Starting phenix.real_space_refine on Wed Sep 17 13:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgt_60090/09_2025/8zgt_60090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgt_60090/09_2025/8zgt_60090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgt_60090/09_2025/8zgt_60090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgt_60090/09_2025/8zgt_60090.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgt_60090/09_2025/8zgt_60090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgt_60090/09_2025/8zgt_60090.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5713 2.51 5 N 1483 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8915 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1729 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1227 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 1, 'TRANS': 156} Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2602 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 300} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2571 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 295} Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} 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: "H" 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.28 Number of scatterers: 8915 At special positions: 0 Unit cell: (80.75, 103.55, 169.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1679 8.00 N 1483 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.04 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 112 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 184 " distance=2.04 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 334 " - pdb=" SG CYS E 396 " distance=2.04 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 184 " distance=2.04 Simple disulfide: pdb=" SG CYS F 230 " - pdb=" SG CYS F 289 " distance=2.03 Simple disulfide: pdb=" SG CYS F 334 " - pdb=" SG CYS F 396 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 301 " - " ASN A 158 " " NAG A 302 " - " ASN A 167 " " NAG D 1 " - " ASN E 265 " " NAG E 501 " - " ASN E 240 " " NAG E 502 " - " ASN E 170 " " NAG F 501 " - " ASN F 170 " " NAG H 1 " - " ASN F 265 " " NAG T 1 " - " ASN A 65 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 352.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 20 sheets defined 29.3% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.544A pdb=" N SER A 86 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.570A pdb=" N SER A 169 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.603A pdb=" N GLN A 204 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 236 removed outlier: 3.892A pdb=" N ILE A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.538A pdb=" N LYS B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 56' Processing helix chain 'B' and resid 58 through 83 removed outlier: 3.977A pdb=" N GLN B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.562A pdb=" N PHE B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.575A pdb=" N TRP B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 160 removed outlier: 3.619A pdb=" N ALA B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 207 removed outlier: 3.505A pdb=" N PHE B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 removed outlier: 4.199A pdb=" N ALA C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 177 Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.744A pdb=" N TRP E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.804A pdb=" N HIS E 360 " --> pdb=" O LYS E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'G' and resid 25 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 64 Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 115 removed outlier: 3.540A pdb=" N ILE A 128 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.433A pdb=" N VAL A 120 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR A 177 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS A 140 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 151 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS A 145 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.433A pdb=" N VAL A 120 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 104 through 109 removed outlier: 5.310A pdb=" N ALA E 163 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 157 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR E 166 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU E 155 " --> pdb=" O TYR E 166 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ARG E 168 " --> pdb=" O ASN E 153 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 153 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 