Starting phenix.real_space_refine on Wed Feb 4 00:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzk_47332/02_2026/9dzk_47332.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzk_47332/02_2026/9dzk_47332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dzk_47332/02_2026/9dzk_47332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzk_47332/02_2026/9dzk_47332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dzk_47332/02_2026/9dzk_47332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzk_47332/02_2026/9dzk_47332.map" } resolution = 2.9 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= 0.001 sd= 0.117 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 Cl 2 4.86 5 C 5186 2.51 5 N 1399 2.21 5 O 1396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s 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: 8015 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3115 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 27, 'TRANS': 399} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 20, 'ARG:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 178 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 905 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 119} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 740 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3062 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 18, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "C" 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: "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: "F" 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: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.19 Number of scatterers: 8015 At special positions: 0 Unit cell: (67.41, 109.14, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 32 16.00 O 1396 8.00 N 1399 7.00 C 5186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1102 " - " ASN A 2 " " NAG A1103 " - " ASN A 354 " " NAG B1102 " - " ASN B 2 " " NAG B1103 " - " ASN B 354 " " NAG C 1 " - " ASN B 13 " " NAG D 1 " - " ASN B 395 " " NAG E 1 " - " ASN A 13 " " NAG F 1 " - " ASN A 395 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 377.8 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 35.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 19 through 36 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 63 through 76 removed outlier: 4.004A pdb=" N LEU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.568A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 193 through 207 removed outlier: 3.779A pdb=" N THR B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Proline residue: B 204 - end of helix Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.957A pdb=" N GLN B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.014A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.522A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 337 removed outlier: 3.618A pdb=" N LEU B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.776A pdb=" N ARG B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.544A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.202A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.763A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 130 through 145 removed outlier: 3.800A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 215 through 229 Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.602A pdb=" N GLN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.753A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 315 through 338 Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.017A pdb=" N LEU B 3 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N VAL B 49 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLY B 51 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 7 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 80 " --> pdb=" O THR B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 104 through 106 removed outlier: 6.201A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.406A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE B 188 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR B 154 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE B 210 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 212 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 355 through 359 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.735A pdb=" N GLU H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.735A pdb=" N GLU H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL H 113 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.343A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR L 86 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 50 removed outlier: 8.781A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE A 81 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 182 through 187 removed outlier: 3.616A pdb=" N ASP A 184 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 210 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 241 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 212 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 355 through 359 357 hydrogen bonds defined for protein. 