Starting phenix.real_space_refine on Sat Jun 14 17:44:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yt8_39568/06_2025/8yt8_39568_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yt8_39568/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yt8_39568/06_2025/8yt8_39568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yt8_39568/06_2025/8yt8_39568.map" model { file = "/net/cci-nas-00/data/ceres_data/8yt8_39568/06_2025/8yt8_39568_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yt8_39568/06_2025/8yt8_39568_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 8, 'ASP:plan': 8, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 11, 'GLU:plan': 10, 'ARG:plan': 9} 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: 10.87, per 1000 atoms: 0.67 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: 4.86 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.95 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: 5.61 Time building geometry restraints manager: 5.63 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.810 ------------------------------------------------------------------------------- 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 : 9.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (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 TRP 0.031 0.001 TRP E3174 HIS 0.003 0.001 HIS G 177 PHE 0.010 0.001 PHE G 151 TYR 0.037 0.001 TYR E3208 ARG 0.008 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 10) link_NAG-ASN : angle 2.76906 ( 30) link_BETA1-4 : bond 0.00554 ( 13) link_BETA1-4 : angle 1.45909 ( 39) hydrogen bonds : bond 0.12974 ( 669) hydrogen bonds : angle 5.38674 ( 1920) metal coordination : bond 0.00619 ( 4) metal coordination : angle 3.28366 ( 6) SS BOND : bond 0.00140 ( 11) SS BOND : angle 1.02571 ( 22) link_BETA1-3 : bond 0.01052 ( 3) link_BETA1-3 : angle 1.78948 ( 9) link_NAG-THR : bond 0.00341 ( 2) link_NAG-THR : angle 3.47364 ( 4) covalent geometry : bond 0.00376 (16634) covalent geometry : angle 0.68624 (22612) *********************** 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 : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 96 MET cc_start: 0.2600 (tpt) cc_final: 0.2108 (tmm) outliers start: 4 outliers final: 4 residues processed: 147 average time/residue: 0.2576 time to fit residues: 59.3643 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 : 1.832 ------------------------------------------------------------------------------- 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 173 optimal weight: 0.9990 chunk 155 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.120102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077164 restraints weight = 34468.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.079593 restraints weight = 20313.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.081145 restraints weight = 14907.428| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0640 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= 0.155 Angle : 0.632 10.994 22722 Z= 0.303 Chirality : 0.043 0.180 2711 Planarity : 0.005 0.099 2852 Dihedral : 11.760 144.258 3056 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.73 % Rotamer: Outliers : 3.02 % Allowed : 31.52 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 2074 helix: 2.41 (0.20), residues: 692 sheet: -0.70 (0.34), residues: 257 loop : -1.33 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E3174 HIS 0.004 0.001 HIS E3078 PHE 0.014 0.001 PHE S 61 TYR 0.036 0.001 TYR E3208 ARG 0.004 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 10) link_NAG-ASN : angle 2.79080 ( 30) link_BETA1-4 : bond 0.00673 ( 13) link_BETA1-4 : angle 2.02559 ( 39) hydrogen bonds : bond 0.03995 ( 669) hydrogen bonds : angle 4.45897 ( 1920) metal coordination : bond 0.00532 ( 4) metal coordination : angle 3.12941 ( 6) SS BOND : bond 0.00175 ( 11) SS BOND : angle 0.86301 ( 22) link_BETA1-3 : bond 0.00890 ( 3) link_BETA1-3 : angle 2.92689 ( 9) link_NAG-THR : bond 0.00241 ( 2) link_NAG-THR : angle 3.14022 ( 4) covalent geometry : bond 0.00351 (16634) covalent geometry : angle 0.61231 (22612) *********************** 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 193 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 MET cc_start: 0.7675 (mtp) cc_final: 0.7395 (mtt) REVERT: D 116 ASP cc_start: 0.8585 (p0) cc_final: 0.8288 (p0) REVERT: D 187 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8437 (t80) REVERT: E 3174 TRP cc_start: 0.9093 (t-100) cc_final: 0.8492 (t-100) REVERT: E 3203 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7809 (t-90) REVERT: S 77 MET cc_start: 0.1512 (tpt) cc_final: 0.1218 (tpt) REVERT: S 94 MET cc_start: 0.8522 (pmm) cc_final: 0.8050 (pmm) REVERT: S 110 MET cc_start: 0.8445 (mmm) cc_final: 0.8130 (tpp) outliers start: 50 outliers final: 32 residues processed: 183 average time/residue: 0.2540 time to fit residues: 72.8515 Evaluate side-chains 165 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 148 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 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 768 ILE Chi-restraints excluded: chain O residue 771 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 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 119 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3109 GLN E3232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.116602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073944 restraints weight = 35153.