213 removed outlier: 3.946A pdb=" N THR E 229 " --> pdb=" O ILE E 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP E 234 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR E 268 " --> pdb=" O ASP E 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AB2, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.843A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.843A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG E 374 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 345 through 350 Processing sheet with id=AB5, first strand: chain 'F' and resid 104 through 109 removed outlier: 4.958A pdb=" N ALA F 163 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU F 158 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER F 164 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 144 through 145 removed outlier: 3.527A pdb=" N ALA F 195 " --> pdb=" O CYS F 184 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 209 through 213 removed outlier: 3.916A pdb=" N ASP F 234 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR F 268 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.864A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.864A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 366 " --> pdb=" O PHE F 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 345 through 350 removed outlier: 3.522A pdb=" N SER F 345 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR F 395 " --> pdb=" O LEU F 349 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1200 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: 1.43 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2304 1.33 - 1.46: 2315 1.46 - 1.58: 4453 1.58 - 1.71: 0 1.71 - 1.84: 49 Bond restraints: 9121 Sorted by residual: bond pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.88e+00 bond pdb=" C1 NAG F 501 " pdb=" O5 NAG F 501 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.93e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C1 NAG E 502 " pdb=" O5 NAG E 502 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 9116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12208 2.83 - 5.65: 150 5.65 - 8.48: 21 8.48 - 11.31: 2 11.31 - 14.13: 2 Bond angle restraints: 12383 Sorted by residual: angle pdb=" C ASP F 134 " pdb=" N VAL F 135 " pdb=" CA VAL F 135 " ideal model delta sigma weight residual 121.97 133.57 -11.60 1.80e+00 3.09e-01 4.15e+01 angle pdb=" C TYR F 368 " pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C GLN F 390 " pdb=" N THR F 391 " pdb=" CA THR F 391 " ideal model delta sigma weight residual 122.46 128.96 -6.50 1.41e+00 5.03e-01 2.13e+01 angle pdb=" C GLN E 390 " pdb=" N THR E 391 " pdb=" CA THR E 391 " ideal model delta sigma weight residual 122.82 128.62 -5.80 1.42e+00 4.96e-01 1.67e+01 angle pdb=" CA LEU B 110 " pdb=" CB LEU B 110 " pdb=" CG LEU B 110 " ideal model delta sigma weight residual 116.30 130.43 -14.13 3.50e+00 8.16e-02 1.63e+01 ... (remaining 12378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5022 21.62 - 43.25: 545 43.25 - 64.87: 112 64.87 - 86.50: 28 86.50 - 108.12: 9 Dihedral angle restraints: 5716 sinusoidal: 2532 harmonic: 3184 Sorted by residual: dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta harmonic sigma weight residual 180.00 138.76 41.24 0 5.00e+00 4.00e-02 6.80e+01 dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TYR F 368 " pdb=" C TYR F 368 " pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1098 0.053 - 0.105: 273 0.105 - 0.158: 71 0.158 - 0.210: 7 0.210 - 0.263: 4 Chirality restraints: 1453 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 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ASN F 369 " pdb=" N ASN F 369 " pdb=" C ASN F 369 " pdb=" CB ASN F 369 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1450 not shown) Planarity restraints: 1527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.90e+01 pdb=" C ILE A 198 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE A 198 " 0.035 2.00e-02 2.50e+03 pdb=" N GLU A 199 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 320 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO F 321 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 321 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 321 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 114 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " 0.030 5.00e-02 4.00e+02 ... (remaining 1524 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1579 2.78 - 3.31: 7156 3.31 - 3.84: 13991 3.84 - 4.37: 15781 4.37 - 4.90: 28932 Nonbonded interactions: 67439 Sorted by model distance: nonbonded pdb=" OG1 THR A 25 " pdb=" OE1 GLN A 26 