993 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: 0.86 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2558 1.34 - 1.46: 2124 1.46 - 1.58: 3505 1.58 - 1.70: 1 1.70 - 1.81: 51 Bond restraints: 8239 Sorted by residual: bond pdb=" CG PRO B 254 " pdb=" CD PRO B 254 " ideal model delta sigma weight residual 1.503 1.364 0.139 3.40e-02 8.65e+02 1.66e+01 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.39e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.566 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" CB PRO B 254 " pdb=" CG PRO B 254 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.84e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 8234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11113 2.25 - 4.49: 154 4.49 - 6.74: 10 6.74 - 8.99: 5 8.99 - 11.23: 1 Bond angle restraints: 11283 Sorted by residual: angle pdb=" N PRO B 254 " pdb=" CD PRO B 254 " pdb=" CG PRO B 254 " ideal model delta sigma weight residual 103.20 91.97 11.23 1.50e+00 4.44e-01 5.61e+01 angle pdb=" CA PRO B 254 " pdb=" N PRO B 254 " pdb=" CD PRO B 254 " ideal model delta sigma weight residual 112.00 103.55 8.45 1.40e+00 5.10e-01 3.64e+01 angle pdb=" CA PRO B 254 " pdb=" CB PRO B 254 " pdb=" CG PRO B 254 " ideal model delta sigma weight residual 104.50 97.64 6.86 1.90e+00 2.77e-01 1.30e+01 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 104.88 8.07 3.00e+00 1.11e-01 7.24e+00 angle pdb=" CB PRO B 254 " pdb=" CG PRO B 254 " pdb=" CD PRO B 254 " ideal model delta sigma weight residual 106.10 99.01 7.09 3.20e+00 9.77e-02 4.91e+00 ... (remaining 11278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 4438 21.33 - 42.65: 375 42.65 - 63.98: 71 63.98 - 85.31: 20 85.31 - 106.63: 10 Dihedral angle restraints: 4914 sinusoidal: 1820 harmonic: 3094 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.92 106.63 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.75 105.46 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C3 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 47.62 -56.88 104.50 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 4911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1106 0.055 - 0.111: 147 0.111 - 0.166: 38 0.166 - 0.221: 0 0.221 - 0.277: 3 Chirality restraints: 1294 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.71 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1291 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 77 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO A 78 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 253 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A 254 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 417 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 418 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 418 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 418 " -0.022 5.00e-02 4.00e+02 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 77 2.64 - 3.21: 7150 3.21 - 3.77: 12174 3.77 - 4.34: 17450 4.34 - 4.90: 29442 Nonbonded interactions: 66293 Sorted by model distance: nonbonded pdb=" O ASN B 13 " pdb=" OG SER B 19 " model vdw 2.078 3.040 nonbonded pdb=" OD1 ASP A 135 " pdb=" N PHE A 136 " model vdw 2.253 3.120 nonbonded pdb=" O LEU B 248 " pdb=" NH1 ARG B 257 " model vdw 2.261 3.120 nonbonded pdb=" O PRO A 204 " pdb=" NH1 ARG A 208 " model vdw 2.265 3.120 nonbonded pdb=" O SER H 77 " pdb=" OG SER H 77 " model vdw 2.285 3.040 ... (remaining 66288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 60 or (resid 61 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 111 or (resid 112 and (n \ ame N or name CA or name C or name O or name CB )) or resid 113 through 176 or ( \ resid 177 and (name N or name CA or name C or name O or name CB )) or resid 178 \ through 189 or (resid 190 through 195 and (name N or name CA or name C or name O \ or name CB )) or resid 196 through 213 or (resid 214 through 215 and (name N or \ name CA or name C or name O or name CB )) or resid 216 through 221 or (resid 22 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 223 through \ 265 or (resid 266 through 270 and (name N or name CA or name C or name O or name \ CB )) or resid 271 through 307 or (resid 308 and (name N or name CA or name C o \ r name O or name CB )) or resid 309 through 322 or (resid 323 and (name N or nam \ e CA or name C or name O or name CB )) or resid 324 through 333 or (resid 334 an \ d (name N or name CA or name C or name O or name CB )) or resid 335 through 367 \ or (resid 368 through 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 381 or (resid 382 and (name N or name CA or name C or na \ me O or name CB )) or resid 383 through 409 or (resid 410 and (name N or name CA \ or name C or name O or name CB )) or resid 411 through 1103)) selection = (chain 'B' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 34 or (resid 35 through 36 and (nam \ e N or name CA or name C or name O or name CB )) or resid 37 through 58 or (resi \ d 59 and (name N or name CA or name C or name O or name CB )) or resid 60 throug \ h 62 or (resid 63 through 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 through 116 or (resid 117 through 119 and (name N or name CA o \ r name C or name O or name CB )) or resid 120 through 172 or (resid 173 and (nam \ e N or name CA or name C or name O or name CB )) or resid 174 through 185 or (re \ sid 186 through 187 and (name N or name CA or name C or name O or name CB )) or \ resid 188 through 193 or (resid 194 through 195 and (name N or name CA or name C \ or name O or name CB )) or resid 196 through 231 or (resid 232 and (name N or n \ ame CA or name C or name O or name CB )) or resid 233 or (resid 234 through 235 \ and (name N or name CA or name C or name O or name CB )) or resid 236 through 25 \ 1 or (resid 252 and (name N or name CA or name C or name O or name CB )) or resi \ d 253 through 268 or (resid 269 through 270 and (name N or name CA or name C or \ name O or name CB )) or resid 271 through 294 or (resid 295 and (name N or name \ CA or name C or name O or name CB )) or resid 296 through 297 or (resid 298 thro \ ugh 299 and (name N or name CA or name C or name O or name CB )) or resid 300 th \ rough 340 or (resid 341 through 344 and (name N or name CA or name C or name O o \ r name CB )) or resid 345 through 372 or (resid 373 and (name N or name CA or na \ me C or name O or name CB )) or resid 374 through 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB )) or resid 386 through 412 or (resid \ 413 and (name N or name CA or name C or name O or name CB )) or resid 414 or (re \ sid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 th \ rough 418 or (resid 419 through 420 and (name N or name CA or name C or name O o \ r name CB )) or resid 421 through 1103)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.740 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 0.139 8256 Z= 0.164 Angle : 0.641 11.492 11331 Z= 0.311 Chirality : 0.044 0.277 1294 Planarity : 0.004 0.053 1437 Dihedral : 17.229 106.634 2937 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 2.67 % Allowed : 20.77 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.27), residues: 1074 helix: 1.07 (0.30), residues: 323 sheet: -0.71 (0.32), residues: 289 loop : -0.46 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.009 0.001 TYR H 95 PHE 0.017 0.001 PHE A 172 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8239) covalent geometry : angle 0.62332 (11283) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.93702 ( 6) hydrogen bonds : bond 0.12918 ( 353) hydrogen bonds : angle 6.96353 ( 993) link_BETA1-4 : bond 0.01013 ( 6) link_BETA1-4 : angle 3.45940 ( 18) link_NAG-ASN : bond 0.00184 ( 8) link_NAG-ASN : angle 1.39777 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.285 Fit side-chains REVERT: A 334 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 358 GLN cc_start: 0.7887 (tp40) cc_final: 0.7519 (tp40) outliers start: 18 outliers final: 16 residues processed: 128 average time/residue: 0.4953 time to fit residues: 67.0152 Evaluate side-chains 119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 368 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 399 GLN A 249 GLN A 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121378 restraints weight = 9599.621| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.49 r_work: 0.3220 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8256 Z= 0.163 Angle : 0.626 9.553 11331 Z= 0.302 Chirality : 0.044 0.260 1294 Planarity : 0.005 0.045 1437 Dihedral : 9.856 80.874 1497 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 5.04 % Allowed : 18.84 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 1074 helix: 1.70 (0.30), residues: 321 sheet: -0.67 (0.32), residues: 286 loop : -0.51 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 257 TYR 0.014 0.001 TYR H 33 PHE 0.018 0.001 PHE A 172 TRP 0.013 0.001 TRP H 50 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8239) covalent geometry : angle 0.60848 (11283) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.40076 ( 6) hydrogen bonds : bond 0.03907 ( 353) hydrogen bonds : angle 5.03349 ( 993) link_BETA1-4 : bond 0.01296 ( 6) link_BETA1-4 : angle 3.23601 ( 18) link_NAG-ASN : bond 0.00159 ( 8) link_NAG-ASN : angle 1.60300 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.216 Fit side-chains REVERT: B 76 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7381 (m90) REVERT: B 176 ARG cc_start: 0.7301 (ttp80) cc_final: 0.6992 (mtp85) REVERT: B 248 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6367 (mt) REVERT: H 34 MET cc_start: 0.8316 (tpp) cc_final: 0.7948 (tpp) REVERT: H 116 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: L 4 MET cc_start: 0.8656 (mmm) cc_final: 0.8437 (mtp) REVERT: A 271 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6829 (tmt90) REVERT: A 358 GLN cc_start: 0.7993 (tp40) cc_final: 0.7604 (tp40) outliers start: 34 outliers final: 11 residues processed: 136 average time/residue: 0.4593 time to fit residues: 66.2299 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 287 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 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 163 HIS B 399 GLN H 39 GLN A 249 GLN A 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120761 restraints weight = 9343.766| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.31 r_work: 0.3250 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8256 Z= 0.126 Angle : 0.578 9.367 11331 Z= 0.276 Chirality : 0.043 0.232 1294 Planarity : 0.004 0.045 1437 Dihedral : 7.003 82.244 1480 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 5.04 % Allowed : 18.99 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.27), residues: 1074 helix: 1.69 (0.29), residues: 326 sheet: -0.65 (0.32), residues: 287 loop : -0.52 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 176 TYR 0.012 0.001 TYR H 33 PHE 0.015 0.001 PHE A 172 TRP 0.011 0.001 TRP H 50 HIS 0.008 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8239) covalent geometry : angle 0.56259 (11283) SS BOND : bond 0.00336 ( 3) SS BOND : angle 0.89110 ( 6) hydrogen bonds : bond 0.03445 ( 353) hydrogen bonds : angle 4.72003 ( 993) link_BETA1-4 : bond 0.01036 ( 6) link_BETA1-4 : angle 2.89004 ( 18) link_NAG-ASN : bond 0.00166 ( 8) link_NAG-ASN : angle 1.50539 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.184 Fit side-chains REVERT: B 76 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7367 (m90) REVERT: B 152 MET cc_start: 0.8373 (mtm) cc_final: 0.8141 (mtm) REVERT: B 248 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6333 (mt) REVERT: H 12 LYS cc_start: 0.7448 (mmtm) cc_final: 0.7181 (mttm) REVERT: H 34 MET cc_start: 0.8194 (tpp) cc_final: 0.7896 (tpp) REVERT: H 80 TYR cc_start: 0.8134 (m-80) cc_final: 0.7656 (m-80) REVERT: H 116 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: A 149 GLN cc_start: 0.8355 (tt0) cc_final: 0.8135 (pt0) REVERT: A 358 GLN cc_start: 0.8036 (tp40) cc_final: 0.7673 (tp40) outliers start: 34 outliers final: 10 residues processed: 140 average time/residue: 0.4898 time to fit residues: 72.6290 Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN A 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117924 restraints weight = 9563.109| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.27 r_work: 0.3210 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8256 Z= 0.210 Angle : 0.633 9.728 11331 Z= 0.303 Chirality : 0.045 0.257 1294 Planarity : 0.005 0.049 1437 Dihedral : 6.728 83.408 1475 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 5.04 % Allowed : 19.44 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1074 helix: 1.43 (0.29), residues: 328 sheet: -0.80 (0.31), residues: 287 loop : -0.64 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 176 TYR 0.016 0.002 TYR H 33 PHE 0.021 0.002 PHE A 172 TRP 0.015 0.001 TRP A 379 HIS 0.007 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8239) covalent geometry : angle 0.61600 (11283) SS BOND : bond 0.00766 ( 3) SS BOND : angle 1.74699 ( 6) hydrogen bonds : bond 0.03883 ( 353) hydrogen bonds : angle 4.78393 ( 993) link_BETA1-4 : bond 0.00795 ( 6) link_BETA1-4 : angle 2.99332 ( 18) link_NAG-ASN : bond 0.00200 ( 8) link_NAG-ASN : angle 1.80905 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.282 Fit side-chains REVERT: B 76 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7425 (m90) REVERT: B 248 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6277 (mt) REVERT: H 12 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7377 (mttm) REVERT: H 34 MET cc_start: 0.8218 (tpp) cc_final: 0.7982 (tpp) REVERT: H 80 TYR cc_start: 0.8259 (m-80) cc_final: 0.7819 (m-80) REVERT: H 116 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: A 149 GLN cc_start: 