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076124 restraints weight = 21657.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077527 restraints weight = 16326.496| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 16677 Z= 0.353 Angle : 0.771 12.271 22722 Z= 0.379 Chirality : 0.048 0.194 2711 Planarity : 0.005 0.097 2852 Dihedral : 10.056 150.820 3053 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.53 % Favored : 91.27 % Rotamer: Outliers : 6.11 % Allowed : 30.43 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2074 helix: 2.18 (0.20), residues: 693 sheet: -0.98 (0.33), residues: 256 loop : -1.59 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 657 HIS 0.005 0.001 HIS A 38 PHE 0.020 0.002 PHE D 149 TYR 0.019 0.002 TYR E3319 ARG 0.006 0.001 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 10) link_NAG-ASN : angle 3.26860 ( 30) link_BETA1-4 : bond 0.00550 ( 13) link_BETA1-4 : angle 2.14013 ( 39) hydrogen bonds : bond 0.05002 ( 669) hydrogen bonds : angle 4.68181 ( 1920) metal coordination : bond 0.01300 ( 4) metal coordination : angle 4.40957 ( 6) SS BOND : bond 0.00444 ( 11) SS BOND : angle 1.17070 ( 22) link_BETA1-3 : bond 0.00876 ( 3) link_BETA1-3 : angle 2.56603 ( 9) link_NAG-THR : bond 0.00426 ( 2) link_NAG-THR : angle 3.06122 ( 4) covalent geometry : bond 0.00816 (16634) covalent geometry : angle 0.75082 (22612) *********************** 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 238 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 137 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 116 ASP cc_start: 0.8527 (p0) cc_final: 0.8251 (p0) REVERT: E 3170 MET cc_start: 0.7599 (mmm) cc_final: 0.6955 (ptt) REVERT: E 3174 TRP cc_start: 0.9149 (t-100) cc_final: 0.8495 (t-100) REVERT: E 3333 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7717 (m) REVERT: O 596 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6979 (mtp85) REVERT: S 77 MET cc_start: 0.2012 (tpt) cc_final: 0.1606 (tpt) REVERT: S 94 MET cc_start: 0.8560 (pmm) cc_final: 0.8290 (pmm) REVERT: S 110 MET cc_start: 0.8501 (mmm) cc_final: 0.8171 (tpp) REVERT: S 172 MET cc_start: 0.8518 (ttm) cc_final: 0.8254 (ttm) REVERT: S 175 ASN cc_start: 0.7954 (m110) cc_final: 0.7667 (m110) outliers start: 101 outliers final: 68 residues processed: 224 average time/residue: 0.2425 time to fit residues: 85.2156 Evaluate side-chains 200 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 130 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 176 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain 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 91 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 C residue 128 SER Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3273 LEU Chi-restraints excluded: chain E residue 3278 MET 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 132 MET Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 535 THR Chi-restraints excluded: chain O residue 554 SER Chi-restraints excluded: chain O residue 596 ARG Chi-restraints excluded: chain O residue 640 CYS Chi-restraints excluded: chain O residue 642 SER Chi-restraints excluded: chain O residue 706 THR Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 758 VAL Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain O residue 771 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 188 VAL Chi-restraints excluded: chain S residue 189 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 141 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 87 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E3109 GLN E3232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.119307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076378 restraints weight = 34725.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078786 restraints weight = 20470.