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 25 " pdb=" N GLN A 26 " model vdw 2.320 3.120 nonbonded pdb=" OD1 ASN E 265 " pdb=" OG1 THR E 267 " model vdw 2.330 3.040 nonbonded pdb=" O THR E 225 " pdb=" OG1 THR E 225 " model vdw 2.332 3.040 nonbonded pdb=" O ASP E 142 " pdb=" O6 NAG D 1 " model vdw 2.350 3.040 ... (remaining 67434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 24 through 57) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 101 through 416 or resid 502)) 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.590 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 0.050 9145 Z= 0.212 Angle : 0.809 14.135 12444 Z= 0.417 Chirality : 0.052 0.263 1453 Planarity : 0.006 0.066 1519 Dihedral : 18.714 108.121 3613 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.14 % Allowed : 25.63 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1065 helix: -1.11 (0.26), residues: 272 sheet: 1.08 (0.28), residues: 337 loop : -1.23 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 206 TYR 0.016 0.001 TYR A 103 PHE 0.018 0.002 PHE F 339 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9121) covalent geometry : angle 0.78863 (12383) SS BOND : bond 0.00513 ( 11) SS BOND : angle 1.19390 ( 22) hydrogen bonds : bond 0.19865 ( 417) hydrogen bonds : angle 7.25767 ( 1200) link_BETA1-4 : bond 0.00517 ( 5) link_BETA1-4 : angle 2.27538 ( 15) link_NAG-ASN : bond 0.00602 ( 8) link_NAG-ASN : angle 3.68174 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 38 residues processed: 125 average time/residue: 0.4663 time to fit residues: 63.4165 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 303 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 405 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 312 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN B 205 GLN E 393 GLN F 189 GLN F 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.189059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132667 restraints weight = 10080.558| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.70 r_work: 0.3306 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9145 Z= 0.138 Angle : 0.602 7.165 12444 Z= 0.312 Chirality : 0.045 0.152 1453 Planarity : 0.004 0.037 1519 Dihedral : 11.289 73.253 1559 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 4.34 % Allowed : 25.13 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1065 helix: 0.52 (0.31), residues: 261 sheet: 1.37 (0.28), residues: 342 loop : -1.06 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 198 TYR 0.015 0.001 TYR A 172 PHE 0.018 0.002 PHE E 339 TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9121) covalent geometry : angle 0.58313 (12383) SS BOND : bond 0.00671 ( 11) SS BOND : angle 1.11974 ( 22) hydrogen bonds : bond 0.04154 ( 417) hydrogen bonds : angle 4.88971 ( 1200) link_BETA1-4 : bond 0.00471 ( 5) link_BETA1-4 : angle 2.51202 ( 15) link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.73229 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 90 time to evaluate : 0.320 Fit side-chains REVERT: E 369 ASN cc_start: 0.7868 (t160) cc_final: 0.7495 (t0) outliers start: 43 outliers final: 23 residues processed: 125 average time/residue: 0.4752 time to fit residues: 64.3975 Evaluate side-chains 108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 0.0060 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS A 173 HIS B 205 GLN E 152 GLN E 223 ASN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.190140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136241 restraints weight = 9926.536| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.90 r_work: 0.3354 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9145 Z= 0.099 Angle : 0.540 7.614 12444 Z= 0.279 Chirality : 0.043 0.180 1453 Planarity : 0.003 0.032 1519 Dihedral : 9.180 59.473 1522 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 4.34 % Allowed : 25.33 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1065 helix: 1.31 (0.31), residues: 267 sheet: 1.40 (0.27), residues: 352 loop : -0.94 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 206 TYR 0.015 0.001 TYR B 158 PHE 0.012 0.001 PHE F 126 TRP 0.015 0.001 TRP B 103 HIS 0.003 0.000 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 9121) covalent geometry : angle 0.52204 (12383) SS BOND : bond 0.00532 ( 11) SS BOND : angle 0.90179 ( 22) hydrogen bonds : bond 0.03611 ( 417) hydrogen bonds : angle 4.42353 ( 1200) link_BETA1-4 : bond 0.00527 ( 5) link_BETA1-4 : angle 2.26065 ( 15) link_NAG-ASN : bond 0.00422 ( 8) link_NAG-ASN : angle 2.55212 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 221 LEU cc_start: 