Starting phenix.real_space_refine on Fri Jul 3 21:39:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yt8_39568/07_2026/8yt8_39568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yt8_39568/07_2026/8yt8_39568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yt8_39568/07_2026/8yt8_39568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yt8_39568/07_2026/8yt8_39568.map" model { file = "/net/cci-nas-00/data/ceres_data/8yt8_39568/07_2026/8yt8_39568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yt8_39568/07_2026/8yt8_39568_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 1 6.06 5 P 1 5.49 5 S 97 5.16 5 C 10362 2.51 5 N 2787 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16309 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2296 Classifications: {'peptide': 291} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 259} Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2009 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 8, 'TRANS': 254} Chain: "C" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1078 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 591 Unresolved non-hydrogen angles: 756 Unresolved non-hydrogen dihedrals: 486 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'TYR:plan': 5, 'ARG:plan': 9, 'PHE:plan': 11, 'GLN:plan1': 8, 'ASN:plan1': 11, 'HIS:plan': 4, 'ASP:plan': 8, 'GLU:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 304 Chain: "D" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2045 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 251} Chain: "E" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2686 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 317} Chain: "G" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2031 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain: "I" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Chain: "O" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2247 Classifications: {'peptide': 289} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 267} Chain: "S" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1390 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "P" 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: "Q" 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: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9376 SG CYS E3306 52.863 81.389 58.749 1.00113.74 S ATOM 9398 SG CYS E3309 49.688 82.844 57.443 1.00132.92 S ATOM 9580 SG CYS E3330 51.804 80.352 55.315 1.00106.64 S ATOM 9601 SG CYS E3333 52.833 83.982 55.861 1.00115.69 S Time building chain proxies: 3.14, per 1000 atoms: 0.19 Number of scatterers: 16309 At special positions: 0 Unit cell: (109.787, 121.744, 259.793, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 1 19.99 S 97 16.00 P 1 15.00 O 3060 8.00 N 2787 7.00 C 10362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 209 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 263 " - pdb=" SG CYS D 281 " distance=2.03 Simple disulfide: pdb=" SG CYS D 265 " - pdb=" SG CYS D 288 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 283 " distance=2.03 Simple disulfide: pdb=" SG CYS G 267 " - pdb=" SG CYS G 290 " distance=2.03 Simple disulfide: pdb=" SG CYS O 667 " - pdb=" SG CYS O 711 " distance=2.03 Simple disulfide: pdb=" SG CYS S 128 " - pdb=" SG CYS S 137 " distance=2.03 Simple disulfide: pdb=" SG CYS S 135 " - pdb=" SG CYS S 157 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG P 2 " - " BMA P 3 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG F 1 " - " ASN A 174 " " NAG H 1 " - " ASN A 246 " " NAG J 1 " - " ASN B 160 " " NAG K 1 " - " ASN B 213 " " NAG L 1 " - " ASN B 260 " " NAG M 1 " - " ASN D 108 " " NAG N 1 " - " ASN G 110 " " NAG O 801 " - " ASN O 647 " " NAG P 1 " - " ASN O 659 " " NAG Q 1 " - " ASN O 639 " NAG-THR " NAG A 401 " - " THR A 279 " " NAG A 402 " - " THR A 263 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 742.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E3401 " pdb="ZN ZN E3401 " - pdb=" SG CYS E3309 " pdb="ZN ZN E3401 " - pdb=" SG CYS E3306 " pdb="ZN ZN E3401 " - pdb=" SG CYS E3333 " pdb="ZN ZN E3401 " - pdb=" SG CYS E3330 " Number of angles added : 6 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3914 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 22 sheets defined 35.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 41 through 47 removed outlier: 3.633A pdb=" N PHE A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.591A pdb=" N ARG A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.585A pdb=" N LEU A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.575A pdb=" N ALA A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 removed outlier: 3.778A pdb=" N GLY A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.872A pdb=" N TYR A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 314 removed outlier: 4.743A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'B' and resid 61 through 93 removed outlier: 3.724A pdb=" N ASN B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 49 Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 78 through 95 removed outlier: 3.778A pdb=" N ARG C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 120 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 143 through 156 Processing helix chain 'C' and resid 163 through 180 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 181 through 182 No H-bonds generated for 'chain 'C' and resid 181 through 182' Processing helix chain 'C' and resid 183 through 188 removed outlier: 3.947A pdb=" N GLY C 188 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 removed outlier: 4.308A pdb=" N ARG C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 219 through 237 Proline residue: C 226 - end of helix Processing helix chain 'D' and resid 29 through 59 removed outlier: 3.633A pdb=" N CYS D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 3078 through 3091 Processing helix chain 'E' and resid 3092 through 3094 No H-bonds generated for 'chain 'E' and resid 3092 through 3094' Processing helix chain 'E' and resid 3096 through 3113 removed outlier: 3.621A pdb=" N ARG E3100 " --> pdb=" O PHE E3096 " (cutoff:3.500A) Processing helix chain 'E' and resid 3118 through 3129 removed outlier: 3.823A pdb=" N HIS E3129 " --> pdb=" O ALA E3125 " (cutoff:3.500A) Processing helix chain 'E' and resid 3139 through 3158 Processing helix chain 'E' and resid 3163 through 3180 Processing helix chain 'E' and resid 3189 through 3200 Processing helix chain 'E' and resid 3204 through 3216 Processing helix chain 'E' and resid 3223 through 3241 