Starting phenix.real_space_refine on Fri Feb 6 11:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p98_71402/02_2026/9p98_71402_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p98_71402/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9p98_71402/02_2026/9p98_71402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p98_71402/02_2026/9p98_71402.map" model { file = "/net/cci-nas-00/data/ceres_data/9p98_71402/02_2026/9p98_71402_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p98_71402/02_2026/9p98_71402_trim.cif" } 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-2.0-5952/lib/python3.9/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, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 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: 4.57, per 1000 atoms: 0.19 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: 2.15 Conformation dependent library (CDL) restraints added in 666.8 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: 0.65 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: 5.91 Time building geometry restraints manager: 2.95 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 2.040 nonbonded pdb="HD22 ASN B 235 " pdb="CA CA B2002 " model vdw 1.743 2.040 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: 3.210 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: 0.150 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 covalent geometry : bond 0.00440 (12562) covalent geometry : angle 0.61231 (17064) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.38822 ( 16) hydrogen bonds : bond 0.21880 ( 415) hydrogen bonds : angle 8.97182 ( 1101) link_BETA1-4 : bond 0.00609 ( 5) link_BETA1-4 : angle 3.22801 ( 15) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 1.31583 ( 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 : 0.614 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: 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: 1.2161 time to fit residues: 277.8388 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 : 0.455 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 122 ASN B 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.202684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142330 restraints weight = 52042.178| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.49 r_work: 0.3461 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 12581 Z= 0.301 Angle : 0.631 6.437 17113 Z= 0.330 Chirality : 0.047 0.167 1947 Planarity : 0.005 0.067 2209 Dihedral : 7.405 61.224 1967 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.33 % Allowed : 14.12 % Favored : 83.55 % 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: -0.87 (0.21), residues: 1572 helix: -0.29 (0.35), residues: 208 sheet: -0.25 (0.22), residues: 553 loop : -0.80 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 200 TYR 0.023 0.002 TYR A 354 PHE 0.021 0.002 PHE A 559 TRP 0.014 0.002 TRP B 258 HIS 0.007 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00716 (12562) covalent geometry : angle 0.62566 (17064) SS BOND : bond 0.00427 ( 8) SS BOND : angle 0.98384 ( 16) hydrogen bonds : bond 0.04833 ( 415) hydrogen bonds : angle 6.43950 ( 1101) link_BETA1-4 : bond 0.00421 ( 5) link_BETA1-4 : angle 2.31874 ( 15) link_NAG-ASN : bond 0.00415 ( 6) link_NAG-ASN : angle 1.33058 ( 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 235 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.494 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: 0.7816 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: A 69 ILE cc_start: 0.8227 (mt) cc_final: 0.7843 (pp) REVERT: A 217 LYS cc_start: 0.7552 (mttp) cc_final: 0.7237 (mttp) REVERT: A 690 GLU cc_start: 0.6917 (tt0) cc_final: 0.6607 (tt0) REVERT: A 772 GLN cc_start: 0.8114 (mt0) cc_final: 0.7690 (mt0) REVERT: B 202 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7433 (mt-10) REVERT: B 225 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: L 54 LEU cc_start: 0.8586 (mt) cc_final: 0.8240 (mt) REVERT: L 82 THR cc_start: 0.6873 (m) cc_final: 0.6653 (m) outliers start: 31 outliers final: 17 residues processed: 218 average time/residue: 1.1805 time to fit residues: 