Starting phenix.real_space_refine on Sun Aug 24 02:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yt8_39568/08_2025/8yt8_39568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yt8_39568/08_2025/8yt8_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yt8_39568/08_2025/8yt8_39568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yt8_39568/08_2025/8yt8_39568_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yt8_39568/08_2025/8yt8_39568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yt8_39568/08_2025/8yt8_39568.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.78, per 1000 atoms: 0.23 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: 1.39 Conformation dependent library (CDL) restraints added in 654.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.59 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: 3.15 Time building geometry restraints manager: 1.84 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: 5.290 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 aren 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 covalent geometry : bond 0.00376 (16634) covalent geometry : angle 0.68624 (22612) SS BOND : bond 0.00140 ( 11) SS BOND : angle 1.02571 ( 22) hydrogen bonds : bond 0.12974 ( 669) hydrogen bonds : angle 5.38674 ( 1920) metal coordination : bond 0.00619 ( 4) metal coordination : angle 3.28366 ( 6) link_BETA1-3 : bond 0.01052 ( 3) link_BETA1-3 : angle 1.78948 ( 9) link_BETA1-4 : bond 0.00554 ( 13) link_BETA1-4 : angle 1.45909 ( 39) link_NAG-ASN : bond 0.00363 ( 10) link_NAG-ASN : angle 2.76906 ( 30) link_NAG-THR : bond 0.00341 ( 2) link_NAG-THR : angle 3.47364 ( 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 : 0.460 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: 0.1151 time to fit residues: 26.4653 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 : 0.730 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.119724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076749 restraints weight = 34670.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079174 restraints weight = 20455.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080722 restraints weight = 15006.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.081669 restraints weight = 12487.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081987 restraints weight = 11202.964| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0686 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= 0.172 Angle : 0.643 10.965 22722 Z= 0.309 Chirality : 0.044 0.186 2711 Planarity : 0.005 0.098 2852 Dihedral : 11.677 144.842 3056 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.36 % Favored : 93.49 % Rotamer: Outliers : 3.57 % Allowed : 31.09 % Favored : 65.34 % 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 aren not related in a simple way. whole: 0.06 (0.19), residues: 2074 helix: 2.39 (0.20), residues: 692 sheet: -0.73 (0.34), residues: 257 loop : -1.35 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 152 TYR 0.036 0.001 TYR E3208 PHE 0.013 0.001 PHE S 61 TRP 0.015 0.001 TRP E3174 HIS 0.004 0.001 HIS E3078 Details of bonding type rmsd covalent geometry : bond 0.00393 (16634) covalent geometry : angle 0.62305 (22612) SS BOND : bond 0.00246 ( 11) SS BOND : angle 0.88560 ( 22) hydrogen bonds : bond 0.04035 ( 669) hydrogen bonds : angle 4.47062 ( 1920) metal coordination : bond 0.00592 ( 4) metal coordination : angle 3.32270 ( 6) link_BETA1-3 : bond 0.00836 ( 3) link_BETA1-3 : angle 3.10313 ( 9) link_BETA1-4 : bond 0.00759 ( 13) link_BETA1-4 : angle 2.11951 ( 39) link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 2.84431 ( 30) link_NAG-THR : bond 0.00192 ( 2) link_NAG-THR : angle 3.11909 ( 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 200 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8554 (p0) cc_final: 0.8249 (p0) REVERT: D 187 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8419 (t80) REVERT: E 3174 TRP cc_start: 0.9078 (t-100) cc_final: 0.8458 (t-100) REVERT: E 3203 HIS cc_start: 0.8062 (OUTLIER) cc_final: 0.7850 (t-90) REVERT: E 3333 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7453 (m) REVERT: S 53 SER cc_start: 0.7025 (OUTLIER) cc_final: 0.6817 (m) REVERT: S 77 MET cc_start: 0.1503 (tpt) cc_final: 0.1210 (tpt) REVERT: S 94 MET cc_start: 0.8531 (pmm) cc_final: 0.8084 (pmm) REVERT: S 110 MET cc_start: 0.8447 (mmm) cc_final: 0.8123 (tpp) outliers start: 59 outliers final: 36 residues processed: 189 average time/residue: 0.0922 time to fit residues: 27.4490 Evaluate side-chains 172 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 E residue 3333 CYS 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 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 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 53 SER 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: 0.8980 chunk 164 optimal weight: 1.9990 chunk 128 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 184 optimal weight: 0.4980 chunk 131 optimal weight: 5.