removed outlier: 4.274A pdb=" N ILE E3237 " --> pdb=" O ASP E3233 " (cutoff:3.500A) Proline residue: E3238 - end of helix Processing helix chain 'E' and resid 3252 through 3263 Processing helix chain 'E' and resid 3270 through 3279 Processing helix chain 'E' and resid 3280 through 3281 No H-bonds generated for 'chain 'E' and resid 3280 through 3281' Processing helix chain 'E' and resid 3282 through 3285 Processing helix chain 'E' and resid 3286 through 3296 removed outlier: 3.550A pdb=" N LEU E3291 " --> pdb=" O TRP E3287 " (cutoff:3.500A) Processing helix chain 'E' and resid 3330 through 3337 removed outlier: 3.543A pdb=" N GLY E3337 " --> pdb=" O CYS E3333 " (cutoff:3.500A) Processing helix chain 'E' and resid 3357 through 3372 Processing helix chain 'G' and resid 30 through 61 removed outlier: 4.095A pdb=" N LEU G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 528 through 532 Processing helix chain 'O' and resid 614 through 619 Processing helix chain 'O' and resid 620 through 636 Processing helix chain 'O' and resid 668 through 680 removed outlier: 3.624A pdb=" N ILE O 672 " --> pdb=" O PRO O 668 " (cutoff:3.500A) Processing helix chain 'O' and resid 687 through 695 Processing helix chain 'O' and resid 709 through 712 removed outlier: 3.706A pdb=" N ARG O 712 " --> pdb=" O GLY O 709 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 709 through 712' Processing helix chain 'O' and resid 745 through 772 removed outlier: 4.044A pdb=" N ILE O 753 " --> pdb=" O LEU O 749 " (cutoff:3.500A) Proline residue: O 754 - end of helix Processing helix chain 'S' and resid 24 through 51 removed outlier: 3.945A pdb=" N SER S 51 " --> pdb=" O MET S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 84 removed outlier: 3.812A pdb=" N TYR S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 124 removed outlier: 3.784A pdb=" N PHE S 92 " --> pdb=" O THR S 88 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE S 97 " --> pdb=" O SER S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 194 removed outlier: 3.582A pdb=" N THR S 163 " --> pdb=" O SER S 159 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS S 165 " --> pdb=" O THR S 161 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU S 166 " --> pdb=" O GLY S 162 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET S 189 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP S 190 " --> pdb=" O CYS S 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.779A pdb=" N GLY A 99 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 177 removed outlier: 5.766A pdb=" N LEU A 172 " --> pdb=" O GLY A 201 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLY A 201 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 174 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 112 removed outlier: 6.582A pdb=" N LEU B 110 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER D 82 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 129 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY G 124 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 171 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 174 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 180 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 117 removed outlier: 6.472A pdb=" N SER B 116 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU D 88 " --> pdb=" O ARG G 96 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN B 142 " --> pdb=" O SER G 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 141 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR D 122 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL D 131 " --> pdb=" O GLN G 141 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN G 143 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA D 133 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 75 through 77 removed outlier: 5.871A pdb=" N LEU D 76 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU G 87 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 150 removed outlier: 3.690A pdb=" N LEU B 155 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 165 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR B 162 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYS D 141 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 164 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 138 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B 199 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL G 167 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN B 201 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 200 " --> pdb=" O GLU D 178 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE D 177 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASN B 219 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B 218 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU D 202 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 220 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 199 " --> pdb=" O HIS G 210 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS G 212 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET D 201 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA G 213 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 241 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU D 227 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE B 243 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 237 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 236 removed outlier: 6.339A pdb=" N PHE B 235 " --> pdb=" O MET G 203 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU D 192 " --> pdb=" O ASP G 204 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B 210 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR D 171 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 182 through 183 removed outlier: 7.112A pdb=" N VAL D 207 " --> pdb=" O GLU G 219 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU G 221 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE D 209 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER G 222 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE D 233 " --> pdb=" O GLY G 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 218 through 220 removed outlier: 6.507A pdb=" N ALA D 218 " --> pdb=" O GLN G 229 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE B 257 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 287 through 292 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 297 through 301 current: chain 'D' and resid 270 through 273 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 