0.8405 (tt0) cc_final: 0.8146 (pt0) REVERT: A 246 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7347 (mp-120) REVERT: A 291 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7165 (mm) REVERT: A 358 GLN cc_start: 0.8111 (tp40) cc_final: 0.7758 (tp40) outliers start: 34 outliers final: 17 residues processed: 132 average time/residue: 0.4734 time to fit residues: 66.1649 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN A 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120462 restraints weight = 9477.099| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.31 r_work: 0.3242 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8256 Z= 0.127 Angle : 0.579 9.648 11331 Z= 0.273 Chirality : 0.042 0.234 1294 Planarity : 0.004 0.047 1437 Dihedral : 6.395 84.170 1475 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.70 % Favored : 97.21 % Rotamer: Outliers : 5.04 % Allowed : 19.29 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1074 helix: 1.69 (0.29), residues: 321 sheet: -0.78 (0.31), residues: 287 loop : -0.56 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.012 0.001 TYR H 33 PHE 0.018 0.001 PHE A 172 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8239) covalent geometry : angle 0.56502 (11283) SS BOND : bond 0.00249 ( 3) SS BOND : angle 1.02730 ( 6) hydrogen bonds : bond 0.03314 ( 353) hydrogen bonds : angle 4.65527 ( 993) link_BETA1-4 : bond 0.00840 ( 6) link_BETA1-4 : angle 2.60040 ( 18) link_NAG-ASN : bond 0.00151 ( 8) link_NAG-ASN : angle 1.60822 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.291 Fit side-chains REVERT: B 76 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7380 (m90) REVERT: B 248 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6354 (mt) REVERT: H 34 MET cc_start: 0.8137 (tpp) cc_final: 0.7846 (tpp) REVERT: H 109 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.8056 (t80) REVERT: H 116 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: L 79 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: A 149 GLN cc_start: 0.8396 (tt0) cc_final: 0.8137 (pt0) REVERT: A 169 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: A 246 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7247 (mp-120) REVERT: A 291 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7090 (mm) REVERT: A 358 GLN cc_start: 0.8101 (tp40) cc_final: 0.7744 (tp40) outliers start: 34 outliers final: 15 residues processed: 127 average time/residue: 0.5018 time to fit residues: 67.6402 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN H 6 GLN H 39 GLN A 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120674 restraints weight = 9330.470| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.30 r_work: 0.3247 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8256 Z= 0.121 Angle : 0.573 9.664 11331 Z= 0.270 Chirality : 0.042 0.235 1294 Planarity : 0.004 0.046 1437 Dihedral : 6.218 85.882 1475 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 4.90 % Allowed : 20.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1074 helix: 1.79 (0.29), residues: 321 sheet: -0.72 (0.31), residues: 287 loop : -0.57 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.022 0.001 TYR H 80 PHE 0.019 0.001 PHE A 172 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8239) covalent geometry : angle 0.56109 (11283) SS BOND : bond 0.00289 ( 3) SS BOND : angle 1.02405 ( 6) hydrogen bonds : bond 0.03193 ( 353) hydrogen bonds : angle 4.54457 ( 993) link_BETA1-4 : bond 0.00791 ( 6) link_BETA1-4 : angle 2.46325 ( 18) link_NAG-ASN : bond 0.00149 ( 8) link_NAG-ASN : angle 1.56580 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.180 Fit side-chains REVERT: B 76 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7391 (m90) REVERT: B 248 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6424 (mt) REVERT: H 34 MET cc_start: 0.8180 (tpp) cc_final: 0.7902 (tpp) REVERT: H 80 TYR cc_start: 0.8058 (m-80) cc_final: 0.7598 (m-80) REVERT: H 109 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.8020 (t80) REVERT: H 116 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: A 7 VAL cc_start: 0.8735 (t) cc_final: 0.8443 (m) REVERT: A 246 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7236 (mp-120) REVERT: A 291 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7114 (mm) REVERT: A 358 GLN cc_start: 0.8084 (tp40) cc_final: 0.7734 (tp40) outliers start: 33 outliers final: 19 residues processed: 133 average time/residue: 0.4845 time to fit residues: 68.3299 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 99 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN H 39 GLN A 249 GLN A 338 HIS A 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117465 restraints weight = 9498.891| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.26 r_work: 0.3200 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 8256 Z= 0.229 Angle : 0.645 9.827 11331 Z= 0.307 Chirality : 0.045 0.255 1294 Planarity : 0.005 0.047 1437 Dihedral : 6.572 87.746 1475 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 5.04 % Allowed : 20.