: 0.7760 (mt0) REVERT: B 225 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7763 (ttp80) REVERT: L 54 LEU cc_start: 0.8583 (mt) cc_final: 0.8262 (mt) REVERT: L 82 THR cc_start: 0.6864 (m) cc_final: 0.6635 (m) outliers start: 34 outliers final: 25 residues processed: 223 average time/residue: 1.2758 time to fit residues: 311.1308 Evaluate side-chains 229 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 152 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.203209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143595 restraints weight = 51785.573| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.41 r_work: 0.3473 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12581 Z= 0.183 Angle : 0.555 9.803 17113 Z= 0.286 Chirality : 0.044 0.157 1947 Planarity : 0.005 0.072 2209 Dihedral : 6.535 59.251 1953 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.85 % Allowed : 14.88 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1572 helix: 0.17 (0.37), residues: 207 sheet: -0.20 (0.22), residues: 573 loop : -0.93 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 97 TYR 0.016 0.001 TYR A 354 PHE 0.017 0.002 PHE A 236 TRP 0.007 0.001 TRP A 34 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (12562) covalent geometry : angle 0.55125 / 0.29 (17064) SS BOND : bond 0.00416 / 0.20 ( 8) SS BOND : angle 1.04396 / 0.62 ( 16) hydrogen bonds : bond 0.03554 / 2.49 ( 415) hydrogen bonds : angle 5.37928 / 3.75 ( 1101) link_BETA1-4 : bond 0.00289 / 0.16 ( 5) link_BETA1-4 : angle 1.85664 / 1.20 ( 15) link_NAG-ASN : bond 0.00211 / 0.10 ( 6) link_NAG-ASN : angle 1.18347 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8103 (p) cc_final: 0.7798 (t) REVERT: A 56 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: A 69 ILE cc_start: 0.8217 (mt) cc_final: 0.7801 (pp) REVERT: A 217 LYS cc_start: 0.7331 (mttp) cc_final: 0.7021 (mttp) REVERT: A 344 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7148 (t70) REVERT: A 394 ASP cc_start: 0.8151 (p0) cc_final: 0.7947 (p0) REVERT: A 480 GLU cc_start: 0.7533 (pm20) cc_final: 0.7313 (pm20) REVERT: A 499 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: A 690 GLU cc_start: 0.6820 (tt0) cc_final: 0.6579 (tt0) REVERT: A 703 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7862 (mtt-85) REVERT: A 772 GLN cc_start: 0.8088 (mt0) cc_final: 0.7814 (mt0) REVERT: B 153 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6815 (mtp180) REVERT: B 154 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: B 225 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7768 (ttp80) REVERT: L 54 LEU cc_start: 0.8585 (mt) cc_final: 0.8262 (mt) REVERT: L 82 THR cc_start: 0.6855 (m) cc_final: 0.6653 (m) outliers start: 38 outliers final: 23 residues processed: 224 average time/residue: 1.2580 time to fit residues: 308.3968 Evaluate side-chains 226 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.201949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142020 restraints weight = 51681.610| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.41 r_work: 0.3468 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12581 Z= 0.194 Angle : 0.562 9.520 17113 Z= 0.291 Chirality : 0.044 0.156 1947 Planarity : 0.005 0.051 2209 Dihedral : 6.463 59.513 1952 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.78 % Allowed : 14.95 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.21), residues: 1572 helix: 0.13 (0.37), residues: 207 sheet: -0.16 (0.21), residues: 579 loop : -0.93 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 229 TYR 0.016 0.001 TYR A 354 PHE 0.018 0.002 PHE A 236 TRP 0.007 0.001 TRP A 34 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (12562) covalent geometry : angle 0.55809 / 0.29 (17064) SS BOND : bond 0.00414 / 0.20 ( 8) SS BOND : angle 1.04675 / 0.62 ( 16) hydrogen bonds : bond 0.03600 / 2.50 ( 415) hydrogen bonds : angle 5.32377 / 3.71 ( 1101) link_BETA1-4 : bond 0.00310 / 0.17 ( 5) link_BETA1-4 : angle 1.82855 / 1.19 ( 15) link_NAG-ASN : bond 0.00227 / 0.11 ( 6) link_NAG-ASN : angle 1.19906 / 0.