0.3668 (OUTLIER) cc_final: 0.3125 (mp) REVERT: E 369 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7519 (t0) REVERT: F 165 THR cc_start: 0.7772 (t) cc_final: 0.7479 (m) outliers start: 43 outliers final: 21 residues processed: 127 average time/residue: 0.4022 time to fit residues: 56.0699 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 55 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 204 GLN B 151 ASN E 152 GLN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127343 restraints weight = 10175.033| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.60 r_work: 0.3143 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9145 Z= 0.222 Angle : 0.675 8.021 12444 Z= 0.343 Chirality : 0.049 0.179 1453 Planarity : 0.004 0.034 1519 Dihedral : 10.282 76.048 1520 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 5.05 % Allowed : 23.92 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1065 helix: 1.42 (0.31), residues: 262 sheet: 1.32 (0.27), residues: 352 loop : -1.05 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 206 TYR 0.015 0.002 TYR A 172 PHE 0.021 0.002 PHE E 339 TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 9121) covalent geometry : angle 0.65126 (12383) SS BOND : bond 0.00808 ( 11) SS BOND : angle 1.60078 ( 22) hydrogen bonds : bond 0.04267 ( 417) hydrogen bonds : angle 4.50931 ( 1200) link_BETA1-4 : bond 0.00646 ( 5) link_BETA1-4 : angle 3.16427 ( 15) link_NAG-ASN : bond 0.00408 ( 8) link_NAG-ASN : angle 2.92957 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: A 221 LEU cc_start: 0.4094 (OUTLIER) cc_final: 0.3460 (mp) REVERT: F 198 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7667 (mtp-110) REVERT: F 315 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: F 338 ASN cc_start: 0.8418 (t0) cc_final: 0.7963 (t0) outliers start: 50 outliers final: 32 residues processed: 138 average time/residue: 0.4146 time to fit residues: 62.8744 Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 351 ASP Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 151 ASN E 347 GLN E 369 ASN ** F 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.182191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128368 restraints weight = 10101.759| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.51 r_work: 0.3221 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9145 Z= 0.127 Angle : 0.574 8.934 12444 Z= 0.295 Chirality : 0.044 0.175 1453 Planarity : 0.003 0.033 1519 Dihedral : 9.196 62.121 1520 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.53 % Allowed : 25.93 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1065 helix: 1.70 (0.31), residues: 268 sheet: 1.40 (0.27), residues: 358 loop : -1.02 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 206 TYR 0.011 0.001 TYR A 144 PHE 0.013 0.001 PHE F 339 TRP 0.019 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9121) covalent geometry : angle 0.55436 (12383) SS BOND : bond 0.00580 ( 11) SS BOND : angle 1.05875 ( 22) hydrogen bonds : bond 0.03601 ( 417) hydrogen bonds : angle 4.25597 ( 1200) link_BETA1-4 : bond 0.00510 ( 5) link_BETA1-4 : angle 2.52896 ( 15) link_NAG-ASN : bond 0.00418 ( 8) link_NAG-ASN : angle 2.70583 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 221 LEU cc_start: 0.3853 (OUTLIER) cc_final: 0.3272 (mp) REVERT: B 167 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: E 213 ILE cc_start: 0.8372 (pt) cc_final: 0.8069 (mt) REVERT: F 338 ASN cc_start: 0.8335 (t0) cc_final: 0.7909 (t0) outliers start: 35 outliers final: 26 residues processed: 117 average time/residue: 0.4880 time to fit residues: 62.1121 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 0.0170 chunk 8 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN F 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.187494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133782 restraints weight = 10042.580| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.93 r_work: 0.3320 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9145 Z= 0.110 Angle : 0.557 9.410 12444 Z= 0.285 Chirality : 0.044 0.169 1453 Planarity : 0.003 0.032 1519 Dihedral : 8.593 58.817 1518 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 3.33 % Allowed : 26.24 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.25), residues: 1065 helix: 1.86 (0.31), residues: 268 sheet: 1.41 (0.27), residues: 358 loop : -0.95 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 198 TYR 0.016 0.001 TYR B 158 PHE 0.012 0.001 PHE F 126 TRP 0.017 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9121) covalent geometry : angle 0.53783 (12383) SS BOND : bond 0.00539 ( 11) SS BOND : angle 