279.3505 Evaluate side-chains 223 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 151 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4400 r_free = 0.4400 target = 0.201802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141894 restraints weight = 52098.977| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.42 r_work: 0.3463 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 12581 Z= 0.314 Angle : 0.625 7.162 17113 Z= 0.326 Chirality : 0.047 0.174 1947 Planarity : 0.006 0.070 2209 Dihedral : 6.962 59.531 1953 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.48 % Allowed : 14.27 % Favored : 83.25 % 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: -1.00 (0.21), residues: 1572 helix: -0.39 (0.35), residues: 206 sheet: -0.29 (0.22), residues: 559 loop : -0.94 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 135 TYR 0.028 0.002 TYR A 354 PHE 0.024 0.002 PHE A 236 TRP 0.013 0.002 TRP B 258 HIS 0.008 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00751 (12562) covalent geometry : angle 0.61804 (17064) SS BOND : bond 0.00857 ( 8) SS BOND : angle 1.83129 ( 16) hydrogen bonds : bond 0.04863 ( 415) hydrogen bonds : angle 6.06748 ( 1101) link_BETA1-4 : bond 0.00417 ( 5) link_BETA1-4 : angle 2.14366 ( 15) link_NAG-ASN : bond 0.00315 ( 6) link_NAG-ASN : angle 1.45969 ( 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: 33 poor density : 200 time to evaluate : 0.554 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: 0.7736 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: A 69 ILE cc_start: 0.8207 (mt) cc_final: 0.7808 (pp) REVERT: A 217 LYS cc_start: 0.7498 (mttp) cc_final: 0.7215 (mttp) REVERT: A 317 GLU cc_start: 0.7503 (mp0) cc_final: 0.7228 (mp0) REVERT: A 690 GLU cc_start: 0.6914 (tt0) cc_final: 0.6611 (tt0) REVERT: A 772 GLN cc_start: 0.8143 (mt0) cc_final: 0.7708 (mt0) REVERT: B 225 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7759 (ttp80) REVERT: L 54 LEU cc_start: 0.8589 (mt) cc_final: 0.8247 (mt) REVERT: L 82 THR cc_start: 0.6848 (m) cc_final: 0.6589 (m) outliers start: 33 outliers final: 22 residues processed: 214 average time/residue: 1.2197 time to fit residues: 283.4298 Evaluate side-chains 216 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 371 MET 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 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 H residue 100 GLU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 97 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4423 r_free = 0.4423 target = 0.203822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144061 restraints weight = 52128.479| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.44 r_work: 0.3476 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12581 Z= 0.141 Angle : 0.545 7.640 17113 Z= 0.281 Chirality : 0.043 0.156 1947 Planarity : 0.005 0.054 2209 Dihedral : 6.667 57.943 1953 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.78 % Allowed : 14.12 % Favored : 83.10 % 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: -0.76 (0.21), residues: 1572 helix: 0.11 (0.38), residues: 207 sheet: -0.18 (0.22), residues: 564 loop : -0.85 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 229 TYR 0.014 0.001 TYR A 354 PHE 0.016 0.001 PHE A 236 TRP 0.007 0.001 TRP H 99 HIS 0.004 0.001 HIS L 197 Details of bonding type rmsd covalent geometry : bond 0.00336 (12562) covalent geometry : angle 0.53997 (17064) SS BOND : bond 0.00517 ( 8) SS BOND : angle 1.21420 ( 16) hydrogen bonds : bond 0.03598 ( 415) hydrogen bonds : angle 5.66239 ( 1101) link_BETA1-4 : bond 0.00270 ( 5) link_BETA1-4 : angle 1.95976 ( 15) link_NAG-ASN : bond 0.00184 ( 6) link_NAG-ASN : angle 1.13047 ( 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 : 0.518 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: 0.7780 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: A 69 ILE cc_start: 0.8198 (mt) cc_final: 0.7802 (pp) REVERT: A 217 LYS cc_start: 0.7340 (mttp) cc_final: 0.7056 (mttp) REVERT: A 394 ASP cc_start: 0.8169 (p0) cc_final: 0.7929 (p0) REVERT: A 690 GLU cc_start: 0.6881 (tt0) cc_final: 0.6604 (tt0) REVERT: A 772 GLN cc_start: 