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080342 restraints weight = 15039.288| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16677 Z= 0.144 Angle : 0.626 11.322 22722 Z= 0.301 Chirality : 0.044 0.191 2711 Planarity : 0.004 0.099 2852 Dihedral : 8.651 153.410 3053 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 4.42 % Allowed : 32.00 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 2074 helix: 2.44 (0.20), residues: 690 sheet: -0.87 (0.33), residues: 266 loop : -1.47 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E3277 HIS 0.004 0.001 HIS E3292 PHE 0.010 0.001 PHE O 589 TYR 0.017 0.001 TYR S 98 ARG 0.005 0.000 ARG B 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 10) link_NAG-ASN : angle 2.67366 ( 30) link_BETA1-4 : bond 0.00650 ( 13) link_BETA1-4 : angle 1.91549 ( 39) hydrogen bonds : bond 0.03900 ( 669) hydrogen bonds : angle 4.36488 ( 1920) metal coordination : bond 0.00643 ( 4) metal coordination : angle 3.48369 ( 6) SS BOND : bond 0.00168 ( 11) SS BOND : angle 0.90269 ( 22) link_BETA1-3 : bond 0.00884 ( 3) link_BETA1-3 : angle 2.59245 ( 9) link_NAG-THR : bond 0.00303 ( 2) link_NAG-THR : angle 3.17119 ( 4) covalent geometry : bond 0.00324 (16634) covalent geometry : angle 0.60777 (22612) *********************** 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 209 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 136 time to evaluate : 1.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7783 (OUTLIER) cc_final: 0.7348 (p) REVERT: D 116 ASP cc_start: 0.8480 (p0) cc_final: 0.8146 (p0) REVERT: D 187 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8386 (t80) REVERT: D 208 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: E 3095 ARG cc_start: 0.7040 (ptt-90) cc_final: 0.6830 (ptt-90) REVERT: E 3170 MET cc_start: 0.7763 (mmm) cc_final: 0.7078 (ptt) REVERT: E 3174 TRP cc_start: 0.9119 (t-100) cc_final: 0.8474 (t-100) REVERT: E 3203 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7779 (t-90) REVERT: E 3333 CYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7489 (m) REVERT: S 175 ASN cc_start: 0.7904 (m110) cc_final: 0.7587 (m110) outliers start: 73 outliers final: 47 residues processed: 197 average time/residue: 0.2468 time to fit residues: 77.4584 Evaluate side-chains 181 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 129 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 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 87 VAL Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 46 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 199 LEU 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 3203 HIS Chi-restraints excluded: chain E residue 3278 MET Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 132 MET 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 658 THR 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 54 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 189 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 118 optimal weight: 0.0020 chunk 73 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 71 optimal weight: 40.0000 chunk 70 optimal weight: 30.0000 chunk 180 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E3109 GLN E3232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.119235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076266 restraints weight = 34991.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078667 restraints weight = 20599.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080212 restraints weight = 15145.302| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1195 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= 0.157 Angle : 0.628 11.280 22722 Z= 0.303 Chirality : 0.043 0.193 2711 Planarity : 0.004 0.100 2852 Dihedral : 7.845 160.075 3051 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.20 % Rotamer: Outliers : 5.14 % Allowed : 30.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 2074 helix: 2.41 (0.20), residues: 693 sheet: -0.90 (0.34), residues: 254 loop : -1.38 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E3277 HIS 0.004 0.001 HIS G 139 PHE 0.011 0.001 PHE G 151 TYR 0.018 0.001 TYR S 120 ARG 0.007 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 10) link_NAG-ASN : angle 2.73253 ( 30) link_BETA1-4 : bond 0.00614 ( 13) link_BETA1-4 : angle 1.74745 ( 39) hydrogen bonds : bond 0.03815 ( 669) hydrogen bonds : angle 4.29395 ( 1920) metal coordination : bond 0.00660 ( 4) metal coordination : angle 3.45975 ( 6) SS BOND : bond 0.00660 ( 11) SS BOND : angle 0.86845 ( 22) link_BETA1-3 : bond 0.00880 ( 3) link_BETA1-3 : angle 2.16343 ( 9) link_NAG-THR : bond 0.00327 ( 2) link_NAG-THR : angle 3.16760 ( 4) covalent geometry : bond 0.00359 (16634) covalent geometry : angle 0.61094 (22612) *********************** 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 224 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 139 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7444 (p) REVERT: D 116 ASP cc_start: 0.8500 (p0) cc_final: 