270 through 273 current: chain 'G' and resid 272 through 276 Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 77 Processing sheet with id=AB4, first strand: chain 'D' and resid 163 through 164 removed outlier: 7.291A pdb=" N LEU D 163 " --> pdb=" O LEU G 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 3066 through 3068 Processing sheet with id=AB6, first strand: chain 'E' and resid 3137 through 3138 removed outlier: 3.584A pdb=" N MET E3138 " --> pdb=" O ILE E3187 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE E3187 " --> pdb=" O MET E3138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 3328 through 3329 Processing sheet with id=AB8, first strand: chain 'G' and resid 67 through 68 Processing sheet with id=AB9, first strand: chain 'O' and resid 504 through 507 removed outlier: 6.437A pdb=" N VAL O 504 " --> pdb=" O HIS O 592 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N HIS O 594 " --> pdb=" O VAL O 504 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA O 506 " --> pdb=" O HIS O 594 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N GLU O 572 " --> pdb=" O ARG O 539 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG O 539 " --> pdb=" O GLU O 572 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG O 539 " --> pdb=" O GLN O 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 512 through 515 Processing sheet with id=AC2, first strand: chain 'O' and resid 643 through 648 removed outlier: 3.576A pdb=" N THR O 644 " --> pdb=" O THR O 658 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLU O 656 " --> pdb=" O GLN O 646 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE O 648 " --> pdb=" O VAL O 654 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL O 654 " --> pdb=" O ILE O 648 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP O 657 " --> pdb=" O PHE O 606 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN O 659 " --> pdb=" O ALA O 604 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA O 604 " --> pdb=" O ASN O 659 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG O 605 " --> pdb=" O THR O 706 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER O 702 " --> pdb=" O ARG O 609 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA O 611 " --> pdb=" O ALA O 700 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA O 700 " --> pdb=" O ALA O 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 776 through 778 removed outlier: 4.119A pdb=" N PHE S 197 " --> pdb=" O LYS O 776 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS O 778 " --> pdb=" O PHE S 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'S' and resid 137 through 138 669 hydrogen bonds defined for protein. 1920 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: 2.55 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2691 1.32 - 1.44: 4242 1.44 - 1.57: 9558 1.57 - 1.69: 3 1.69 - 1.82: 140 Bond restraints: 16634 Sorted by residual: bond pdb=" C20 P5S G 301 " pdb=" C21 P5S G 301 " ideal model delta sigma weight residual 1.540 1.501 0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" CB GLN E3072 " pdb=" CG GLN E3072 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.43e+00 bond pdb=" C42 P5S G 301 " pdb=" C43 P5S G 301 " ideal model delta sigma weight residual 1.538 1.504 0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 ... (remaining 16629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 22247 2.38 - 4.76: 291 4.76 - 7.14: 56 7.14 - 9.52: 13 9.52 - 11.90: 5 Bond angle restraints: 22612 Sorted by residual: angle pdb=" N MET A 312 " pdb=" CA MET A 312 " pdb=" C MET A 312 " ideal model delta sigma weight residual 114.62 105.37 9.25 1.14e+00 7.69e-01 6.58e+01 angle pdb=" C ALA G 186 " pdb=" N ASP G 187 " pdb=" CA ASP G 187 " ideal model delta sigma weight residual 121.80 133.00 -11.20 2.44e+00 1.68e-01 2.11e+01 angle pdb=" CA GLN E3072 " pdb=" CB GLN E3072 " pdb=" CG GLN E3072 " ideal model delta sigma weight residual 114.10 122.53 -8.43 2.00e+00 2.50e-01 1.78e+01 angle pdb=" N ILE O 501 " pdb=" CA ILE O 501 " pdb=" C ILE O 501 " ideal model delta sigma weight residual 111.48 108.13 3.35 9.40e-01 1.13e+00 1.27e+01 angle pdb=" CB MET E3285 " pdb=" CG MET E3285 " pdb=" SD MET E3285 " ideal model delta sigma weight residual 112.70 123.22 -10.52 3.00e+00 1.11e-01 1.23e+01 ... (remaining 22607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 9976 32.54 - 65.08: 495 65.08 - 97.61: 69 97.61 - 130.15: 28 130.15 - 162.69: 2 Dihedral angle restraints: 10570 sinusoidal: 4520 harmonic: 6050 Sorted by residual: dihedral pdb=" CB CYS O 667 " pdb=" SG CYS O 667 " pdb=" SG CYS O 711 " pdb=" CB CYS O 711 " ideal model delta sinusoidal sigma weight residual 93.00 167.38 -74.38 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS S 135 " pdb=" SG CYS S 135 " pdb=" SG CYS S 157 " pdb=" CB CYS S 157 " ideal model delta sinusoidal sigma weight residual 93.00 165.53 -72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 290 " pdb=" SG CYS B 290 " pdb=" SG CYS B 309 " pdb=" CB CYS B 309 " ideal model delta sinusoidal sigma weight residual 93.00 162.96 -69.96 1 1.00e+01 1.00e-02 6.31e+01 ... (remaining 10567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2234 0.055 - 0.110: 388 0.110 - 0.165: 77 0.165 - 0.220: 5 0.220 - 0.275: 7 Chirality restraints: 2711 Sorted by residual: chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2708 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 187 " 0.065 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO G 188 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO G 188 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO G 188 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E3072 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C GLN E3072 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN E3072 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E3073 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E3208 " 0.020 2.00e-02 2.50e+03 1.53e-02 4.69e+00 pdb=" CG TYR E3208 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR E3208 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E3208 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E3208 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E3208 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E3208 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR E3208 " 0.003 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 382 2.68 - 3.24: 15565 3.24 - 3.79: 25025 3.79 - 4.35: 30478 4.35 - 4.90: 51696 Nonbonded interactions: 123146 Sorted by model distance: nonbonded pdb=" O LEU I 213 " pdb=" OH TYR O 773 " model vdw 2.129 3.040 nonbonded pdb=" OD1 ASN E3092 " pdb=" NZ LYS E3104 " model vdw 2.170 3.120 nonbonded pdb=" NE2 GLN G 141 " pdb=" OD1 ASN G 143 " model vdw 2.194 3.120 nonbonded pdb=" O ILE E3252 " pdb=" OG SER E3255 " model vdw 2.204 3.040 nonbonded pdb=" O LEU E3141 " pdb=" ND2 ASN E3145 " model vdw 2.207 3.120 ... (remaining 123141 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 'F' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'J' selection = chain 'Q' } 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 group one per residue 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: 6.