Starting phenix.real_space_refine on Mon May 12 10:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgt_60090/05_2025/8zgt_60090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgt_60090/05_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_60090/05_2025/8zgt_60090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgt_60090/05_2025/8zgt_60090.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgt_60090/05_2025/8zgt_60090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgt_60090/05_2025/8zgt_60090.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.32, per 1000 atoms: 0.60 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: 2.08 Conformation dependent library (CDL) restraints added in 940.3 milliseconds 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: 1.22 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: 2.79 Time building geometry restraints manager: 2.45 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: 2.100 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.450 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- 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 : 2.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), 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 TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.018 0.002 PHE F 339 TYR 0.016 0.001 TYR A 103 ARG 0.017 0.001 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 8) link_NAG-ASN : angle 3.68174 ( 24) link_BETA1-4 : bond 0.00517 ( 5) link_BETA1-4 : angle 2.27538 ( 15) hydrogen bonds : bond 0.19865 ( 417) hydrogen bonds : angle 7.25767 ( 1200) SS BOND : bond 0.00513 ( 11) SS BOND : angle 1.19390 ( 22) covalent geometry : bond 0.00424 ( 9121) covalent geometry : angle 0.78863 (12383) *********************** 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 : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 38 residues processed: 125 average time/residue: 0.8540 time to fit residues: 117.0888 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 : 0.900 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.187381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135078 restraints weight = 10020.668| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.79 r_work: 0.3327 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9145 Z= 0.131 Angle : 0.595 7.399 12444 Z= 0.309 Chirality : 0.045 0.151 1453 Planarity : 0.004 0.038 1519 Dihedral : 11.412 74.959 1559 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 4.14 % Allowed : 25.23 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1065 helix: 0.49 (0.31), residues: 261 sheet: 1.38 (0.28), residues: 342 loop : -1.05 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS A 173 PHE 0.015 0.002 PHE E 339 TYR 0.014 0.001 TYR A 172 ARG 0.005 0.000 ARG F 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 8) link_NAG-ASN : angle 2.74142 ( 24) link_BETA1-4 : bond 0.00495 ( 5) link_BETA1-4 : angle 2.41110 ( 15) hydrogen bonds : bond 0.04200 ( 417) hydrogen bonds : angle 4.93301 ( 1200) SS BOND : bond 0.00660 ( 11) SS BOND : angle 1.13494 ( 22) covalent geometry : bond 0.00300 ( 9121) covalent geometry : angle 0.57659 (12383) *********************** 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: 41 poor density : 92 time to evaluate : 0.977 Fit side-chains REVERT: E 369 ASN cc_start: 0.7903 (t160) cc_final: 0.7525 (t0) outliers start: 41 outliers final: 23 residues processed: 125 average time/residue: 0.9166 time to fit residues: 125.0794 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 79 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 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 17 optimal weight: 0.0060 chunk 84 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN E 223 ASN ** F 350 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 = 0.4105 r_free = 0.4105 target = 0.187313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.134753 restraints weight = 10037.834| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.79 r_work: 0.3312 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1115 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= 0.129 Angle : 0.576 7.274 12444 Z= 0.297 Chirality : 0.045 0.178 1453 Planarity : 0.004 0.031 1519 Dihedral : 9.917 66.460 1522 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 4.44 % Allowed : 25.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1065 helix: 1.19 (0.31), residues: 267 sheet: 1.35 (0.27), residues: 358 loop : -1.02 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 PHE 0.015 0.002 PHE E 339 TYR 0.012 0.001 TYR A 172 ARG 0.004 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 8) link_NAG-ASN : angle 2.65195 ( 24) link_BETA1-4 : bond 0.00547 ( 5) link_BETA1-4 : angle 2.54238 ( 15) hydrogen bonds : bond 0.03883 ( 417) hydrogen bonds : angle 4.55427 ( 1200) SS BOND : bond 0.00642 ( 11) SS BOND : angle 1.13779 ( 22) covalent geometry : bond 0.00299 ( 9121) covalent geometry : angle 0.55600 (12383) *********************** 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 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 95 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 221 LEU cc_start: 0.3708 (OUTLIER) cc_final: 0.3181 (mp) REVERT: E 369 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7553 (t0) REVERT: F 165 THR cc_start: 0.7606 (t) cc_final: 0.7347 (m) REVERT: F 338 ASN cc_start: 0.8261 (t0) cc_final: 0.7986 (t0) outliers start: 44 outliers final: 24 residues processed: 127 average time/residue: 0.8367 time to fit residues: 116.9656 Evaluate side-chains 113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 361 SER 