0.8178 (p0) REVERT: D 187 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8367 (t80) REVERT: E 3095 ARG cc_start: 0.7146 (ptt-90) cc_final: 0.6769 (ptt-90) REVERT: E 3170 MET cc_start: 0.7815 (mmm) cc_final: 0.7113 (ptt) REVERT: E 3174 TRP cc_start: 0.9118 (OUTLIER) cc_final: 0.8723 (t60) REVERT: E 3203 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7865 (t-90) REVERT: E 3333 CYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7477 (m) REVERT: G 177 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7441 (t-170) REVERT: S 54 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7375 (pp) REVERT: S 94 MET cc_start: 0.8415 (pmm) cc_final: 0.8191 (pmm) REVERT: S 110 MET cc_start: 0.8459 (mmm) cc_final: 0.8153 (tpp) outliers start: 85 outliers final: 61 residues processed: 211 average time/residue: 0.2449 time to fit residues: 81.9058 Evaluate side-chains 200 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 132 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 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 94 ILE Chi-restraints excluded: chain B residue 109 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 27 TYR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 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 3241 LEU Chi-restraints excluded: chain E residue 3278 MET Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 177 HIS 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 642 SER Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain O residue 761 ILE Chi-restraints excluded: chain O residue 763 LEU Chi-restraints excluded: chain O residue 768 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 59 THR Chi-restraints excluded: chain S residue 92 PHE Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 6 optimal weight: 0.0570 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 0.0040 chunk 15 optimal weight: 0.0170 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.121118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078088 restraints weight = 34444.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.080596 restraints weight = 20114.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082183 restraints weight = 14707.967| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 16677 Z= 0.104 Angle : 0.600 11.492 22722 Z= 0.288 Chirality : 0.042 0.195 2711 Planarity : 0.004 0.101 2852 Dihedral : 7.261 163.508 3051 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 3.69 % Allowed : 32.73 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2074 helix: 2.54 (0.20), residues: 691 sheet: -0.64 (0.33), residues: 265 loop : -1.32 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E3277 HIS 0.003 0.001 HIS E3292 PHE 0.009 0.001 PHE G 151 TYR 0.020 0.001 TYR S 98 ARG 0.006 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 10) link_NAG-ASN : angle 2.43064 ( 30) link_BETA1-4 : bond 0.00701 ( 13) link_BETA1-4 : angle 1.57232 ( 39) hydrogen bonds : bond 0.03318 ( 669) hydrogen bonds : angle 4.13515 ( 1920) metal coordination : bond 0.00334 ( 4) metal coordination : angle 3.00426 ( 6) SS BOND : bond 0.00221 ( 11) SS BOND : angle 1.05506 ( 22) link_BETA1-3 : bond 0.00929 ( 3) link_BETA1-3 : angle 2.11616 ( 9) link_NAG-THR : bond 0.00356 ( 2) link_NAG-THR : angle 3.19140 ( 4) covalent geometry : bond 0.00227 (16634) covalent geometry : angle 0.58509 (22612) *********************** 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 203 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 MET cc_start: 0.7894 (tpt) cc_final: 0.7501 (tpt) REVERT: D 187 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8366 (t80) REVERT: E 3170 MET cc_start: 0.7952 (mmm) cc_final: 0.7357 (ptt) REVERT: E 3174 TRP cc_start: 0.9097 (t-100) cc_final: 0.8755 (t60) REVERT: E 3203 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7715 (t-90) REVERT: E 3241 LEU cc_start: 0.8920 (tp) cc_final: 0.8616 (mt) REVERT: E 3333 CYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7171 (m) REVERT: S 110 MET cc_start: 0.8456 (mmm) cc_final: 0.8140 (tpp) REVERT: S 147 ARG cc_start: 0.8819 (mtp180) cc_final: 0.8546 (mtp-110) outliers start: 61 outliers final: 37 residues processed: 193 average time/residue: 0.2435 time to fit residues: 74.1445 Evaluate side-chains 171 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE 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 68 ILE Chi-restraints excluded: chain B residue 94 ILE 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 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 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 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 3333 CYS Chi-restraints excluded: chain E residue 3392 THR Chi-restraints excluded: chain G residue 