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.130 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.056 16677 Z= 0.175 Angle : 0.700 11.897 22722 Z= 0.326 Chirality : 0.046 0.275 2711 Planarity : 0.004 0.099 2852 Dihedral : 19.496 162.688 6623 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.92 % Rotamer: Outliers : 0.24 % Allowed : 34.36 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 2074 helix: 2.45 (0.20), residues: 681 sheet: -0.53 (0.35), residues: 242 loop : -1.33 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 152 TYR 0.037 0.001 TYR E3208 PHE 0.010 0.001 PHE G 151 TRP 0.031 0.001 TRP E3174 HIS 0.003 0.001 HIS G 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (16634) covalent geometry : angle 0.68624 / 0.32 (22612) SS BOND : bond 0.00140 / 0.08 ( 11) SS BOND : angle 1.02571 / 0.63 ( 22) hydrogen bonds : bond 0.12974 / 8.82 ( 669) hydrogen bonds : angle 5.38674 / 3.80 ( 1920) metal coordination : bond 0.00619 / 0.31 ( 4) metal coordination : angle 3.28366 / 2.00 ( 6) link_BETA1-3 : bond 0.01052 / 0.55 ( 3) link_BETA1-3 : angle 1.78948 / 1.06 ( 9) link_BETA1-4 : bond 0.00554 / 0.32 ( 13) link_BETA1-4 : angle 1.45909 / 0.90 ( 39) link_NAG-ASN : bond 0.00363 / 0.18 ( 10) link_NAG-ASN : angle 2.76906 / 1.80 ( 30) link_NAG-THR : bond 0.00341 / 0.17 ( 2) link_NAG-THR : angle 3.47364 / 1.88 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 MET cc_start: 0.2600 (tpt) cc_final: 0.2109 (tmm) REVERT: E 3241 LEU cc_start: 0.8753 (tp) cc_final: 0.8346 (mp) outliers start: 4 outliers final: 4 residues processed: 147 average time/residue: 0.1105 time to fit residues: 25.7046 Evaluate side-chains 142 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain G residue 288 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E3145 ASN E3159 ASN O 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.119714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076797 restraints weight = 34683.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079214 restraints weight = 20450.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080760 restraints weight = 15021.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.081731 restraints weight = 12491.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.082160 restraints weight = 11179.440| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16677 Z= 0.173 Angle : 0.640 10.942 22722 Z= 0.307 Chirality : 0.044 0.187 2711 Planarity : 0.005 0.098 2852 Dihedral : 11.789 144.586 3056 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.73 % Rotamer: Outliers : 3.33 % Allowed : 31.28 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 2074 helix: 2.40 (0.20), residues: 692 sheet: -0.74 (0.34), residues: 257 loop : -1.35 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 152 TYR 0.035 0.001 TYR E3208 PHE 0.013 0.001 PHE S 61 TRP 0.014 0.001 TRP E3174 HIS 0.004 0.001 HIS E3078 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (16634) covalent geometry : angle 0.62070 / 0.30 (22612) SS BOND : bond 0.00184 / 0.12 ( 11) SS BOND : angle 0.87279 / 0.55 ( 22) hydrogen bonds : bond 0.04169 / 2.90 ( 669) hydrogen bonds : angle 4.49099 / 3.18 ( 1920) metal coordination : bond 0.00560 / 0.28 ( 4) metal coordination : angle 3.29528 / 2.27 ( 6) link_BETA1-3 : bond 0.00928 / 0.47 ( 3) link_BETA1-3 : angle 2.96742 / 1.67 ( 9) link_BETA1-4 : bond 0.00868 / 0.50 ( 13) link_BETA1-4 : angle 2.03596 / 1.29 ( 39) link_NAG-ASN : bond 0.00377 / 0.21 ( 10) link_NAG-ASN : angle 2.82850 / 1.82 ( 30) link_NAG-THR : bond 0.00200 / 0.10 ( 2) link_NAG-THR : angle 3.13908 / 1.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8541 (p0) cc_final: 0.8236 (p0) REVERT: D 187 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8410 (t80) REVERT: E 3174 TRP cc_start: 0.9082 (t-100) cc_final: 0.8471 (t-100) REVERT: E 3203 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7839 (t-90) REVERT: S 77 MET cc_start: 0.1507 (tpt) cc_final: 0.1211 (tpt) REVERT: S 94 MET cc_start: 0.8493 (pmm) cc_final: 0.8022 (pmm) REVERT: S 110 MET cc_start: 0.8446 (mmm) cc_final: 0.8122 (tpp) outliers start: 55 outliers final: 36 residues processed: 186 average time/residue: 0.1173 time to fit residues: 34.5901 Evaluate side-chains 170 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain O residue 771 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 189 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 75 optimal weight: 0.0570 chunk 164 optimal weight: 0.0030 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 overall best weight: 0.6910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E3109 GLN E3232 HIS O 646 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.120473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077531 restraints weight = 34734.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079994 restraints weight = 20314.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081565 restraints weight = 14834.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082560 restraints weight = 12310.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083142 restraints weight = 10993.325| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16677 Z= 0.129 Angle : 0.614 12.120 22722 Z= 0.293 Chirality : 0.044 0.233 2711 Planarity : 0.004 0.099 2852 Dihedral : 9.718 147.971 3053 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.40 % Favored : 94.46 % Rotamer: Outliers : 3.45 % Allowed : 31.28 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 2074 helix: 2.46 (0.20), residues: 691 sheet: -0.68 (0.34), residues: 257 loop : -1.30 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 152 TYR 0.016 0.001 TYR S 98 PHE 0.012 0.001 PHE E3262 TRP 0.010 0.001 TRP E3277 HIS 0.003 0.001 HIS E3078 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16634) covalent geometry : angle 0.59545 / 0.29 (22612) SS BOND : bond 0.00307 / 0.16 ( 11) SS BOND : angle 0.72836 / 0.46 ( 22) hydrogen bonds : bond 0.03713 / 2.55 ( 669) hydrogen bonds : angle 4.32720 / 3.05 ( 1920) metal coordination : bond 0.00514 / 0.26 ( 4) metal coordination : angle 2.95888 / 1.99 ( 6) link_BETA1-3 : bond 0.00914 / 0.46 ( 3) link_BETA1-3 : angle 2.74268 / 1.60 ( 9) link_BETA1-4 : bond 0.00663 / 0.39 ( 13) link_BETA1-4 : angle 1.94981 / 1.25 ( 39) link_NAG-ASN : bond 0.00322 / 0.16 ( 10) link_NAG-ASN : angle 2.68564 / 1.74 ( 30) link_NAG-THR : bond 0.00275 / 0.14 ( 2) link_NAG-THR : angle 3.14284 / 1.