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.121090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.078051 restraints weight = 34644.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080519 restraints weight = 20351.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.082087 restraints weight = 14898.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083069 restraints weight = 12397.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.083666 restraints weight = 11097.546| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16677 Z= 0.113 Angle : 0.607 12.341 22722 Z= 0.288 Chirality : 0.043 0.218 2711 Planarity : 0.004 0.093 2852 Dihedral : 9.635 147.803 3053 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 2.96 % Allowed : 32.00 % Favored : 65.03 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 2074 helix: 2.48 (0.20), residues: 691 sheet: -0.66 (0.34), residues: 257 loop : -1.27 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 132 TYR 0.016 0.001 TYR S 98 PHE 0.011 0.001 PHE E3262 TRP 0.009 0.001 TRP E3277 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00247 (16634) covalent geometry : angle 0.58881 (22612) SS BOND : bond 0.00166 ( 11) SS BOND : angle 0.78127 ( 22) hydrogen bonds : bond 0.03576 ( 669) hydrogen bonds : angle 4.29285 ( 1920) metal coordination : bond 0.00439 ( 4) metal coordination : angle 2.89514 ( 6) link_BETA1-3 : bond 0.00933 ( 3) link_BETA1-3 : angle 2.75699 ( 9) link_BETA1-4 : bond 0.00704 ( 13) link_BETA1-4 : angle 1.94297 ( 39) link_NAG-ASN : bond 0.00310 ( 10) link_NAG-ASN : angle 2.64952 ( 30) link_NAG-THR : bond 0.00283 ( 2) link_NAG-THR : angle 3.13904 ( 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 192 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8491 (p0) cc_final: 0.8218 (p0) REVERT: D 187 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8352 (t80) REVERT: E 3170 MET cc_start: 0.7705 (mmm) cc_final: 0.7095 (ptt) REVERT: E 3174 TRP cc_start: 0.9095 (t-100) cc_final: 0.8367 (t-100) REVERT: E 3203 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7606 (t-90) REVERT: G 83 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: G 235 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7817 (mp) REVERT: S 94 MET cc_start: 0.8518 (pmm) cc_final: 0.8213 (pmm) REVERT: S 110 MET cc_start: 0.8436 (mmm) cc_final: 0.8135 (tpp) outliers start: 49 outliers final: 26 residues processed: 180 average time/residue: 0.1086 time to fit residues: 31.0614 Evaluate side-chains 161 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 86 LEU 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 78 LEU 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 G residue 83 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 92 PHE 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: 0.4980 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 148 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075272 restraints weight = 35139.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077562 restraints weight = 21261.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.079012 restraints weight = 15815.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.079912 restraints weight = 13270.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080418 restraints weight = 11960.607| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16677 Z= 0.263 Angle : 0.680 11.556 22722 Z= 0.333 Chirality : 0.045 0.184 2711 Planarity : 0.005 0.092 2852 Dihedral : 8.634 153.693 3053 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.33 % Favored : 92.53 % Rotamer: Outliers : 5.51 % Allowed : 30.13 % Favored : 64.37 % 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 aren not related in a simple way. whole: -0.00 (0.19), residues: 2074 helix: 2.40 (0.20), residues: 692 sheet: -0.84 (0.33), residues: 266 loop : -1.42 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 152 TYR 0.018 0.001 TYR S 120 PHE 0.015 0.001 PHE D 84 TRP 0.010 0.001 TRP O 657 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00611 (16634) covalent geometry : angle 0.66179 (22612) SS BOND : bond 0.00233 ( 11) SS BOND : angle 1.07984 ( 22) hydrogen bonds : bond 0.04282 ( 669) hydrogen bonds : angle 4.42669 ( 1920) metal coordination : bond 0.01022 ( 4) metal coordination : angle 3.74436 ( 6) link_BETA1-3 : bond 0.00822 ( 3) link_BETA1-3 : angle 2.45231 ( 9) link_BETA1-4 : bond 0.00609 ( 13) link_BETA1-4 : angle 