29 TYR Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain G residue 288 HIS Chi-restraints excluded: chain O residue 701 LEU Chi-restraints excluded: chain O residue 717 ILE Chi-restraints excluded: chain O residue 723 SER Chi-restraints excluded: chain 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 137 CYS Chi-restraints excluded: chain S residue 145 LEU Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 105 optimal weight: 4.9990 chunk 39 optimal weight: 0.0870 chunk 3 optimal weight: 0.8980 chunk 198 optimal weight: 0.0870 chunk 63 optimal weight: 20.0000 chunk 191 optimal weight: 0.0470 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 194 optimal weight: 3.9990 chunk 160 optimal weight: 0.0070 chunk 126 optimal weight: 2.9990 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E3232 HIS G 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078676 restraints weight = 34519.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081182 restraints weight = 20206.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.082790 restraints weight = 14772.735| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16677 Z= 0.102 Angle : 0.604 11.516 22722 Z= 0.289 Chirality : 0.042 0.252 2711 Planarity : 0.004 0.100 2852 Dihedral : 6.824 163.936 3051 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.26 % Rotamer: Outliers : 3.87 % Allowed : 32.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2074 helix: 2.52 (0.20), residues: 691 sheet: -0.48 (0.34), residues: 260 loop : -1.23 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E3277 HIS 0.003 0.001 HIS E3078 PHE 0.010 0.001 PHE G 151 TYR 0.040 0.001 TYR E3208 ARG 0.004 0.000 ARG B 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 10) link_NAG-ASN : angle 2.47205 ( 30) link_BETA1-4 : bond 0.00635 ( 13) link_BETA1-4 : angle 1.52272 ( 39) hydrogen bonds : bond 0.03196 ( 669) hydrogen bonds : angle 4.07781 ( 1920) metal coordination : bond 0.00280 ( 4) metal coordination : angle 2.92762 ( 6) SS BOND : bond 0.00311 ( 11) SS BOND : angle 1.26445 ( 22) link_BETA1-3 : bond 0.00890 ( 3) link_BETA1-3 : angle 1.98666 ( 9) link_NAG-THR : bond 0.00352 ( 2) link_NAG-THR : angle 3.17206 ( 4) covalent geometry : bond 0.00218 (16634) covalent geometry : angle 0.58921 (22612) *********************** 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 206 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 142 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 MET cc_start: 0.7894 (tpt) cc_final: 0.7467 (tpt) REVERT: D 59 MET cc_start: 0.9235 (tpp) cc_final: 0.9006 (tpt) REVERT: D 187 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8347 (t80) REVERT: E 3138 MET cc_start: 0.7536 (mmm) cc_final: 0.7116 (mmm) REVERT: E 3174 TRP cc_start: 0.9110 (t-100) cc_final: 0.8716 (t60) REVERT: E 3203 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7487 (t-90) REVERT: E 3241 LEU cc_start: 0.8795 (tp) cc_final: 0.8553 (mt) REVERT: E 3333 CYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7007 (m) REVERT: S 46 LEU cc_start: 0.8504 (mm) cc_final: 0.7879 (tt) REVERT: S 94 MET cc_start: 0.8388 (pmm) cc_final: 0.7976 (pmm) REVERT: S 110 MET cc_start: 0.8497 (mmm) cc_final: 0.8090 (tpp) outliers start: 64 outliers final: 42 residues processed: 197 average time/residue: 0.2317 time to fit residues: 72.8723 Evaluate side-chains 175 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE 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 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 309 CYS 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 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 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 58 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 163 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 170 optimal weight: 0.0970 chunk 51 optimal weight: 0.0070 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 71 optimal weight: 50.0000 chunk 78 optimal weight: 2.9990 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 GLN E3232 HIS E3236 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.117723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075051 restraints weight = 35020.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.077306 restraints weight = 21298.