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8441 (p0) cc_final: 0.8176 (p0) REVERT: D 187 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8373 (t80) REVERT: E 3170 MET cc_start: 0.7691 (mmm) cc_final: 0.7071 (ptt) REVERT: E 3174 TRP cc_start: 0.9096 (t-100) cc_final: 0.8364 (t-100) REVERT: E 3203 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: E 3333 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7278 (m) REVERT: G 235 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7842 (mp) REVERT: S 77 MET cc_start: 0.2189 (tpt) cc_final: 0.1975 (tpt) REVERT: S 94 MET cc_start: 0.8525 (pmm) cc_final: 0.8222 (pmm) REVERT: S 110 MET cc_start: 0.8438 (mmm) cc_final: 0.8131 (tpp) outliers start: 57 outliers final: 33 residues processed: 188 average time/residue: 0.1156 time to fit residues: 34.9342 Evaluate side-chains 168 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3278 MET Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E3232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.118073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075285 restraints weight = 35093.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077571 restraints weight = 21188.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079019 restraints weight = 15805.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079913 restraints weight = 13262.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080425 restraints weight = 11951.228| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16677 Z= 0.251 Angle : 0.674 11.504 22722 Z= 0.330 Chirality : 0.045 0.186 2711 Planarity : 0.005 0.096 2852 Dihedral : 8.525 154.500 3053 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.52 % Favored : 92.33 % Rotamer: Outliers : 5.75 % Allowed : 30.07 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 2074 helix: 2.38 (0.20), residues: 692 sheet: -0.87 (0.33), residues: 266 loop : -1.44 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.018 0.001 TYR S 120 PHE 0.015 0.001 PHE D 149 TRP 0.010 0.001 TRP O 657 HIS 0.007 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.25 (16634) covalent geometry : angle 0.65528 / 0.33 (22612) SS BOND : bond 0.00239 / 0.16 ( 11) SS BOND : angle 1.04809 / 0.66 ( 22) hydrogen bonds : bond 0.04300 / 2.98 ( 669) hydrogen bonds : angle 4.43125 / 3.13 ( 1920) metal coordination : bond 0.01021 / 0.51 ( 4) metal coordination : angle 3.71095 / 2.43 ( 6) link_BETA1-3 : bond 0.00829 / 0.42 ( 3) link_BETA1-3 : angle 2.38644 / 1.36 ( 9) link_BETA1-4 : bond 0.00573 / 0.34 ( 13) link_BETA1-4 : angle 1.96792 / 1.23 ( 39) link_NAG-ASN : bond 0.00499 / 0.29 ( 10) link_NAG-ASN : angle 2.90955 / 1.84 ( 30) link_NAG-THR : bond 0.00368 / 0.18 ( 2) link_NAG-THR : angle 3.08119 / 1.63 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 131 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8421 (p0) cc_final: 0.8143 (p0) REVERT: D 187 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8411 (t80) REVERT: E 3170 MET cc_start: 0.7807 (mmm) cc_final: 0.7083 (ptt) REVERT: E 3174 TRP cc_start: 0.9115 (t-100) cc_final: 0.8446 (t-100) REVERT: E 3203 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7845 (t-90) REVERT: E 3333 CYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7551 (m) REVERT: O 596 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: S 110 MET cc_start: 0.8479 (mmm) cc_final: 0.8166 (tpp) outliers start: 95 outliers final: 64 residues processed: 213 average time/residue: 0.1173 time to fit residues: 39.6465 Evaluate side-chains 192 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 124 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 284 TRP Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3241 LEU Chi-restraints excluded: chain E residue 3274 PHE Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 596 ARG Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 758 VAL Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain O residue 771 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain S residue 189 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 118 optimal weight: 0.0570 chunk 202 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.119416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076460 restraints weight = 34686.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078886 restraints weight = 20506.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080416 restraints weight = 15045.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081360 restraints weight = 12560.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.081949 restraints weight = 11285.064| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16677 Z= 0.157 Angle : 0.623 10.885 22722 Z= 0.301 Chirality : 0.043 0.189 2711 Planarity : 0.004 0.102 2852 Dihedral : 7.832 158.583 3051 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 5.26 % Allowed : 30.55 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.19), residues: 2074 helix: 2.48 (0.20), residues: 691 sheet: -0.89 (0.34), residues: 254 loop : -1.35 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 93 TYR 0.016 0.001 TYR S 120 PHE 0.011 0.001 PHE G 151 TRP 0.011 0.001 TRP E3277 HIS 0.004 0.001 HIS E3292 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16634) covalent geometry : angle 0.60595 / 0.30 (22612) SS BOND : bond 0.00237 / 0.14 ( 11) SS BOND : angle 0.91292 / 0.55 ( 22) hydrogen bonds : bond 0.03814 / 2.61 ( 669) hydrogen bonds : angle 4.30502 / 3.04 ( 1920) metal coordination : bond 0.00684 / 0.34 ( 4) metal coordination : angle 3.38802 / 2.22 ( 6) link_BETA1-3 : bond 0.00879 / 0.44 ( 3) link_BETA1-3 : angle 2.22844 / 1.27 ( 9) link_BETA1-4 : bond 0.00616 / 0.36 ( 13) link_BETA1-4 : angle 1.73714 / 1.08 ( 39) link_NAG-ASN : bond 0.00304 / 0.16 ( 10) link_NAG-ASN : angle 2.67249 / 1.72 ( 30) link_NAG-THR : bond 0.00307 / 0.16 ( 2) link_NAG-THR : angle 3.15860 / 1.