1.98740 ( 39) link_NAG-ASN : bond 0.00516 ( 10) link_NAG-ASN : angle 2.92593 ( 30) link_NAG-THR : bond 0.00367 ( 2) link_NAG-THR : angle 3.05472 ( 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 221 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 130 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8443 (p0) cc_final: 0.8117 (p0) REVERT: D 187 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8400 (t80) REVERT: E 3170 MET cc_start: 0.7812 (mmm) cc_final: 0.7116 (ptt) REVERT: E 3174 TRP cc_start: 0.9118 (t-100) cc_final: 0.8462 (t-100) REVERT: E 3203 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7783 (t-90) REVERT: E 3333 CYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7493 (m) REVERT: S 94 MET cc_start: 0.8469 (pmm) cc_final: 0.8245 (pmm) REVERT: S 110 MET cc_start: 0.8478 (mmm) cc_final: 0.8164 (tpp) outliers start: 91 outliers final: 60 residues processed: 208 average time/residue: 0.0998 time to fit residues: 32.6502 Evaluate side-chains 187 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 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 126 VAL 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 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 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 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: 2.9990 chunk 202 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 183 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4038 r_free = 0.4038 target = 0.119909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076928 restraints weight = 34603.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079383 restraints weight = 20342.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080933 restraints weight = 14912.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081822 restraints weight = 12420.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082466 restraints weight = 11164.159| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16677 Z= 0.134 Angle : 0.609 11.064 22722 Z= 0.294 Chirality : 0.043 0.189 2711 Planarity : 0.004 0.099 2852 Dihedral : 7.857 156.931 3051 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 4.96 % Allowed : 30.85 % 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 aren not related in a simple way. whole: 0.14 (0.19), residues: 2074 helix: 2.50 (0.20), residues: 691 sheet: -0.73 (0.33), residues: 266 loop : -1.33 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.011 0.001 TYR E3208 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 covalent geometry : bond 0.00301 (16634) covalent geometry : angle 0.59216 (22612) SS BOND : bond 0.00225 ( 11) SS BOND : angle 0.83911 ( 22) hydrogen bonds : bond 0.03698 ( 669) hydrogen bonds : angle 4.26772 ( 1920) metal coordination : bond 0.00541 ( 4) metal coordination : angle 3.28700 ( 6) link_BETA1-3 : bond 0.00878 ( 3) link_BETA1-3 : angle 2.28776 ( 9) link_BETA1-4 : bond 0.00632 ( 13) link_BETA1-4 : angle 1.74371 ( 39) link_NAG-ASN : bond 0.00278 ( 10) link_NAG-ASN : angle 2.64457 ( 30) link_NAG-THR : bond 0.00312 ( 2) link_NAG-THR : angle 3.15157 ( 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 219 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 137 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8406 (p0) cc_final: 0.8092 (p0) REVERT: D 187 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8388 (t80) REVERT: D 208 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: E 3170 MET cc_start: 0.7772 (mmm) cc_final: 0.7045 (ptt) REVERT: E 3174 TRP cc_start: 0.9112 (t-100) cc_final: 0.8692 (t60) REVERT: E 3203 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: E 3333 CYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7162 (m) REVERT: G 177 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7407 (t-170) REVERT: O 646 GLN cc_start: 0.7473 (mt0) cc_final: 0.7250 (mt0) REVERT: S 110 MET cc_start: 0.8448 (mmm) cc_final: 0.8147 (tpp) outliers start: 82 outliers final: 47 residues processed: 203 average time/residue: 0.0941 time to fit residues: 30.3819 Evaluate side-chains 183 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 C residue 98 THR 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 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 3241 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 60 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 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 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 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 118 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 111 optimal weight: 0.3980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 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 = 0.4038 r_free = 0.4038 target = 0.119929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076828 restraints weight = 34726.