0.97811 ( 22) hydrogen bonds : bond 0.03443 ( 417) hydrogen bonds : angle 4.14992 ( 1200) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 2.44322 ( 15) link_NAG-ASN : bond 0.00408 ( 8) link_NAG-ASN : angle 2.63968 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8187 (t0) REVERT: A 221 LEU cc_start: 0.3998 (OUTLIER) cc_final: 0.3403 (mp) REVERT: B 108 PHE cc_start: 0.7149 (m-80) cc_final: 0.6845 (m-80) REVERT: B 167 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: E 213 ILE cc_start: 0.8288 (pt) cc_final: 0.7988 (mt) REVERT: F 131 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6963 (mm) REVERT: F 338 ASN cc_start: 0.8316 (t0) cc_final: 0.7908 (t0) outliers start: 33 outliers final: 24 residues processed: 117 average time/residue: 0.4751 time to fit residues: 60.4712 Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN E 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.187801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133870 restraints weight = 10027.229| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.86 r_work: 0.3322 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9145 Z= 0.119 Angle : 0.612 13.013 12444 Z= 0.300 Chirality : 0.050 0.844 1453 Planarity : 0.003 0.032 1519 Dihedral : 8.311 59.793 1516 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 3.94 % Allowed : 25.93 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.25), residues: 1065 helix: 1.95 (0.31), residues: 268 sheet: 1.40 (0.27), residues: 358 loop : -0.92 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 198 TYR 0.011 0.001 TYR F 124 PHE 0.012 0.001 PHE F 126 TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9121) covalent geometry : angle 0.57759 (12383) SS BOND : bond 0.00551 ( 11) SS BOND : angle 1.01834 ( 22) hydrogen bonds : bond 0.03422 ( 417) hydrogen bonds : angle 4.10554 ( 1200) link_BETA1-4 : bond 0.00539 ( 5) link_BETA1-4 : angle 2.49724 ( 15) link_NAG-ASN : bond 0.00365 ( 8) link_NAG-ASN : angle 4.14535 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 LEU cc_start: 0.4094 (OUTLIER) cc_final: 0.3486 (mp) REVERT: B 108 PHE cc_start: 0.7385 (m-80) cc_final: 0.6876 (m-80) REVERT: B 167 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: E 213 ILE cc_start: 0.8322 (pt) cc_final: 0.8046 (mt) REVERT: E 369 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7552 (t0) REVERT: F 131 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.7000 (mm) REVERT: F 315 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: F 338 ASN cc_start: 0.8328 (t0) cc_final: 0.7945 (t0) outliers start: 39 outliers final: 26 residues processed: 122 average time/residue: 0.4637 time to fit residues: 61.8129 Evaluate side-chains 120 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 361 SER Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 0.0010 chunk 13 optimal weight: 0.0270 chunk 11 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135731 restraints weight = 9989.824| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.78 r_work: 0.3362 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9145 Z= 0.092 Angle : 0.561 14.846 12444 Z= 0.280 Chirality : 0.047 0.732 1453 Planarity : 0.003 0.033 1519 Dihedral : 7.443 57.802 1516 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 2.83 % Allowed : 27.55 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1065 helix: 1.98 (0.32), residues: 274 sheet: 1.41 (0.27), residues: 361 loop : -0.82 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 198 TYR 0.027 0.001 TYR E 166 PHE 0.012 0.001 PHE F 376 TRP 0.014 0.001 TRP B 103 HIS 0.003 0.000 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 9121) covalent geometry : angle 0.52748 (12383) SS BOND : bond 0.00379 ( 11) SS BOND : angle 0.67439 ( 22) hydrogen bonds : bond 0.03080 ( 417) hydrogen bonds : angle 3.96148 ( 1200) link_BETA1-4 : bond 0.00531 ( 5) link_BETA1-4 : angle 2.04655 ( 15) link_NAG-ASN : bond 0.00389 ( 8) link_NAG-ASN : angle 4.09789 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7825 (mttt) REVERT: B 167 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: E 271 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8730 (m) REVERT: F 131 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.7028 (mm) REVERT: F 174 GLN cc_start: 0.7093 (mp10) cc_final: 0.6681 (mp10) REVERT: F 338 ASN cc_start: 0.8144 (t0) cc_final: 0.7760 (t0) outliers start: 28 outliers final: 16 residues processed: 114 average time/residue: 0.4744 time to fit residues: 58.8564 Evaluate side-chains 104 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN E 223 ASN E 369 ASN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.187022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131610 