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.26), residues: 1074 helix: 1.40 (0.29), residues: 327 sheet: -0.92 (0.31), residues: 280 loop : -0.69 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 176 TYR 0.016 0.002 TYR H 33 PHE 0.019 0.002 PHE A 172 TRP 0.014 0.002 TRP A 379 HIS 0.008 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8239) covalent geometry : angle 0.63071 (11283) SS BOND : bond 0.00416 ( 3) SS BOND : angle 1.79068 ( 6) hydrogen bonds : bond 0.03929 ( 353) hydrogen bonds : angle 4.72686 ( 993) link_BETA1-4 : bond 0.00637 ( 6) link_BETA1-4 : angle 2.68385 ( 18) link_NAG-ASN : bond 0.00205 ( 8) link_NAG-ASN : angle 1.84699 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.304 Fit side-chains REVERT: B 76 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7371 (m90) REVERT: B 248 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6372 (mt) REVERT: H 34 MET cc_start: 0.8203 (tpp) cc_final: 0.7966 (tpp) REVERT: H 109 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8055 (t80) REVERT: H 116 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: A 246 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7237 (mp-120) REVERT: A 291 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7151 (mm) REVERT: A 358 GLN cc_start: 0.8141 (tp40) cc_final: 0.7686 (tp-100) outliers start: 34 outliers final: 18 residues processed: 132 average time/residue: 0.5118 time to fit residues: 71.4445 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN H 39 GLN A 249 GLN A 338 HIS A 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119191 restraints weight = 9456.413| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.29 r_work: 0.3222 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8256 Z= 0.157 Angle : 0.599 9.706 11331 Z= 0.284 Chirality : 0.043 0.239 1294 Planarity : 0.004 0.047 1437 Dihedral : 6.414 88.828 1475 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 4.45 % Allowed : 21.07 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 1074 helix: 1.51 (0.29), residues: 327 sheet: -0.94 (0.30), residues: 280 loop : -0.69 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 176 TYR 0.016 0.001 TYR H 80 PHE 0.014 0.001 PHE A 172 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8239) covalent geometry : angle 0.58637 (11283) SS BOND : bond 0.00303 ( 3) SS BOND : angle 1.33413 ( 6) hydrogen bonds : bond 0.03491 ( 353) hydrogen bonds : angle 4.61337 ( 993) link_BETA1-4 : bond 0.00684 ( 6) link_BETA1-4 : angle 2.43351 ( 18) link_NAG-ASN : bond 0.00136 ( 8) link_NAG-ASN : angle 1.69115 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.184 Fit side-chains REVERT: B 76 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7373 (m90) REVERT: B 152 MET cc_start: 0.8512 (mtm) cc_final: 0.8230 (mtm) REVERT: B 248 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6369 (mt) REVERT: H 34 MET cc_start: 0.8138 (tpp) cc_final: 0.7847 (tpp) REVERT: H 109 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7982 (t80) REVERT: H 116 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: A 246 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7122 (mp-120) REVERT: A 291 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7072 (mm) REVERT: A 358 GLN cc_start: 0.8103 (tp40) cc_final: 0.7745 (tp40) outliers start: 30 outliers final: 20 residues processed: 127 average time/residue: 0.5023 time to fit residues: 67.5281 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN H 39 GLN A 185 HIS A 249 GLN A 338 HIS A 399 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120750 restraints weight = 9379.171| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.32 r_work: 0.3247 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8256 Z= 0.119 Angle : 0.570 9.647 11331 Z= 0.269 Chirality : 0.042 0.232 1294 Planarity : 0.004 0.046 1437 Dihedral : 6.180 89.337 1475 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.98 % Favored : 96.93 % Rotamer: Outliers : 4.15 % Allowed : 21.81 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1074 helix: 1.80 (0.29), residues: 321 sheet: -0.91 (0.30), residues: 280 loop : -0.64 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 176 TYR 0.012 0.001 TYR H 33 PHE 0.009 0.001 PHE B 172 TRP 0.011 0.001 TRP H 50 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8239) covalent geometry : angle 0.55961 (11283) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.91633 ( 6) hydrogen bonds : bond 0.03131 ( 353) hydrogen bonds : angle 4.49634 ( 993) link_BETA1-4 : bond 0.00685 ( 6) link_BETA1-4 : angle 2.20987 ( 18) link_NAG-ASN : bond 0.00149 ( 8) link_NAG-ASN : angle 1.54057 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.296 Fit side-chains REVERT: B 76 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.6984 (m90) REVERT: B 152 MET cc_start: 0.8475 (mtm) cc_final: 0.8152 (mtm) REVERT: B 248 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6351 (mt) REVERT: H 34 MET cc_start: 0.8127 (tpp) cc_final: 0.7786 (tpp) REVERT: H 90 ASP cc_start: 0.7709 (m-30) cc_final: 0.7507 (m-30) REVERT: H 109 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7955 (t80) REVERT: H 116 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7487 (pm20) REVERT: A 246 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7098 (mp-120) REVERT: A 291 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7105 (mm) REVERT: A 358 GLN cc_start: 0.8099 (tp40) cc_final: 0.7753 (tp40) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.5592 time to fit residues: 80.2348 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 47 optimal weight: 0.0970 chunk 35 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN H 39 GLN A 249 GLN A 338 HIS A 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123558 restraints weight = 9323.405| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.30 r_work: 0.3285 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8256 Z= 0.097 Angle : 0.559 9.591 11331 Z= 0.261 Chirality : 0.041 0.226 1294 Planarity : 0.004 0.046 1437 Dihedral : 5.951 87.587 1475 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.42 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 23.29 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1074 helix: 1.97 (0.29), residues: 323 sheet: -0.81 (0.31), residues: 280 loop : -0.60 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 176 TYR 0.010 0.001 TYR A 154 PHE 0.009 0.001 PHE A 172 TRP 0.011 0.001 TRP H 50 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8239) covalent geometry : angle 0.55050 (11283) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.68499 ( 6) hydrogen bonds : bond 0.02846 ( 353) hydrogen bonds : angle 4.37257 ( 993) link_BETA1-4 : bond 0.00698 ( 6) link_BETA1-4 : angle 2.01020 ( 18) link_NAG-ASN : bond 0.00151 ( 8) link_NAG-ASN : angle 1.41390 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.269 Fit side-chains REVERT: B 76 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7312 (m90) REVERT: B 152 MET cc_start: 0.8413 (mtm) cc_final: 0.8103 (mtm) REVERT: H 80 TYR cc_start: 0.7956 (m-80) cc_final: 0.7493 (m-80) REVERT: H 109 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7900 (t80) REVERT: H 116 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: A 7 VAL cc_start: 0.8744 (t) cc_final: 0.8470 (m) REVERT: A 237 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8444 (m) REVERT: A 246 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.6957 (mp-120) REVERT: A 358 GLN cc_start: 0.8059 (tp40) cc_final: 0.7611 (tp-100) outliers start: 19 outliers final: 9 residues processed: 125 average time/residue: 0.5548 time to fit residues: 73.4111 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 55 GLN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 246 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 chunk 69 optimal weight: 0.0570 chunk 102 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 249 GLN A 338 HIS A 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.151564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122950 restraints weight = 9353.851| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.31 r_work: 0.3274 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8256 Z= 0.108 Angle : 0.561 9.665 11331 Z= 0.263 Chirality : 0.042 0.232 1294 Planarity : 0.004 0.047 1437 Dihedral : 5.936 87.093 1475 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 2.52 % Allowed : 24.04 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1074 helix: 2.00 (0.29), residues: 323 sheet: -0.77 (0.30), residues: 280 loop : -0.61 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 176 TYR 0.011 0.001 TYR H 33 PHE 0.008 0.001 PHE B 388 TRP 0.012 0.001 TRP H 50 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8239) covalent geometry : angle 0.55217 (11283) SS BOND : bond 0.00093 ( 3) SS BOND : angle 1.07297 ( 6) hydrogen bonds : bond 0.02949 ( 353) hydrogen bonds : angle 4.36762 ( 993) link_BETA1-4 : bond 0.00661 ( 6) link_BETA1-4 : angle 2.00284 ( 18) link_NAG-ASN : bond 0.00136 ( 8) link_NAG-ASN : angle 1.44042 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.62 seconds wall clock time: 48 minutes 37.32 seconds (2917.32 seconds total)