0.8122 (mt0) cc_final: 0.7818 (mt0) REVERT: B 224 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7747 (mp0) REVERT: B 225 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7740 (ttp80) REVERT: L 54 LEU cc_start: 0.8591 (mt) cc_final: 0.8265 (mt) REVERT: L 82 THR cc_start: 0.6861 (m) cc_final: 0.6641 (m) outliers start: 37 outliers final: 19 residues processed: 221 average time/residue: 1.2709 time to fit residues: 304.3570 Evaluate side-chains 224 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 218 CYS 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 645 ILE Chi-restraints excluded: chain A residue 649 THR 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 100 GLU Chi-restraints excluded: chain H residue 159 THR 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: 0.0770 chunk 152 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4420 r_free = 0.4420 target = 0.203472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143901 restraints weight = 51826.254| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.41 r_work: 0.3476 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12581 Z= 0.183 Angle : 0.555 8.864 17113 Z= 0.285 Chirality : 0.044 0.158 1947 Planarity : 0.005 0.070 2209 Dihedral : 6.483 58.958 1951 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.63 % Allowed : 14.12 % Favored : 83.25 % 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: -0.75 (0.21), residues: 1572 helix: 0.13 (0.37), residues: 207 sheet: -0.13 (0.22), residues: 558 loop : -0.86 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 40 TYR 0.016 0.001 TYR A 354 PHE 0.017 0.002 PHE A 236 TRP 0.007 0.001 TRP H 99 HIS 0.005 0.001 HIS L 197 Details of bonding type rmsd covalent geometry : bond 0.00440 (12562) covalent geometry : angle 0.55010 (17064) SS BOND : bond 0.00440 ( 8) SS BOND : angle 1.13546 ( 16) hydrogen bonds : bond 0.03678 ( 415) hydrogen bonds : angle 5.50527 ( 1101) link_BETA1-4 : bond 0.00296 ( 5) link_BETA1-4 : angle 1.91320 ( 15) link_NAG-ASN : bond 0.00205 ( 6) link_NAG-ASN : angle 1.20665 ( 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: 35 poor density : 202 time to evaluate : 0.600 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: symmetry clash REVERT: A 56 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: A 69 ILE cc_start: 0.8196 (mt) cc_final: 0.7798 (pp) REVERT: A 217 LYS cc_start: 0.7335 (mttp) cc_final: 0.7039 (mttp) REVERT: A 394 ASP cc_start: 0.8160 (p0) cc_final: 0.7948 (p0) REVERT: A 690 GLU cc_start: 0.6884 (tt0) cc_final: 0.6590 (tt0) REVERT: A 772 GLN cc_start: 0.8086 (mt0) cc_final: 0.7811 (mt0) REVERT: B 225 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7745 (ttp80) REVERT: L 54 LEU cc_start: 0.8582 (mt) cc_final: 0.8247 (mt) REVERT: L 82 THR cc_start: 0.6846 (m) cc_final: 0.6618 (m) outliers start: 35 outliers final: 24 residues processed: 223 average time/residue: 1.3232 time to fit residues: 318.5394 Evaluate side-chains 225 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 218 CYS 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 645 ILE Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 702 LEU 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 97 ARG 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: 0.8980 chunk 7 optimal weight: 0.3980 chunk 152 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4417 r_free = 0.4417 target = 0.203170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143450 restraints weight = 51901.785| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.40 r_work: 0.3472 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12581 Z= 0.222 Angle : 0.574 9.189 17113 Z= 0.296 Chirality : 0.044 0.157 1947 Planarity : 0.005 0.056 2209 Dihedral : 6.441 59.647 1950 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.78 % Allowed : 14.27 % Favored : 82.95 % 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: 0.08 (0.37), residues: 207 sheet: -0.19 (0.22), residues: 574 loop : -0.92 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 229 TYR 0.019 0.002 TYR A 354 PHE 0.019 0.002 PHE A 236 TRP 0.008 0.001 TRP A 34 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00533 (12562) covalent geometry : angle 0.56959 (17064) SS BOND : bond 0.00432 ( 8) SS BOND : angle 1.12642 ( 16) hydrogen bonds : bond 0.03711 ( 415) hydrogen bonds : angle 5.39231 ( 1101) link_BETA1-4 : bond 0.00333 ( 5) link_BETA1-4 : angle 1.85438 ( 15) link_NAG-ASN : bond 0.00242 ( 6) link_NAG-ASN : angle 1.24926 ( 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 236 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: A 69 ILE cc_start: 0.8212 (mt) cc_final: 0.7796 (pp) REVERT: A 217 LYS cc_start: 0.7307 (mttp) cc_final: 0.7004 (mttp) REVERT: A 317 GLU cc_start: 0.7372 (mp0) cc_final: 0.7116 (mp0) REVERT: A 394 ASP cc_start: 0.8149 (p0) cc_final: 0.7947 (p0) REVERT: A 499 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: A 690 GLU cc_start: 0.6846 (tt0) cc_final: 0.6586 (tt0) REVERT: A 703 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7857 (mtt-85) REVERT: A 772 GLN cc_start: 0.8090 (mt0) cc_final: 0.7814 (mt0) REVERT: B 225 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7740 (ttp80) REVERT: L 54 LEU cc_start: 0.8563 (mt) cc_final: 0.8224 (mt) REVERT: L 82 THR cc_start: 0.6830 (m) cc_final: 0.6597 (m) outliers start: 37 outliers final: 26 residues processed: 223 average time/residue: 1.3629 time to fit residues: 329.1051 Evaluate side-chains 227 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 184 GLU 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 631 MET 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 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: 5.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4417 r_free = 0.4417 target = 0.203254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143236 restraints weight = 51651.013| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.40 r_work: 0.3474 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 12581 Z= 0.230 Angle : 0.573 9.446 17113 Z= 0.296 Chirality : 0.045 0.157 1947 Planarity : 0.005 0.068 2209 Dihedral : 6.410 59.887 1950 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.70 % Allowed : 14.43 % Favored : 82.87 % 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: 0.07 (0.37), residues: 207 sheet: -0.19 (0.22), residues: 576 loop : -0.95 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 229 TYR 0.018 0.002 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 covalent geometry : bond 0.00551 (12562) covalent geometry : angle 0.56864 (17064) SS BOND : bond 0.00432 ( 8) SS BOND : angle 1.10354 ( 16) hydrogen bonds : bond 0.03681 ( 415) hydrogen bonds : angle 5.32859 ( 1101) link_BETA1-4 : bond 0.00325 ( 5) link_BETA1-4 : angle 1.83071 ( 15) link_NAG-ASN : bond 0.00270 ( 6) link_NAG-ASN : angle 1.25675 ( 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 237 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.527 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: 0.7701 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: A 69 ILE cc_start: 0.8215 (mt) cc_final: 0.7791 (pp) REVERT: A 217 LYS cc_start: 0.7315 (mttp) cc_final: 0.7038 (mttp) REVERT: A 499 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: A 690 GLU cc_start: 0.6859 (tt0) cc_final: 0.6653 (tt0) REVERT: A 703 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7866 (mtt-85) REVERT: A 772 GLN cc_start: 0.8096 (mt0) cc_final: 0.7834 (mt0) REVERT: B 225 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7749 (ttp80) REVERT: L 54 LEU cc_start: 0.8568 (mt) cc_final: 0.8242 (mt) REVERT: L 82 THR cc_start: 0.6804 (m) cc_final: 0.6597 (m) outliers start: 36 outliers final: 25 residues processed: 222 average time/residue: 1.2067 time to fit residues: 290.8600 Evaluate side-chains 230 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 321 ILE 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 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 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: 1.9990 chunk 67 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 148 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4406 r_free = 0.4406 target = 0.202159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141502 restraints weight = 