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 242 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 B 205 GLN E 152 GLN ** 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 = 0.4061 r_free = 0.4061 target = 0.183802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131290 restraints weight = 9994.741| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.80 r_work: 0.3279 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9145 Z= 0.177 Angle : 0.620 7.871 12444 Z= 0.317 Chirality : 0.047 0.179 1453 Planarity : 0.004 0.033 1519 Dihedral : 9.953 70.829 1521 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 5.05 % Allowed : 24.02 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1065 helix: 1.45 (0.31), residues: 267 sheet: 1.34 (0.27), residues: 359 loop : -1.02 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.007 0.001 HIS A 173 PHE 0.019 0.002 PHE E 339 TYR 0.014 0.002 TYR A 172 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 8) link_NAG-ASN : angle 2.80767 ( 24) link_BETA1-4 : bond 0.00586 ( 5) link_BETA1-4 : angle 2.90383 ( 15) hydrogen bonds : bond 0.03995 ( 417) hydrogen bonds : angle 4.44615 ( 1200) SS BOND : bond 0.00717 ( 11) SS BOND : angle 1.38714 ( 22) covalent geometry : bond 0.00437 ( 9121) covalent geometry : angle 0.59782 (12383) *********************** 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 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8172 (t0) REVERT: A 199 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: A 221 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3540 (mp) REVERT: E 213 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7973 (mt) REVERT: F 338 ASN cc_start: 0.8344 (t0) cc_final: 0.7911 (t0) outliers start: 50 outliers final: 29 residues processed: 134 average time/residue: 0.7862 time to fit residues: 116.4745 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 105 ASN 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 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 213 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 184 CYS 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 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 89 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN E 223 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 = 0.4026 r_free = 0.4026 target = 0.181943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127639 restraints weight = 10024.461| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.59 r_work: 0.3209 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9145 Z= 0.133 Angle : 0.580 8.573 12444 Z= 0.297 Chirality : 0.045 0.175 1453 Planarity : 0.004 0.031 1519 Dihedral : 9.244 62.238 1521 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.79 % Favored : 95.12 % Rotamer: Outliers : 4.24 % Allowed : 25.13 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1065 helix: 1.65 (0.31), residues: 268 sheet: 1.40 (0.27), residues: 358 loop : -1.02 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS A 173 PHE 0.014 0.002 PHE F 339 TYR 0.011 0.001 TYR A 172 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 8) link_NAG-ASN : angle 2.71538 ( 24) link_BETA1-4 : bond 0.00454 ( 5) link_BETA1-4 : angle 2.62532 ( 15) hydrogen bonds : bond 0.03662 ( 417) hydrogen bonds : angle 4.26934 ( 1200) SS BOND : bond 0.00618 ( 11) SS BOND : angle 1.13675 ( 22) covalent geometry : bond 0.00313 ( 9121) covalent geometry : angle 0.55954 (12383) *********************** 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 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 186 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8279 (m-30) REVERT: A 221 LEU cc_start: 0.3882 (OUTLIER) cc_final: 0.3318 (mp) REVERT: B 167 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: E 213 ILE cc_start: 0.8343 (pt) cc_final: 0.8037 (mt) REVERT: F 338 ASN cc_start: 0.8351 (t0) cc_final: 0.7903 (t0) outliers start: 42 outliers final: 32 residues processed: 126 average time/residue: 0.8322 time to fit residues: 115.2057 Evaluate side-chains 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 186 ASP 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 38 VAL 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 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 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 369 ASN Chi-restraints excluded: chain F residue 131 ILE 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 220 LEU Chi-restraints excluded: chain F residue 242 THR 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 47 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 69 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.182966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128694 restraints weight = 9986.842| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.55 r_work: 0.3192 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1532 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= 0.112 Angle : 0.560 9.364 12444 Z= 0.286 Chirality : 0.044 0.169 1453 Planarity : 0.003 0.029 1519 Dihedral : 8.620 58.812 1518 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 4.44 % Allowed : 25.