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079273 restraints weight = 20417.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080779 restraints weight = 14976.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081807 restraints weight = 12462.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082413 restraints weight = 11179.032| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16677 Z= 0.140 Angle : 0.613 11.293 22722 Z= 0.295 Chirality : 0.043 0.190 2711 Planarity : 0.004 0.098 2852 Dihedral : 7.419 161.935 3051 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.22 % Favored : 93.64 % Rotamer: Outliers : 4.48 % Allowed : 31.34 % 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 aren not related in a simple way. whole: 0.17 (0.19), residues: 2074 helix: 2.52 (0.20), residues: 691 sheet: -0.67 (0.33), residues: 266 loop : -1.32 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 152 TYR 0.041 0.001 TYR E3208 PHE 0.010 0.001 PHE G 151 TRP 0.013 0.001 TRP E3277 HIS 0.003 0.001 HIS G 139 Details of bonding type rmsd covalent geometry : bond 0.00318 (16634) covalent geometry : angle 0.59832 (22612) SS BOND : bond 0.00140 ( 11) SS BOND : angle 0.75595 ( 22) hydrogen bonds : bond 0.03616 ( 669) hydrogen bonds : angle 4.22048 ( 1920) metal coordination : bond 0.00585 ( 4) metal coordination : angle 3.22855 ( 6) link_BETA1-3 : bond 0.00846 ( 3) link_BETA1-3 : angle 2.10036 ( 9) link_BETA1-4 : bond 0.00614 ( 13) link_BETA1-4 : angle 1.64308 ( 39) link_NAG-ASN : bond 0.00284 ( 10) link_NAG-ASN : angle 2.55682 ( 30) link_NAG-THR : bond 0.00318 ( 2) link_NAG-THR : angle 3.14493 ( 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 208 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 134 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7548 (p) REVERT: D 116 ASP cc_start: 0.8387 (p0) cc_final: 0.8067 (p0) REVERT: D 187 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8380 (t80) REVERT: E 3170 MET cc_start: 0.7787 (mmm) cc_final: 0.7184 (ptt) REVERT: E 3174 TRP cc_start: 0.9103 (t-100) cc_final: 0.8746 (t60) REVERT: E 3203 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: E 3241 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8673 (mt) REVERT: G 177 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7375 (t-170) REVERT: O 646 GLN cc_start: 0.7457 (mt0) cc_final: 0.7243 (mt0) REVERT: S 94 MET cc_start: 0.8432 (pmm) cc_final: 0.8208 (pmm) REVERT: S 110 MET cc_start: 0.8463 (mmm) cc_final: 0.8163 (tpp) outliers start: 74 outliers final: 56 residues processed: 199 average time/residue: 0.0904 time to fit residues: 28.4832 Evaluate side-chains 191 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 130 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 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 262 VAL 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 3291 LEU 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 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 G residue 288 HIS Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 640 CYS 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 S residue 38 ILE 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: 5.9990 chunk 156 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 chunk 99 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 14 optimal weight: 0.0770 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4063 r_free = 0.4063 target = 0.121568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.078672 restraints weight = 34255.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.081194 restraints weight = 19967.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082817 restraints weight = 14566.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083821 restraints weight = 12042.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.084383 restraints weight = 10769.954| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16677 Z= 0.101 Angle : 0.611 12.446 22722 Z= 0.289 Chirality : 0.042 0.250 2711 Planarity : 0.004 0.099 2852 Dihedral : 6.845 163.291 3051 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.16 % Favored : 94.70 % Rotamer: Outliers : 3.93 % Allowed : 32.06 % 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 aren not related in a simple way. whole: 0.33 (0.19), residues: 2074 helix: 2.58 (0.20), residues: 693 sheet: -0.44 (0.35), residues: 251 loop : -1.21 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 152 TYR 0.038 0.001 TYR E3208 PHE 0.010 0.001 PHE E3262 TRP 0.017 0.001 TRP E3277 HIS 0.003 0.001 HIS E3078 Details of bonding type