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8072 (p) cc_final: 0.7793 (t) REVERT: A 56 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: A 69 ILE cc_start: 0.8217 (mt) cc_final: 0.7793 (pp) REVERT: A 217 LYS cc_start: 0.7302 (mttp) cc_final: 0.6988 (mttp) REVERT: A 480 GLU cc_start: 0.7530 (pm20) cc_final: 0.7311 (pm20) REVERT: A 499 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 690 GLU cc_start: 0.6838 (tt0) cc_final: 0.6578 (tt0) REVERT: A 703 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7872 (mtt-85) REVERT: A 772 GLN cc_start: 0.8089 (mt0) cc_final: 0.7817 (mt0) REVERT: B 153 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6766 (mtp180) REVERT: B 154 GLN cc_start: 0.8212 (mt0) cc_final: 0.7988 (mt0) REVERT: B 168 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6938 (t70) REVERT: B 225 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: L 54 LEU cc_start: 0.8532 (mt) cc_final: 0.8196 (mt) REVERT: L 82 THR cc_start: 0.6878 (m) cc_final: 0.6652 (m) outliers start: 37 outliers final: 23 residues processed: 226 average time/residue: 1.2455 time to fit residues: 308.6385 Evaluate side-chains 229 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.201562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141286 restraints weight = 51619.338| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.41 r_work: 0.3442 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 12581 Z= 0.392 Angle : 0.656 8.829 17113 Z= 0.343 Chirality : 0.049 0.187 1947 Planarity : 0.006 0.061 2209 Dihedral : 6.748 59.541 1952 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.78 % Allowed : 15.03 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1572 helix: -0.39 (0.35), residues: 205 sheet: -0.26 (0.21), residues: 572 loop : -1.14 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 229 TYR 0.027 0.002 TYR A 771 PHE 0.027 0.003 PHE A 236 TRP 0.014 0.002 TRP B 258 HIS 0.009 0.002 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00936 / 0.39 (12562) covalent geometry : angle 0.65117 / 0.34 (17064) SS BOND : bond 0.00525 / 0.26 ( 8) SS BOND : angle 1.38099 / 0.81 ( 16) hydrogen bonds : bond 0.04367 / 3.01 ( 415) hydrogen bonds : angle 5.46334 / 3.83 ( 1101) link_BETA1-4 : bond 0.00406 / 0.22 ( 5) link_BETA1-4 : angle 1.88701 / 1.25 ( 15) link_NAG-ASN : bond 0.00493 / 0.25 ( 6) link_NAG-ASN : angle 1.52109 / 0.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8032 (p) cc_final: 0.7755 (t) REVERT: A 56 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: A 69 ILE cc_start: 0.8246 (mt) cc_final: 0.7797 (pp) REVERT: A 477 GLU cc_start: 0.6778 (pp20) cc_final: 0.6498 (pp20) REVERT: A 480 GLU cc_start: 0.7565 (pm20) cc_final: 0.7151 (pm20) REVERT: A 499 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: A 665 LYS cc_start: 0.7384 (tttt) cc_final: 0.7180 (tttt) REVERT: A 703 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7886 (mmt-90) REVERT: A 772 GLN cc_start: 0.8178 (mt0) cc_final: 0.7806 (mt0) REVERT: B 225 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: L 54 LEU cc_start: 0.8578 (mt) cc_final: 0.8244 (mt) REVERT: L 82 THR cc_start: 0.6823 (m) cc_final: 0.6606 (m) outliers start: 37 outliers final: 24 residues processed: 228 average time/residue: 1.1987 time to fit residues: 299.8900 Evaluate side-chains 228 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 452 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.2980 chunk 131 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.202220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142049 restraints weight = 51780.490| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.42 r_work: 0.3454 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12581 Z= 0.216 Angle : 0.591 12.944 17113 Z= 0.303 Chirality : 0.045 0.149 1947 Planarity : 0.005 0.073 2209 Dihedral : 6.536 59.923 1950 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.55 % Allowed : 15.85 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.21), residues: 1572 helix: -0.09 (0.36), residues: 205 sheet: -0.22 (0.21), residues: 580 loop : -1.08 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 229 TYR 0.017 0.002 TYR A 354 PHE 0.021 0.002 PHE A 236 TRP 0.010 0.001 TRP A 34 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (12562) covalent geometry : angle 0.58606 / 0.30 (17064) SS BOND : bond 0.00409 / 0.20 ( 8) SS BOND : angle 1.09168 / 0.64 ( 16) hydrogen bonds : bond 0.03658 / 2.54 ( 415) hydrogen bonds : angle 5.28940 / 3.68 ( 1101) link_BETA1-4 : bond 0.00268 / 0.14 ( 5) link_BETA1-4 : angle 1.78407 / 1.18 ( 15) link_NAG-ASN : bond 0.00392 / 0.18 ( 6) link_NAG-ASN : angle 1.59496 / 0.91 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8101 (p) cc_final: 0.7813 (t) REVERT: A 56 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: A 69 ILE cc_start: 0.8238 (mt) cc_final: 0.7800 (pp) REVERT: A 499 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: A 665 LYS cc_start: 0.7357 (tttt) cc_final: 0.7140 (tttt) REVERT: A 703 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7890 (mtt-85) REVERT: A 772 GLN cc_start: 0.8130 (mt0) cc_final: 0.7780 (mt0) REVERT: B 225 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7760 (ttp80) REVERT: L 54 LEU cc_start: 0.8583 (mt) cc_final: 0.8273 (mt) REVERT: L 82 THR cc_start: 0.6896 (m) cc_final: 0.6671 (m) outliers start: 34 outliers final: 21 residues processed: 227 average time/residue: 1.2199 time to fit residues: 302.8700 Evaluate side-chains 227 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 225 ARG Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.202659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.142601 restraints weight = 51423.354| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.41 r_work: 0.3465 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12581 Z= 0.166 Angle : 0.567 13.391 17113 Z= 0.289 Chirality : 0.043 0.149 1947 Planarity : 0.005 0.077 2209 Dihedral : 6.350 59.843 1950 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.95 % Allowed : 16.45 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.21), residues: 1572 helix: 0.20 (0.37), residues: 206 sheet: -0.12 (0.21), residues: 581 loop : -1.02 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 229 TYR 0.012 0.001 TYR B 337 PHE 0.018 0.002 PHE A 236 TRP 0.008 0.001 TRP A 34 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (12562) covalent geometry : angle 0.56283 / 0.29 (17064) SS BOND : bond 0.00366 / 0.18 ( 8) SS BOND : angle 1.03265 / 0.61 ( 16) hydrogen bonds : bond 0.03369 / 2.36 ( 415) hydrogen bonds : angle 5.15963 / 3.59 ( 1101) link_BETA1-4 : bond 0.00296 / 0.16 ( 5) link_BETA1-4 : angle 1.74905 / 1.14 ( 15) link_NAG-ASN : bond 0.00631 / 0.28 ( 6) link_NAG-ASN : angle 1.27386 / 0.72 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8073 (p) cc_final: 0.7792 (t) REVERT: A 56 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: A 69 ILE cc_start: 0.8236 (mt) cc_final: 0.7790 (pp) REVERT: A 480 GLU cc_start: 0.7659 (pm20) cc_final: 0.7312 (pm20) REVERT: A 499 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 703 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7883 (mtt-85) REVERT: A 772 GLN cc_start: 0.8096 (mt0) cc_final: 0.7836 (mt0) REVERT: B 254 GLU cc_start: 0.7919 (pm20) cc_final: 0.7707 (pm20) REVERT: L 54 LEU cc_start: 0.8572 (mt) cc_final: 0.8260 (mt) REVERT: L 82 THR cc_start: 0.6853 (m) cc_final: 0.6615 (m) outliers start: 26 outliers final: 21 residues processed: 222 average time/residue: 1.1524 time to fit residues: 280.2871 Evaluate side-chains 226 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 703 ARG Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 174 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 316 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.202321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141897 restraints weight = 51482.919| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.48 r_work: 0.3448 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12581 Z= 0.238 Angle : 0.599 10.980 17113 Z= 0.307 Chirality : 0.045 0.180 1947 Planarity : 0.005 0.074 2209 Dihedral : 6.514 59.804 1950 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.95 % Allowed : 16.75 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1572 helix: 0.14 (0.36), residues: 206 sheet: -0.12 (0.21), residues: 580 loop : -1.05 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 229 TYR 0.018 0.002 TYR A 354 PHE 0.019 0.002 PHE A 236 TRP 0.011 0.001 TRP B 258 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (12562) covalent geometry : angle 0.59427 / 0.31 (17064) SS BOND : bond 0.00410 / 0.20 ( 8) SS BOND : angle 1.12442 / 0.66 ( 16) hydrogen bonds : bond 0.03606 / 2.51 ( 415) hydrogen bonds : angle 5.17107 / 3.60 ( 1101) link_BETA1-4 : bond 0.00317 / 0.17 ( 5) link_BETA1-4 : angle 1.74701 / 1.15 ( 15) link_NAG-ASN : bond 0.00578 / 0.26 ( 6) link_NAG-ASN : angle 1.67353 / 0.97 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10582.93 seconds wall clock time: 179 minutes 37.24 seconds (10777.24 seconds total)