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 135 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8421 (p0) cc_final: 0.8140 (p0) REVERT: D 187 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8372 (t80) REVERT: D 208 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: E 3170 MET cc_start: 0.7769 (mmm) cc_final: 0.7072 (ptt) REVERT: E 3174 TRP cc_start: 0.9107 (t-100) cc_final: 0.8464 (t-100) REVERT: E 3203 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7816 (t-90) REVERT: E 3333 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7212 (m) REVERT: G 177 HIS cc_start: 0.8070 (OUTLIER) cc_final: 0.7422 (t-170) REVERT: O 646 GLN cc_start: 0.7428 (mt0) cc_final: 0.7203 (mt0) REVERT: S 54 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7377 (pp) REVERT: S 94 MET cc_start: 0.8407 (pmm) cc_final: 0.8179 (pmm) REVERT: S 110 MET cc_start: 0.8455 (mmm) cc_final: 0.8154 (tpp) outliers start: 87 outliers final: 56 residues processed: 208 average time/residue: 0.1123 time to fit residues: 37.3498 Evaluate side-chains 191 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3274 PHE Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain O residue 501 ILE Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 701 LEU Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain O residue 770 MET Chi-restraints excluded: chain O residue 771 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 118 optimal weight: 0.0670 chunk 149 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3232 HIS O 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.120411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077420 restraints weight = 34679.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079892 restraints weight = 20276.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081459 restraints weight = 14818.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082431 restraints weight = 12317.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083043 restraints weight = 11032.260| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16677 Z= 0.118 Angle : 0.604 11.384 22722 Z= 0.290 Chirality : 0.042 0.192 2711 Planarity : 0.004 0.099 2852 Dihedral : 7.271 163.137 3051 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.98 % Favored : 93.88 % Rotamer: Outliers : 4.84 % Allowed : 31.22 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 2074 helix: 2.52 (0.20), residues: 691 sheet: -0.62 (0.33), residues: 266 loop : -1.31 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.039 0.001 TYR E3208 PHE 0.011 0.001 PHE E3262 TRP 0.015 0.001 TRP E3277 HIS 0.003 0.001 HIS E3292 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16634) covalent geometry : angle 0.58972 / 0.29 (22612) SS BOND : bond 0.00149 / 0.09 ( 11) SS BOND : angle 0.66504 / 0.42 ( 22) hydrogen bonds : bond 0.03492 / 2.39 ( 669) hydrogen bonds : angle 4.18341 / 2.96 ( 1920) metal coordination : bond 0.00471 / 0.24 ( 4) metal coordination : angle 3.12822 / 1.95 ( 6) link_BETA1-3 : bond 0.00891 / 0.45 ( 3) link_BETA1-3 : angle 2.08292 / 1.19 ( 9) link_BETA1-4 : bond 0.00629 / 0.36 ( 13) link_BETA1-4 : angle 1.59684 / 0.98 ( 39) link_NAG-ASN : bond 0.00253 / 0.13 ( 10) link_NAG-ASN : angle 2.48232 / 1.61 ( 30) link_NAG-THR : bond 0.00337 / 0.18 ( 2) link_NAG-THR : angle 3.16549 / 1.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 138 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7564 (p) REVERT: B 291 MET cc_start: 0.7987 (tpt) cc_final: 0.7610 (tpt) REVERT: D 116 ASP cc_start: 0.8435 (p0) cc_final: 0.8163 (p0) REVERT: D 187 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8408 (t80) REVERT: E 3170 MET cc_start: 0.7776 (mmm) cc_final: 0.7197 (ptt) REVERT: E 3174 TRP cc_start: 0.9097 (OUTLIER) cc_final: 0.8762 (t60) REVERT: E 3203 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7657 (t-90) REVERT: E 3241 LEU cc_start: 0.8935 (tp) cc_final: 0.8677 (mt) REVERT: E 3333 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7091 (m) REVERT: G 177 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7350 (t-170) REVERT: S 110 MET cc_start: 0.8459 (mmm) cc_final: 0.8158 (tpp) outliers start: 80 outliers final: 56 residues processed: 206 average time/residue: 0.1109 time to fit residues: 36.7749 Evaluate side-chains 193 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 501 ILE Chi-restraints excluded: chain O residue 535 THR Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain O residue 770 MET Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 111 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.120277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077351 restraints weight = 34474.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079804 restraints weight = 20265.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081377 restraints weight = 14868.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082352 restraints weight = 12364.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082951 restraints weight = 11075.062| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16677 Z= 0.129 Angle : 0.619 12.597 22722 Z= 0.296 Chirality : 0.043 0.239 2711 Planarity : 0.004 0.100 2852 Dihedral : 6.951 164.494 3051 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.50 % Favored : 94.36 % Rotamer: Outliers : 4.90 % Allowed : 31.28 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 2074 helix: 2.52 (0.20), residues: 691 sheet: -0.50 (0.35), residues: 252 loop : -1.29 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 152 TYR 0.038 0.001 TYR E3208 PHE 0.011 0.001 PHE G 151 TRP 0.015 0.001 TRP E3277 HIS 0.003 0.001 HIS E3078 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16634) covalent geometry : angle 0.60484 / 0.29 (22612) SS BOND : bond 0.00125 / 0.08 ( 11) SS BOND : angle 0.83995 / 0.51 ( 22) hydrogen bonds : bond 0.03506 / 2.41 ( 669) hydrogen bonds : angle 4.17355 / 2.95 ( 1920) metal coordination : bond 0.00509 / 0.25 ( 4) metal coordination : angle 3.18028 / 1.99 ( 6) link_BETA1-3 : bond 0.00896 / 0.45 ( 3) link_BETA1-3 : angle 2.00030 / 1.14 ( 9) link_BETA1-4 : bond 0.00616 / 0.36 ( 13) link_BETA1-4 : angle 1.57237 / 0.97 ( 39) link_NAG-ASN : bond 0.00255 / 0.14 ( 10) link_NAG-ASN : angle 2.57201 / 1.67 ( 30) link_NAG-THR : bond 0.00333 / 0.18 ( 2) link_NAG-THR : angle 3.15493 / 1.