51860.637| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.44 r_work: 0.3456 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 12581 Z= 0.272 Angle : 0.603 10.842 17113 Z= 0.312 Chirality : 0.046 0.163 1947 Planarity : 0.005 0.059 2209 Dihedral : 6.463 59.647 1950 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % 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: -0.95 (0.21), residues: 1572 helix: -0.03 (0.37), residues: 205 sheet: -0.21 (0.21), residues: 574 loop : -1.05 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 229 TYR 0.020 0.002 TYR A 771 PHE 0.021 0.002 PHE A 236 TRP 0.010 0.001 TRP B 258 HIS 0.006 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00653 (12562) covalent geometry : angle 0.59868 (17064) SS BOND : bond 0.00458 ( 8) SS BOND : angle 1.20199 ( 16) hydrogen bonds : bond 0.03857 ( 415) hydrogen bonds : angle 5.33992 ( 1101) link_BETA1-4 : bond 0.00327 ( 5) link_BETA1-4 : angle 1.80936 ( 15) link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 1.34349 ( 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 240 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7715 (OUTLIER) cc_final: 0.7211 (mp10) REVERT: A 69 ILE cc_start: 0.8234 (mt) cc_final: 0.7791 (pp) REVERT: A 499 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: A 690 GLU cc_start: 0.6874 (tt0) cc_final: 0.6655 (tt0) REVERT: A 703 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7868 (mtt-85) REVERT: A 772 GLN cc_start: 0.8128 (mt0) cc_final: 0.7843 (mt0) REVERT: B 225 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7752 (ttp80) REVERT: L 54 LEU cc_start: 0.8556 (mt) cc_final: 0.8223 (mt) REVERT: L 82 THR cc_start: 0.6884 (m) cc_final: 0.6656 (m) outliers start: 37 outliers final: 28 residues processed: 226 average time/residue: 1.2493 time to fit residues: 306.6671 Evaluate side-chains 233 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 90 ILE 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 210 MET 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 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 605 ASP 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 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 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: 0.5980 chunk 43 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4413 r_free = 0.4413 target = 0.202726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142251 restraints weight = 51875.796| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.42 r_work: 0.3456 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12581 Z= 0.200 Angle : 0.577 10.958 17113 Z= 0.296 Chirality : 0.044 0.147 1947 Planarity : 0.005 0.054 2209 Dihedral : 6.407 59.915 1950 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.93 % Allowed : 14.80 % 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: -0.87 (0.21), residues: 1572 helix: 0.06 (0.36), residues: 205 sheet: -0.17 (0.21), residues: 577 loop : -1.00 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 229 TYR 0.017 0.002 TYR A 354 PHE 0.020 0.002 PHE A 236 TRP 0.009 0.001 TRP A 34 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00482 (12562) covalent geometry : angle 0.57327 (17064) SS BOND : bond 0.00410 ( 8) SS BOND : angle 1.08228 ( 16) hydrogen bonds : bond 0.03562 ( 415) hydrogen bonds : angle 5.24612 ( 1101) link_BETA1-4 : bond 0.00303 ( 5) link_BETA1-4 : angle 1.74921 ( 15) link_NAG-ASN : bond 0.00535 ( 6) link_NAG-ASN : angle 1.34446 ( 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 241 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.651 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: symmetry clash REVERT: A 42 THR cc_start: 0.8050 (p) cc_final: 0.7772 (t) REVERT: A 56 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: A 69 ILE cc_start: 0.8228 (mt) cc_final: 0.7786 (pp) REVERT: A 499 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: A 690 GLU cc_start: 0.6840 (tt0) cc_final: 0.6623 (tt0) REVERT: A 703 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7866 (mtt-85) REVERT: A 772 GLN cc_start: 0.8088 (mt0) cc_final: 0.7792 (mt0) REVERT: L 54 LEU cc_start: 0.8564 (mt) cc_final: 