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1065 helix: 1.83 (0.31), residues: 268 sheet: 1.43 (0.26), residues: 358 loop : -0.93 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.004 0.001 HIS A 173 PHE 0.012 0.001 PHE F 126 TYR 0.011 0.001 TYR F 124 ARG 0.005 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 8) link_NAG-ASN : angle 2.65540 ( 24) link_BETA1-4 : bond 0.00526 ( 5) link_BETA1-4 : angle 2.46980 ( 15) hydrogen bonds : bond 0.03466 ( 417) hydrogen bonds : angle 4.16666 ( 1200) SS BOND : bond 0.00551 ( 11) SS BOND : angle 1.00172 ( 22) covalent geometry : bond 0.00255 ( 9121) covalent geometry : angle 0.54028 (12383) *********************** 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 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 89 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 221 LEU cc_start: 0.3943 (OUTLIER) cc_final: 0.3369 (mp) REVERT: B 108 PHE cc_start: 0.6977 (m-80) cc_final: 0.6744 (m-80) REVERT: B 167 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: E 213 ILE cc_start: 0.8296 (pt) cc_final: 0.8021 (mt) REVERT: F 131 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6961 (mm) REVERT: F 338 ASN cc_start: 0.8314 (t0) cc_final: 0.7902 (t0) outliers start: 44 outliers final: 30 residues processed: 125 average time/residue: 0.7817 time to fit residues: 107.6478 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 : 0.904 ------------------------------------------------------------------------------- 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 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 38 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU 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 F residue 131 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 0.0060 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.185486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130604 restraints weight = 10051.856| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.02 r_work: 0.3285 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9145 Z= 0.179 Angle : 0.675 14.004 12444 Z= 0.332 Chirality : 0.052 0.839 1453 Planarity : 0.004 0.035 1519 Dihedral : 9.201 65.270 1516 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 4.04 % Allowed : 25.23 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1065 helix: 1.70 (0.31), residues: 269 sheet: 1.36 (0.27), residues: 351 loop : -0.97 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.007 0.001 HIS A 173 PHE 0.020 0.002 PHE E 339 TYR 0.019 0.002 TYR B 158 ARG 0.005 0.000 ARG C 51 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 8) link_NAG-ASN : angle 4.35355 ( 24) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 2.95721 ( 15) hydrogen bonds : bond 0.03841 ( 417) hydrogen bonds : angle 4.26708 ( 1200) SS BOND : bond 0.00711 ( 11) SS BOND : angle 1.37556 ( 22) covalent geometry : bond 0.00440 ( 9121) covalent geometry : angle 0.63846 (12383) *********************** 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 132 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8104 (t0) REVERT: A 221 LEU cc_start: 0.3942 (OUTLIER) cc_final: 0.3324 (mp) REVERT: B 108 PHE cc_start: 0.7175 (m-80) cc_final: 0.6937 (m-80) REVERT: B 167 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: E 213 ILE cc_start: 0.8393 (pt) cc_final: 0.8044 (mt) REVERT: E 369 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7606 (t0) REVERT: F 338 ASN cc_start: 0.8417 (t0) cc_final: 0.7952 (t0) outliers start: 40 outliers final: 30 residues processed: 124 average time/residue: 0.8074 time to fit residues: 110.5056 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 105 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 107 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 38 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 46 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 15 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS B 151 ASN E 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.188356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133597 restraints weight = 10145.753| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.12 r_work: 0.3315 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9145 Z= 0.105 Angle : 0.590 13.787 12444 Z= 0.295 Chirality : 0.049 0.819 1453 Planarity : 0.003 0.031 1519 Dihedral : 8.303 58.015 1516 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 3.13 % Allowed : 26.24 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1065 helix: 1.94 (0.31), residues: 269 sheet: 1.38 (0.26), residues: 358 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.003 0.000 HIS A 173 PHE 0.011 0.001 PHE F 339 TYR 0.012 0.001 TYR F 166 ARG 0.006 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 8) link_NAG-ASN : angle 4.09803 ( 24) link_BETA1-4 : bond 0.00481 ( 5) link_BETA1-4 : angle 2.33400 ( 15) hydrogen bonds : bond 0.03317 ( 417) hydrogen bonds : angle 4.12243 ( 1200) SS BOND : bond 0.00472 ( 11) SS BOND : angle 0.87707 ( 22) covalent geometry : bond 0.00232 ( 9121) covalent geometry : angle 0.55586 (12383) *********************** 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 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8038 (t0) REVERT: A 163 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7855 (mttt) REVERT: A 221 LEU cc_start: 0.3761 (OUTLIER) cc_final: 0.3119 (mp) REVERT: B 167 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: E 213 ILE cc_start: 0.8293 (pt) cc_final: 0.8026 (mt) REVERT: F 131 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6978 (mm) REVERT: F 338 ASN cc_start: 0.8302 (t0) cc_final: 0.7896 (t0) outliers start: 31 outliers final: 20 residues processed: 111 average time/residue: 0.8480 time to fit residues: 103.3608 Evaluate side-chains 108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 124 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 E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE 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 354 LEU Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 70 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN F 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133921 restraints weight = 9978.873| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.55 r_work: 0.3327 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9145 Z= 0.107 Angle : 0.592 10.367 12444 Z= 0.297 Chirality : 0.051 0.940 1453 Planarity : 0.003 0.044 1519 Dihedral : 7.849 58.087 1515 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.72 % Allowed : 26.84 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1065 helix: 1.95 (0.31), residues: 268 sheet: 1.43 (0.27), residues: 353 loop : -0.81 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 PHE 0.012 0.001 PHE F 339 TYR 0.016 0.001 TYR B 158 ARG 0.006 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 8) link_NAG-ASN : angle 3.67027 ( 24) link_BETA1-4 : bond 0.00508 ( 5) link_BETA1-4 : angle 2.32467 ( 15) hydrogen bonds : bond 0.03349 ( 417) hydrogen bonds : angle 4.08533 ( 1200) SS BOND : bond 0.00490 ( 11) SS BOND : angle 0.87001 ( 22) covalent geometry : bond 0.00234 ( 9121) covalent geometry : angle 0.56371 (12383) *********************** 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 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7839 (mttt) REVERT: A 221 LEU cc_start: 0.3738 (OUTLIER) cc_final: 0.3163 (mp) REVERT: B 167 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: F 131 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.7055 (mm) REVERT: F 338 ASN cc_start: 0.8273 (t0) cc_final: 0.7871 (t0) outliers start: 27 outliers final: 21 residues processed: 109 average time/residue: 0.9255 time to fit residues: 110.2432 Evaluate side-chains 108 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 46 LEU 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 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 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 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 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.0040 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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** F 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.186712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129976 restraints weight = 10007.668| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.65 r_work: 0.3312 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9145 Z= 0.147 Angle : 0.623 10.958 12444 Z= 0.314 Chirality : 0.052 0.901 1453 Planarity : 0.004 0.038 1519 Dihedral : 8.164 58.060 1515 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 3.03 % Allowed : 26.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1065 helix: 1.88 (0.31), residues: 268 sheet: 1.35 (0.26), residues: 359 loop : -0.92 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.004 0.001 HIS E 360 PHE 0.016 0.002 PHE E 339 TYR 0.025 0.002 TYR E 166 ARG 0.006 0.000 ARG E 206 Details of bonding type rmsd link_NAG-ASN : bond 0.01083 ( 8) link_NAG-ASN : angle 3.75344 ( 24) link_BETA1-4 : bond 0.00530 ( 5) link_BETA1-4 : angle 2.70369 ( 15) hydrogen bonds : bond 0.03606 ( 417) hydrogen bonds : angle 4.18911 ( 1200) SS BOND : bond 0.00633 ( 11) SS BOND : angle 1.18710 ( 22) covalent geometry : bond 0.00351 ( 9121) covalent geometry : angle 0.59291 (12383) ********************** 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 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7918 (mttt) REVERT: A 221 LEU cc_start: 0.4037 (OUTLIER) cc_final: 0.3379 (mp) REVERT: B 108 PHE cc_start: 0.7408 (m-80) cc_final: 0.7065 (m-80) REVERT: B 167 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: E 369 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7696 (t0) REVERT: F 131 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.7026 (mm) REVERT: F 238 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7258 (tt0) REVERT: F 338 ASN cc_start: 0.8354 (t0) cc_final: 0.7916 (t0) outliers start: 30 outliers final: 23 residues processed: 109 average time/residue: 0.9237 time to fit residues: 110.0734 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 197 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 209 ILE 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 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 71 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.0170 chunk 8 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.189813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133236 restraints weight = 10033.664| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.68 r_work: 0.3325 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1814 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= 0.114 Angle : 0.587 10.109 12444 Z= 0.297 Chirality : 0.049 0.759 1453 Planarity : 0.003 0.033 1519 Dihedral : 7.783 57.598 1515 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 3.13 % Allowed : 26.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1065 helix: 1.95 (0.31), residues: 268 sheet: 1.36 (0.27), residues: 359 loop : -0.86 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.003 0.001 HIS A 173 PHE 0.012 0.001 PHE F 339 TYR 0.028 0.001 TYR E 166 ARG 0.009 0.000 ARG F 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00997 ( 8) link_NAG-ASN : angle 3.52425 ( 24) link_BETA1-4 : bond 0.00516 ( 5) link_BETA1-4 : angle 2.41164 ( 15) hydrogen bonds : bond 0.03417 ( 417) hydrogen bonds : angle 4.14791 ( 1200) SS BOND : bond 0.00527 ( 11) SS BOND : angle 0.94604 ( 22) covalent geometry : bond 0.00256 ( 9121) covalent geometry : angle 0.55986 (12383) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5517.76 seconds wall clock time: 96 minutes 10.01 seconds (5770.01 seconds total)