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 137 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 26 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7664 (p) REVERT: B 291 MET cc_start: 0.7977 (tpt) cc_final: 0.7596 (tpt) REVERT: D 187 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8377 (t80) REVERT: E 3170 MET cc_start: 0.7990 (mmm) cc_final: 0.7246 (ptt) REVERT: E 3174 TRP cc_start: 0.9104 (OUTLIER) cc_final: 0.8704 (t60) REVERT: E 3203 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7687 (t-90) REVERT: E 3241 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8677 (mt) REVERT: E 3333 CYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7077 (m) REVERT: G 177 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7340 (t-170) REVERT: S 94 MET cc_start: 0.8352 (pmm) cc_final: 0.7914 (pmm) REVERT: S 110 MET cc_start: 0.8464 (mmm) cc_final: 0.8149 (tpp) REVERT: S 171 GLN cc_start: 0.6468 (tm-30) cc_final: 0.6235 (tm-30) outliers start: 81 outliers final: 62 residues processed: 204 average time/residue: 0.1132 time to fit residues: 37.1435 Evaluate side-chains 199 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 130 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3241 LEU Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 501 ILE Chi-restraints excluded: chain O residue 535 THR Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain O residue 770 MET Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 189 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 123 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 64 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E3232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.118810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.076099 restraints weight = 35193.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078441 restraints weight = 21025.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079945 restraints weight = 15582.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080818 restraints weight = 13038.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081457 restraints weight = 11745.851| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16677 Z= 0.198 Angle : 0.659 13.644 22722 Z= 0.318 Chirality : 0.044 0.265 2711 Planarity : 0.004 0.099 2852 Dihedral : 6.784 165.411 3051 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.99 % Favored : 92.91 % Rotamer: Outliers : 4.96 % Allowed : 31.09 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 2074 helix: 2.43 (0.20), residues: 691 sheet: -0.64 (0.34), residues: 266 loop : -1.36 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 152 TYR 0.036 0.001 TYR E3208 PHE 0.012 0.001 PHE G 151 TRP 0.015 0.001 TRP E3277 HIS 0.004 0.001 HIS E3078 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (16634) covalent geometry : angle 0.64480 / 0.32 (22612) SS BOND : bond 0.00265 / 0.14 ( 11) SS BOND : angle 0.81342 / 0.51 ( 22) hydrogen bonds : bond 0.03869 / 2.66 ( 669) hydrogen bonds : angle 4.25952 / 3.02 ( 1920) metal coordination : bond 0.00846 / 0.42 ( 4) metal coordination : angle 3.66810 / 2.38 ( 6) link_BETA1-3 : bond 0.00887 / 0.45 ( 3) link_BETA1-3 : angle 1.94122 / 1.12 ( 9) link_BETA1-4 : bond 0.00577 / 0.34 ( 13) link_BETA1-4 : angle 1.60789 / 0.98 ( 39) link_NAG-ASN : bond 0.00377 / 0.22 ( 10) link_NAG-ASN : angle 2.59516 / 1.68 ( 30) link_NAG-THR : bond 0.00336 / 0.17 ( 2) link_NAG-THR : angle 3.12385 / 1.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 134 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7675 (p) REVERT: B 291 MET cc_start: 0.7945 (tpt) cc_final: 0.7581 (tpt) REVERT: D 59 MET cc_start: 0.9285 (tpp) cc_final: 0.9060 (tpt) REVERT: D 187 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8388 (t80) REVERT: E 3170 MET cc_start: 0.7971 (mmm) cc_final: 0.7251 (ptt) REVERT: E 3174 TRP cc_start: 0.9115 (OUTLIER) cc_final: 0.8672 (t60) REVERT: E 3203 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7731 (t-90) REVERT: E 3333 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7272 (m) REVERT: G 177 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7416 (t-170) REVERT: G 246 LYS cc_start: 0.8723 (tptt) cc_final: 0.8348 (tptp) REVERT: S 94 MET cc_start: 0.8302 (pmm) cc_final: 0.7910 (pmm) REVERT: S 110 MET cc_start: 0.8496 (mmm) cc_final: 0.8197 (tpp) REVERT: S 171 GLN cc_start: 0.6689 (tm-30) cc_final: 0.6456 (tm-30) outliers start: 82 outliers final: 63 residues processed: 204 average time/residue: 0.1106 time to fit residues: 36.4936 Evaluate side-chains 197 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 128 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 535 THR Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain S residue 189 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E3232 HIS ** S 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.119270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076423 restraints weight = 34823.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078841 restraints weight = 20529.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080390 restraints weight = 15085.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081312 restraints weight = 12572.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.081920 restraints weight = 11309.356| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16677 Z= 0.167 Angle : 0.658 14.160 22722 Z= 0.317 Chirality : 0.043 0.253 2711 Planarity : 0.004 0.101 2852 Dihedral : 6.558 163.657 3051 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 4.60 % Allowed : 31.40 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2074 helix: 2.42 (0.20), residues: 691 sheet: -0.65 (0.33), residues: 266 loop : -1.36 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 152 TYR 0.036 0.001 TYR E3208 PHE 0.011 0.001 PHE G 151 TRP 0.020 0.001 TRP E3277 HIS 0.004 0.001 HIS E3292 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16634) covalent geometry : angle 0.64318 / 0.31 (22612) SS BOND : bond 0.00318 / 0.15 ( 11) SS BOND : angle 1.59698 / 0.91 ( 22) hydrogen bonds : bond 0.03733 / 2.57 ( 669) hydrogen bonds : angle 4.22606 / 2.99 ( 1920) metal coordination : bond 0.00679 / 0.34 ( 4) metal coordination : angle 3.43023 / 2.20 ( 6) link_BETA1-3 : bond 0.00882 / 0.45 ( 3) link_BETA1-3 : angle 1.94629 / 1.12 ( 9) link_BETA1-4 : bond 0.00573 / 0.34 ( 13) link_BETA1-4 : angle 1.54304 / 0.95 ( 39) link_NAG-ASN : bond 0.00299 / 0.17 ( 10) link_NAG-ASN : angle 2.57942 / 1.67 ( 30) link_NAG-THR : bond 0.00329 / 0.17 ( 2) link_NAG-THR : angle 3.13968 / 1.