0.8248 (mt) REVERT: L 82 THR cc_start: 0.6926 (m) cc_final: 0.6670 (m) outliers start: 39 outliers final: 23 residues processed: 222 average time/residue: 1.3289 time to fit residues: 319.0765 Evaluate side-chains 227 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 321 ILE 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 153 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4416 r_free = 0.4416 target = 0.202977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142695 restraints weight = 51501.460| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.41 r_work: 0.3464 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12581 Z= 0.188 Angle : 0.571 11.439 17113 Z= 0.291 Chirality : 0.044 0.151 1947 Planarity : 0.005 0.056 2209 Dihedral : 6.294 59.813 1950 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.25 % Allowed : 15.48 % 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: -0.78 (0.21), residues: 1572 helix: 0.17 (0.36), residues: 206 sheet: -0.11 (0.22), residues: 575 loop : -0.97 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 229 TYR 0.014 0.001 TYR A 354 PHE 0.018 0.002 PHE A 236 TRP 0.008 0.001 TRP A 34 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00453 (12562) covalent geometry : angle 0.56683 (17064) SS BOND : bond 0.00382 ( 8) SS BOND : angle 1.04317 ( 16) hydrogen bonds : bond 0.03415 ( 415) hydrogen bonds : angle 5.13797 ( 1101) link_BETA1-4 : bond 0.00308 ( 5) link_BETA1-4 : angle 1.73938 ( 15) link_NAG-ASN : bond 0.00484 ( 6) link_NAG-ASN : angle 1.30639 ( 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 232 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 THR cc_start: 0.8076 (p) cc_final: 0.7806 (t) REVERT: A 56 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7119 (mp10) REVERT: A 69 ILE cc_start: 0.8228 (mt) cc_final: 0.7785 (pp) REVERT: A 499 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: A 690 GLU cc_start: 0.6835 (tt0) cc_final: 0.6631 (tt0) REVERT: A 703 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7872 (mtt-85) REVERT: A 772 GLN cc_start: 0.8094 (mt0) cc_final: 0.7842 (mt0) REVERT: L 54 LEU cc_start: 0.8559 (mt) cc_final: 0.8268 (mt) REVERT: L 82 THR cc_start: 0.6963 (m) cc_final: 0.6704 (m) outliers start: 30 outliers final: 24 residues processed: 221 average time/residue: 1.3435 time to fit residues: 322.9128 Evaluate side-chains 228 residues out of total 1331 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 321 ILE 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 153 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 100 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain L residue 57 TRP 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: 0.1980 chunk 35 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 316 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 = 0.4414 r_free = 0.4414 target = 0.202817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142658 restraints weight = 51656.318| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.41 r_work: 0.3464 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12581 Z= 0.193 Angle : 0.580 10.831 17113 Z= 0.295 Chirality : 0.044 0.174 1947 Planarity : 0.005 0.052 2209 Dihedral : 6.434 59.799 1950 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.25 % Allowed : 15.78 % Favored : 81.97 % 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: -0.78 (0.21), residues: 1572 helix: 0.20 (0.36), residues: 206 sheet: -0.11 (0.22), residues: 578 loop : -0.98 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 229 TYR 0.015 0.001 TYR A 354 PHE 0.018 0.002 PHE A 236 TRP 0.008 0.001 TRP B 258 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00465 (12562) covalent geometry : angle 0.57585 (17064) SS BOND : bond 0.00390 ( 8) SS BOND : angle 1.06411 ( 16) hydrogen bonds : bond 0.03406 ( 415) hydrogen bonds : angle 5.10923 ( 1101) link_BETA1-4 : bond 0.00281 ( 5) link_BETA1-4 : angle 1.71989 ( 15) link_NAG-ASN : bond 0.00569 ( 6) link_NAG-ASN : angle 1.45642 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10568.14 seconds wall clock time: 178 minutes 56.39 seconds (10736.39 seconds total)