rmsd covalent geometry : bond 0.00215 (16634) covalent geometry : angle 0.59754 (22612) SS BOND : bond 0.00244 ( 11) SS BOND : angle 0.67309 ( 22) hydrogen bonds : bond 0.03231 ( 669) hydrogen bonds : angle 4.09451 ( 1920) metal coordination : bond 0.00352 ( 4) metal coordination : angle 2.85897 ( 6) link_BETA1-3 : bond 0.00876 ( 3) link_BETA1-3 : angle 2.05594 ( 9) link_BETA1-4 : bond 0.00663 ( 13) link_BETA1-4 : angle 1.52145 ( 39) link_NAG-ASN : bond 0.00265 ( 10) link_NAG-ASN : angle 2.48670 ( 30) link_NAG-THR : bond 0.00367 ( 2) link_NAG-THR : angle 3.19611 ( 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 209 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 MET cc_start: 0.7909 (tpt) cc_final: 0.7501 (tpt) REVERT: D 59 MET cc_start: 0.9285 (tpp) cc_final: 0.8763 (tpt) REVERT: D 187 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8336 (t80) REVERT: E 3174 TRP cc_start: 0.9097 (t-100) cc_final: 0.8709 (t60) REVERT: E 3203 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7503 (t-90) REVERT: E 3241 LEU cc_start: 0.8864 (tp) cc_final: 0.8629 (mt) REVERT: E 3333 CYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6946 (m) REVERT: S 94 MET cc_start: 0.8362 (pmm) cc_final: 0.8150 (pmm) REVERT: S 110 MET cc_start: 0.8519 (mmm) cc_final: 0.8095 (tpp) outliers start: 65 outliers final: 44 residues processed: 198 average time/residue: 0.1049 time to fit residues: 32.9589 Evaluate side-chains 180 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 218 SER 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 73 LEU 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 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 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 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 68 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 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 92 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 123 optimal weight: 0.0040 chunk 58 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 177 optimal weight: 0.0670 chunk 64 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 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 = 0.4042 r_free = 0.4042 target = 0.120117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077114 restraints weight = 34987.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079526 restraints weight = 20867.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.081054 restraints weight = 15422.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082018 restraints weight = 12881.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082609 restraints weight = 11576.594| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16677 Z= 0.162 Angle : 0.631 12.991 22722 Z= 0.302 Chirality : 0.043 0.275 2711 Planarity : 0.004 0.098 2852 Dihedral : 6.661 163.782 3051 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.92 % Rotamer: Outliers : 3.87 % Allowed : 31.76 % Favored : 64.37 % 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 aren not related in a simple way. whole: 0.24 (0.19), residues: 2074 helix: 2.51 (0.20), residues: 693 sheet: -0.52 (0.35), residues: 256 loop : -1.26 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 47 TYR 0.037 0.001 TYR E3208 PHE 0.012 0.001 PHE G 151 TRP 0.017 0.001 TRP E3277 HIS 0.003 0.001 HIS E3078 Details of bonding type rmsd covalent geometry : bond 0.00373 (16634) covalent geometry : angle 0.61730 (22612) SS BOND : bond 0.00125 ( 11) SS BOND : angle 0.85587 ( 22) hydrogen bonds : bond 0.03511 ( 669) hydrogen bonds : angle 4.13171 ( 1920) metal coordination : bond 0.00591 ( 4) metal coordination : angle 3.21645 ( 6) link_BETA1-3 : bond 0.00867 ( 3) link_BETA1-3 : angle 1.93107 ( 9) link_BETA1-4 : bond 0.00586 ( 13) link_BETA1-4 : angle 1.56722 ( 39) link_NAG-ASN : bond 0.00288 ( 10) link_NAG-ASN : angle 2.50042 ( 30) link_NAG-THR : bond 0.00314 ( 2) link_NAG-THR : angle 3.10172 ( 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 199 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 135 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.9300 (tpp) cc_final: 0.9052 (tpt) REVERT: D 116 ASP cc_start: 0.8434 (p0) cc_final: 0.8169 (p0) REVERT: D 187 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8397 (t80) REVERT: E 3138 MET cc_start: 0.7088 (mmm) cc_final: 0.6879 (mmm) REVERT: E 3170 MET cc_start: 0.8003 (mmm) cc_final: 0.7336 (ptt) REVERT: E 3174 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8686 (t60) REVERT: E 3203 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7674 (t-90) REVERT: G 177 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7366 (t-170) REVERT: G 246 LYS cc_start: 0.8642 (tptt) cc_final: 0.8253 (tptp) REVERT: S 110 MET cc_start: 0.8550 (mmm) cc_final: 0.8233 (tpp) outliers start: 64 outliers final: 51 residues processed: 189 average time/residue: 0.1005 time to fit residues: 30.6365 Evaluate side-chains 182 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 ILE 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 187 PHE Chi-restraints excluded: chain D residue 262 VAL 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 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 191 ASP 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3232 HIS ** G 156 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 = 0.4017 r_free = 0.4017 target = 0.118396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075606 restraints weight = 35057.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077925 restraints weight = 21188.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079402 restraints weight = 15794.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080315 restraints weight = 13258.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.080865 restraints weight = 11953.485| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16677 Z= 0.232 Angle : 0.684 13.516 22722 Z= 0.331 Chirality : 0.045 0.247 2711 Planarity : 0.005 0.100 2852 Dihedral : 6.607 163.775 3051 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.18 % Favored : 92.72 % Rotamer: Outliers : 4.30 % Allowed : 31.52 % 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 aren not related in a simple way. whole: 0.06 (0.19), residues: 2074 helix: 2.36 (0.20), residues: 692 sheet: -0.66 (0.34), residues: 266 loop : -1.37 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E3107 TYR 0.035 0.001 TYR E3208 PHE 0.013 0.001 PHE S 197 TRP 0.016 0.002 TRP E3277 HIS 0.004 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00536 (16634) covalent geometry : angle 0.66910 (22612) SS BOND : bond 0.00191 ( 11) SS BOND : angle 1.16590 ( 22) hydrogen bonds : bond 0.03992 ( 669) hydrogen bonds : angle 4.28397 ( 1920) metal coordination : bond 0.01013 ( 4) metal coordination : angle 3.68572 ( 6) link_BETA1-3 : bond 0.00888 ( 3) link_BETA1-3 : angle 1.90045 ( 9) link_BETA1-4 : bond 0.00530 ( 13) link_BETA1-4 : angle 1.59805 ( 39) link_NAG-ASN : bond 0.00457 ( 10) link_NAG-ASN : angle 2.73245 ( 30) link_NAG-THR : bond 0.00349 ( 2) link_NAG-THR : angle 3.10363 ( 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 202 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7638 (p) REVERT: B 291 MET cc_start: 0.8406 (tpt) cc_final: 0.7174 (tpt) REVERT: D 116 ASP cc_start: 0.8358 (p0) cc_final: 0.8045 (p0) REVERT: D 187 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8423 (t80) REVERT: E 3138 MET cc_start: 0.7143 (mmm) cc_final: 0.6904 (mmm) REVERT: E 3170 MET cc_start: 0.8058 (mmm) cc_final: 0.7304 (ptt) REVERT: E 3174 TRP cc_start: 0.9116 (OUTLIER) cc_final: 0.8660 (t60) REVERT: E 3203 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7896 (t-90) REVERT: E 3333 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7302 (m) REVERT: G 177 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7428 (t-170) REVERT: G 189 PHE cc_start: 0.8464 (m-80) cc_final: 0.8105 (m-80) REVERT: S 54 LEU cc_start: 0.7476 (pp) cc_final: 0.7216 (pp) REVERT: S 94 MET cc_start: 0.8372 (pmm) cc_final: 0.7993 (pmm) REVERT: S 110 MET cc_start: 0.8508 (mmm) cc_final: 0.8206 (tpp) outliers start: 71 outliers final: 55 residues processed: 192 average time/residue: 0.1116 time to fit residues: 34.0718 Evaluate side-chains 189 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 128 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 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 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 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 262 VAL 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 61 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 191 ASP 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 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 189 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 172 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 201 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 0.0870 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN E3232 HIS ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.120301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.077429 restraints weight = 34495.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079879 restraints weight = 20257.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.081440 restraints weight = 14860.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082341 restraints weight = 12364.