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 134 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7644 (p) REVERT: B 291 MET cc_start: 0.7938 (tpt) cc_final: 0.7570 (tpt) REVERT: D 59 MET cc_start: 0.9305 (tpp) cc_final: 0.9085 (tpt) REVERT: D 187 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8377 (t80) REVERT: E 3170 MET cc_start: 0.8018 (mmm) cc_final: 0.7312 (ptt) REVERT: E 3174 TRP cc_start: 0.9106 (OUTLIER) cc_final: 0.8715 (t60) REVERT: E 3203 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7823 (t-90) REVERT: E 3243 GLU cc_start: 0.8551 (tt0) cc_final: 0.8336 (tt0) REVERT: E 3333 CYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7174 (m) REVERT: G 177 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7388 (t-170) REVERT: S 77 MET cc_start: 0.1609 (tpt) cc_final: 0.1210 (tpt) REVERT: S 94 MET cc_start: 0.8331 (pmm) cc_final: 0.7905 (pmm) REVERT: S 110 MET cc_start: 0.8464 (mmm) cc_final: 0.8165 (tpp) REVERT: S 171 GLN cc_start: 0.6662 (tm-30) cc_final: 0.6068 (tm-30) outliers start: 76 outliers final: 62 residues processed: 200 average time/residue: 0.1192 time to fit residues: 38.2823 Evaluate side-chains 197 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 129 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 61 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 535 THR Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 172 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 201 optimal weight: 0.0070 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 GLN E3232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.119451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076647 restraints weight = 34705.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079059 restraints weight = 20471.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080613 restraints weight = 15070.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.081576 restraints weight = 12546.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.082173 restraints weight = 11248.558| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16677 Z= 0.157 Angle : 0.654 14.093 22722 Z= 0.316 Chirality : 0.043 0.253 2711 Planarity : 0.004 0.100 2852 Dihedral : 6.405 162.964 3051 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.64 % Rotamer: Outliers : 4.36 % Allowed : 31.58 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 2074 helix: 2.38 (0.20), residues: 692 sheet: -0.62 (0.33), residues: 266 loop : -1.34 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E3107 TYR 0.013 0.001 TYR E3208 PHE 0.011 0.001 PHE G 151 TRP 0.023 0.001 TRP E3277 HIS 0.003 0.001 HIS G 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16634) covalent geometry : angle 0.63553 / 0.31 (22612) SS BOND : bond 0.00198 / 0.10 ( 11) SS BOND : angle 2.75948 / 1.46 ( 22) hydrogen bonds : bond 0.03675 / 2.52 ( 669) hydrogen bonds : angle 4.23167 / 2.99 ( 1920) metal coordination : bond 0.00625 / 0.31 ( 4) metal coordination : angle 3.44939 / 2.17 ( 6) link_BETA1-3 : bond 0.00863 / 0.44 ( 3) link_BETA1-3 : angle 1.92878 / 1.11 ( 9) link_BETA1-4 : bond 0.00568 / 0.33 ( 13) link_BETA1-4 : angle 1.51028 / 0.93 ( 39) link_NAG-ASN : bond 0.00310 / 0.17 ( 10) link_NAG-ASN : angle 2.46927 / 1.61 ( 30) link_NAG-THR : bond 0.00326 / 0.17 ( 2) link_NAG-THR : angle 3.14989 / 1.66 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 133 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7671 (p) REVERT: B 291 MET cc_start: 0.7942 (tpt) cc_final: 0.7570 (tpt) REVERT: C 96 MET cc_start: 0.4020 (tpt) cc_final: 0.3249 (tmm) REVERT: D 59 MET cc_start: 0.9283 (tpp) cc_final: 0.9052 (tpt) REVERT: D 187 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8367 (t80) REVERT: E 3170 MET cc_start: 0.7940 (mmm) cc_final: 0.7278 (ptt) REVERT: E 3174 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.8700 (t60) REVERT: E 3203 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7505 (t-90) REVERT: E 3243 GLU cc_start: 0.8542 (tt0) cc_final: 0.8328 (tt0) REVERT: E 3333 CYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7126 (m) REVERT: G 177 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7367 (t-170) REVERT: G 189 PHE cc_start: 0.8419 (m-80) cc_final: 0.8115 (m-80) REVERT: G 246 LYS cc_start: 0.8784 (tptt) cc_final: 0.8444 (tptp) REVERT: S 110 MET cc_start: 0.8472 (mmm) cc_final: 0.8157 (tpp) REVERT: S 171 GLN cc_start: 0.6775 (tm-30) cc_final: 0.6170 (tm-30) outliers start: 72 outliers final: 61 residues processed: 197 average time/residue: 0.1089 time to fit residues: 35.0195 Evaluate side-chains 196 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 129 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 288 CYS Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3197 ILE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 535 THR Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 135 CYS Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 200 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 189 optimal weight: 9.9990 chunk 74 optimal weight: 50.0000 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E3232 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.120005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077090 restraints weight = 34744.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.079552 restraints weight = 20391.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081128 restraints weight = 14959.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082116 restraints weight = 12432.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082650 restraints weight = 11132.788| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16677 Z= 0.136 Angle : 0.640 14.452 22722 Z= 0.307 Chirality : 0.043 0.252 2711 Planarity : 0.004 0.101 2852 Dihedral : 6.274 162.757 3051 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 4.54 % Allowed : 31.40 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 2074 helix: 2.42 (0.20), residues: 691 sheet: -0.50 (0.34), residues: 261 loop : -1.30 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E3107 TYR 0.020 0.001 TYR S 120 PHE 0.010 0.001 PHE G 151 TRP 0.021 0.001 TRP E3277 HIS 0.003 0.001 HIS E3292 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16634) covalent geometry : angle 0.62636 / 0.31 (22612) SS BOND : bond 0.00354 / 0.16 ( 11) SS BOND : angle 0.83935 / 0.51 ( 22) hydrogen bonds : bond 0.03527 / 2.42 ( 669) hydrogen bonds : angle 4.19028 / 2.96 ( 1920) metal coordination : bond 0.00544 / 0.27 ( 4) metal coordination : angle 3.31965 / 2.07 ( 6) link_BETA1-3 : bond 0.00913 / 0.46 ( 3) link_BETA1-3 : angle 1.92762 / 1.11 ( 9) link_BETA1-4 : bond 0.00581 / 0.34 ( 13) link_BETA1-4 : angle 1.47708 / 0.92 ( 39) link_NAG-ASN : bond 0.00236 / 0.13 ( 10) link_NAG-ASN : angle 2.50944 / 1.64 ( 30) link_NAG-THR : bond 0.00332 / 0.17 ( 2) link_NAG-THR : angle 3.15498 / 1.66 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3844.60 seconds wall clock time: 67 minutes 2.08 seconds (4022.08 seconds total)