restraints weight = 9947.248| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.57 r_work: 0.3301 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9145 Z= 0.157 Angle : 0.624 13.171 12444 Z= 0.310 Chirality : 0.049 0.686 1453 Planarity : 0.004 0.033 1519 Dihedral : 7.819 58.242 1513 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.62 % Allowed : 27.65 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1065 helix: 1.99 (0.31), residues: 268 sheet: 1.43 (0.27), residues: 359 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 198 TYR 0.027 0.002 TYR E 166 PHE 0.019 0.002 PHE E 339 TRP 0.017 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9121) covalent geometry : angle 0.59215 (12383) SS BOND : bond 0.00623 ( 11) SS BOND : angle 1.20888 ( 22) hydrogen bonds : bond 0.03497 ( 417) hydrogen bonds : angle 4.06713 ( 1200) link_BETA1-4 : bond 0.00467 ( 5) link_BETA1-4 : angle 2.72793 ( 15) link_NAG-ASN : bond 0.00349 ( 8) link_NAG-ASN : angle 3.85213 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7851 (mttt) REVERT: B 108 PHE cc_start: 0.7404 (m-80) cc_final: 0.6928 (m-80) REVERT: B 167 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: F 131 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.7057 (mm) REVERT: F 338 ASN cc_start: 0.8357 (t0) cc_final: 0.7910 (t0) outliers start: 26 outliers final: 18 residues processed: 110 average time/residue: 0.5005 time to fit residues: 59.8669 Evaluate side-chains 105 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN E 369 ASN ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.187130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132315 restraints weight = 10030.907| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.98 r_work: 0.3296 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9145 Z= 0.146 Angle : 0.643 15.107 12444 Z= 0.321 Chirality : 0.053 1.022 1453 Planarity : 0.004 0.034 1519 Dihedral : 8.070 57.777 1513 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.62 % Allowed : 27.75 % Favored : 69.63 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1065 helix: 1.96 (0.31), residues: 267 sheet: 1.47 (0.27), residues: 353 loop : -0.89 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 198 TYR 0.027 0.001 TYR E 166 PHE 0.015 0.002 PHE E 339 TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9121) covalent geometry : angle 0.61267 (12383) SS BOND : bond 0.00592 ( 11) SS BOND : angle 1.13698 ( 22) hydrogen bonds : bond 0.03491 ( 417) hydrogen bonds : angle 4.12599 ( 1200) link_BETA1-4 : bond 0.00520 ( 5) link_BETA1-4 : angle 2.65359 ( 15) link_NAG-ASN : bond 0.01112 ( 8) link_NAG-ASN : angle 3.91342 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7910 (mttt) REVERT: B 108 PHE cc_start: 0.7331 (m-80) cc_final: 0.6869 (m-80) REVERT: B 167 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: F 131 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.7044 (mm) REVERT: F 338 ASN cc_start: 0.8358 (t0) cc_final: 0.7921 (t0) outliers start: 26 outliers final: 20 residues processed: 112 average time/residue: 0.4587 time to fit residues: 56.1111 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 345 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 184 CYS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 264 HIS Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 57 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 GLN F 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130754 restraints weight = 9877.703| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.57 r_work: 0.3319 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9145 Z= 0.109 Angle : 0.575 11.725 12444 Z= 0.291 Chirality : 0.046 0.530 1453 Planarity : 0.003 0.033 1519 Dihedral : 7.552 57.356 1513 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 2.42 % Allowed : 27.95 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1065 helix: 2.05 (0.31), residues: 267 sheet: 1.41 (0.27), residues: 359 loop : -0.85 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 198 TYR 0.027 0.001 TYR E 166 PHE 0.012 0.001 PHE F 126 TRP 0.016 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9121) covalent geometry : angle 0.54900 (12383) SS BOND : bond 0.00486 ( 11) SS BOND : angle 0.90130 ( 22) hydrogen bonds : bond 0.03262 ( 417) hydrogen bonds : angle 4.04847 ( 1200) link_BETA1-4 : bond 0.00511 ( 5) link_BETA1-4 : angle 2.34258 ( 15) link_NAG-ASN : bond 0.00563 ( 8) link_NAG-ASN : angle 3.42746 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.55 seconds wall clock time: 53 minutes 52.66 seconds (3232.66 seconds total)