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082989 restraints weight = 11116.741| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16677 Z= 0.124 Angle : 0.655 19.649 22722 Z= 0.311 Chirality : 0.043 0.195 2711 Planarity : 0.004 0.100 2852 Dihedral : 6.322 161.768 3051 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 3.33 % Allowed : 32.43 % Favored : 64.25 % 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 aren not related in a simple way. whole: 0.21 (0.19), residues: 2074 helix: 2.48 (0.20), residues: 691 sheet: -0.53 (0.34), residues: 260 loop : -1.27 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 152 TYR 0.034 0.001 TYR E3208 PHE 0.010 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 covalent geometry : bond 0.00277 (16634) covalent geometry : angle 0.64221 (22612) SS BOND : bond 0.00490 ( 11) SS BOND : angle 1.46419 ( 22) hydrogen bonds : bond 0.03452 ( 669) hydrogen bonds : angle 4.16313 ( 1920) metal coordination : bond 0.00474 ( 4) metal coordination : angle 3.24995 ( 6) link_BETA1-3 : bond 0.00902 ( 3) link_BETA1-3 : angle 1.97089 ( 9) link_BETA1-4 : bond 0.00604 ( 13) link_BETA1-4 : angle 1.46577 ( 39) link_NAG-ASN : bond 0.00277 ( 10) link_NAG-ASN : angle 2.35406 ( 30) link_NAG-THR : bond 0.00342 ( 2) link_NAG-THR : angle 3.16684 ( 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 189 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 MET cc_start: 0.9335 (tpp) cc_final: 0.9064 (tpt) REVERT: D 187 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8375 (t80) REVERT: E 3138 MET cc_start: 0.7160 (mmm) cc_final: 0.6920 (mmm) REVERT: E 3170 MET cc_start: 0.7974 (mmm) cc_final: 0.7355 (ptt) REVERT: E 3174 TRP cc_start: 0.9056 (OUTLIER) cc_final: 0.8664 (t60) REVERT: E 3203 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7839 (t-90) REVERT: E 3333 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7079 (m) REVERT: G 177 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7364 (t-170) REVERT: G 189 PHE cc_start: 0.8498 (m-80) cc_final: 0.8169 (m-80) REVERT: G 246 LYS cc_start: 0.8746 (tptt) cc_final: 0.8403 (tptp) REVERT: S 94 MET cc_start: 0.8354 (pmm) cc_final: 0.7994 (pmm) REVERT: S 110 MET cc_start: 0.8473 (mmm) cc_final: 0.8164 (tpp) outliers start: 55 outliers final: 46 residues processed: 184 average time/residue: 0.1064 time to fit residues: 31.7185 Evaluate side-chains 180 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 86 LEU 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 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 262 VAL 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 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 191 ASP 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 200 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 74 optimal weight: 50.0000 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3232 HIS G 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.119319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076426 restraints weight = 34937.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.078823 restraints weight = 20602.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.080363 restraints weight = 15168.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.081322 restraints weight = 12648.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.081905 restraints weight = 11364.644| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16677 Z= 0.175 Angle : 0.669 17.490 22722 Z= 0.321 Chirality : 0.043 0.194 2711 Planarity : 0.004 0.100 2852 Dihedral : 6.315 163.065 3051 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 3.75 % Allowed : 32.30 % 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 aren not related in a simple way. whole: 0.14 (0.19), residues: 2074 helix: 2.41 (0.20), residues: 693 sheet: -0.62 (0.34), residues: 266 loop : -1.31 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 152 TYR 0.011 0.001 TYR E3319 PHE 0.011 0.001 PHE G 151 TRP 0.021 0.001 TRP E3277 HIS 0.003 0.001 HIS G 139 Details of bonding type rmsd covalent geometry : bond 0.00403 (16634) covalent geometry : angle 0.64915 (22612) SS BOND : bond 0.00281 ( 11) SS BOND : angle 3.01538 ( 22) hydrogen bonds : bond 0.03656 ( 669) hydrogen bonds : angle 4.20047 ( 1920) metal coordination : bond 0.00705 ( 4) metal coordination : angle 3.45537 ( 6) link_BETA1-3 : bond 0.00870 ( 3) link_BETA1-3 : angle 1.89004 ( 9) link_BETA1-4 : bond 0.00546 ( 13) link_BETA1-4 : angle 1.51625 ( 39) link_NAG-ASN : bond 0.00311 ( 10) link_NAG-ASN : angle 2.57486 ( 30) link_NAG-THR : bond 0.00319 ( 2) link_NAG-THR : angle 3.13979 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3561.24 seconds wall clock time: 62 minutes 0.26 seconds (3720.26 seconds total)