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.078750 restraints weight = 15952.777| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 16677 Z= 0.282 Angle : 0.709 10.654 22722 Z= 0.347 Chirality : 0.046 0.256 2711 Planarity : 0.005 0.096 2852 Dihedral : 6.984 166.388 3051 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 3.99 % Allowed : 32.18 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 2074 helix: 2.39 (0.20), residues: 691 sheet: -0.75 (0.34), residues: 266 loop : -1.45 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E3277 HIS 0.004 0.001 HIS A 38 PHE 0.016 0.002 PHE D 84 TYR 0.041 0.002 TYR E3208 ARG 0.012 0.001 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00583 ( 10) link_NAG-ASN : angle 2.78772 ( 30) link_BETA1-4 : bond 0.00512 ( 13) link_BETA1-4 : angle 1.66599 ( 39) hydrogen bonds : bond 0.04223 ( 669) hydrogen bonds : angle 4.32792 ( 1920) metal coordination : bond 0.01129 ( 4) metal coordination : angle 3.90157 ( 6) SS BOND : bond 0.00205 ( 11) SS BOND : angle 1.66804 ( 22) link_BETA1-3 : bond 0.00880 ( 3) link_BETA1-3 : angle 1.86750 ( 9) link_NAG-THR : bond 0.00399 ( 2) link_NAG-THR : angle 3.08817 ( 4) covalent geometry : bond 0.00654 (16634) covalent geometry : angle 0.69286 (22612) *********************** 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 200 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7515 (p) REVERT: B 291 MET cc_start: 0.7986 (tpt) cc_final: 0.7614 (tpt) REVERT: C 96 MET cc_start: 0.3347 (tpt) cc_final: 0.2539 (tmm) REVERT: D 59 MET cc_start: 0.9295 (tpp) cc_final: 0.9026 (tpt) REVERT: D 116 ASP cc_start: 0.8411 (p0) cc_final: 0.8129 (p0) REVERT: E 3138 MET cc_start: 0.7451 (mmm) cc_final: 0.7246 (mmm) REVERT: E 3170 MET cc_start: 0.8052 (mmm) cc_final: 0.7308 (ptt) REVERT: E 3174 TRP cc_start: 0.9141 (OUTLIER) cc_final: 0.8546 (t-100) REVERT: E 3203 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: E 3241 LEU cc_start: 0.8926 (tp) cc_final: 0.8695 (mt) REVERT: E 3333 CYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7500 (m) REVERT: G 177 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7435 (t-170) REVERT: S 94 MET cc_start: 0.8347 (pmm) cc_final: 0.7933 (pmm) REVERT: S 110 MET cc_start: 0.8498 (mmm) cc_final: 0.8193 (tpp) REVERT: S 147 ARG cc_start: 0.8636 (mtp180) cc_final: 0.8412 (mtp-110) outliers start: 66 outliers final: 58 residues processed: 191 average time/residue: 0.2364 time to fit residues: 73.2617 Evaluate side-chains 189 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 126 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 27 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 176 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 291 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 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 150 SER Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 288 CYS Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 3203 HIS Chi-restraints excluded: chain E residue 3291 LEU Chi-restraints excluded: chain E residue 3329 ILE 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 68 MET Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain 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 658 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 7 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 68 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 183 optimal weight: 0.0030 chunk 160 optimal weight: 0.9980 chunk 187 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.120196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.077298 restraints weight = 34590.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079775 restraints weight = 20262.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.081339 restraints weight = 14838.599| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16677 Z= 0.123 Angle : 0.633 12.464 22722 Z= 0.305 Chirality : 0.043 0.237 2711 Planarity : 0.004 0.097 2852 Dihedral : 6.453 163.235 3051 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.40 % Favored : 94.50 % Rotamer: Outliers : 3.69 % Allowed : 32.18 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 2074 helix: 2.48 (0.20), residues: 691 sheet: -0.72 (0.34), residues: 254 loop : -1.31 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E3277 HIS 0.004 0.001 HIS E3292 PHE 0.010 0.001 PHE G 151 TYR 0.039 0.001 TYR E3208 ARG 0.006 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 10) link_NAG-ASN : angle 2.47471 ( 30) link_BETA1-4 : bond 0.00612 ( 13) link_BETA1-4 : angle 1.48320 ( 39) hydrogen bonds : bond 0.03532 ( 669) hydrogen bonds : angle 4.18256 ( 1920) metal coordination : bond 0.00460 ( 4) metal coordination : angle 3.16574 ( 6) SS BOND : bond 0.00158 ( 11) SS BOND : angle 1.30087 ( 22) link_BETA1-3 : bond 0.01022 ( 3) link_BETA1-3 : angle 1.96287 ( 9) link_NAG-THR : bond 0.00334 ( 2) link_NAG-THR : angle 3.21874 ( 4) covalent geometry : bond 0.00272 (16634) covalent geometry : angle 0.61938 (22612) *********************** 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 196 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 291 MET cc_start: 0.7928 (tpt) cc_final: 0.7541 (tpt) REVERT: C 96 MET cc_start: 0.2978 (tpt) cc_final: 0.2289 (tmm) REVERT: D 59 MET cc_start: 0.9290 (tpp) cc_final: 0.9042 (tpt) REVERT: D 187 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8328 (t80) REVERT: E 3138 MET cc_start: 0.7483 (mmm) cc_final: 0.7072 (mmm) REVERT: E 3174 TRP cc_start: 0.9118 (OUTLIER) cc_final: 0.8729 (t60) REVERT: E 3203 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7580 (t-90) REVERT: E 3241 LEU cc_start: 0.8858 (tp) cc_final: 0.8625 (mt) REVERT: E 3243 GLU cc_start: 0.8473 (tt0) cc_final: 0.8267 (tt0) REVERT: E 3333 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7178 (m) REVERT: G 177 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7369 (t-170) REVERT: G 246 LYS cc_start: 0.8716 (tptt) cc_final: 0.8343 (tptp) REVERT: S 77 MET cc_start: 0.1567 (tpt) cc_final: 0.1204 (tpt) REVERT: S 94 MET cc_start: 0.8368 (pmm) cc_final: 0.8001 (pmm) REVERT: S 110 MET cc_start: 0.8487 (mmm) cc_final: 0.8163 (tpp) REVERT: S 147 ARG cc_start: 0.8684 (mtp180) cc_final: 0.8460 (mtp180) outliers start: 61 outliers final: 44 residues processed: 187 average time/residue: 0.2469 time to fit residues: 73.7838 Evaluate side-chains 181 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 27 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 125 TYR Chi-restraints excluded: chain B residue 160 ASN 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 58 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 288 CYS Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 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 122 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain 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 72 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 177 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.120562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077690 restraints weight = 34627.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080165 restraints weight = 20267.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081741 restraints weight = 14826.125| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16677 Z= 0.118 Angle : 0.628 13.012 22722 Z= 0.302 Chirality : 0.043 0.247 2711 Planarity : 0.004 0.096 2852 Dihedral : 6.229 162.164 3051 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 3.39 % Allowed : 32.49 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2074 helix: 2.54 (0.20), residues: 691 sheet: -0.57 (0.34), residues: 265 loop : -1.28 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E3287 HIS 0.003 0.001 HIS G 139 PHE 0.010 0.001 PHE G 151 TYR 0.020 0.001 TYR S 120 ARG 0.005 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 10) link_NAG-ASN : angle 2.37019 ( 30) link_BETA1-4 : bond 0.00562 ( 13) link_BETA1-4 : angle 1.45465 ( 39) hydrogen bonds : bond 0.03350 ( 669) hydrogen bonds : angle 4.11815 ( 1920) metal coordination : bond 0.00437 ( 4) metal coordination : angle 3.19120 ( 6) SS BOND : bond 0.00111 ( 11) SS BOND : angle 1.03907 ( 22) link_BETA1-3 : bond 0.00884 ( 3) link_BETA1-3 : angle 1.92921 ( 9) link_NAG-THR : bond 0.00322 ( 2) link_NAG-THR : angle 3.19722 ( 4) covalent geometry : bond 0.00265 (16634) covalent geometry : angle 0.61493 (22612) ********************** 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 193 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7664 (p) REVERT: B 291 MET cc_start: 0.7910 (tpt) cc_final: 0.7507 (tpt) REVERT: C 96 MET cc_start: 0.3766 (tpt) cc_final: 0.2953 (tmm) REVERT: D 59 MET cc_start: 0.9257 (tpp) cc_final: 0.9006 (tpt) REVERT: D 187 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8319 (t80) REVERT: E 3138 MET cc_start: 0.7546 (mmm) cc_final: 0.7164 (mmm) REVERT: E 3174 TRP cc_start: 0.9100 (OUTLIER) cc_final: 0.8705 (t60) REVERT: E 3203 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7323 (t-90) REVERT: E 3243 GLU cc_start: 0.8499 (tt0) cc_final: 0.8297 (tt0) REVERT: E 3333 CYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7071 (m) REVERT: G 246 LYS cc_start: 0.8739 (tptt) cc_final: 0.8373 (tptp) REVERT: S 77 MET cc_start: 0.1441 (tpt) cc_final: 0.1078 (tpt) REVERT: S 94 MET cc_start: 0.8334 (pmm) cc_final: 0.7927 (pmm) REVERT: S 110 MET cc_start: 0.8538 (mmm) cc_final: 0.8225 (tpp) REVERT: S 147 ARG cc_start: 0.8692 (mtp180) cc_final: 0.8431 (mtp180) outliers start: 56 outliers final: 47 residues processed: 186 average time/residue: 0.3096 time to fit residues: 95.0996 Evaluate side-chains 185 residues out of total 1821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 27 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 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 C residue 98 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 288 CYS Chi-restraints excluded: chain E residue 3108 LEU Chi-restraints excluded: chain E residue 3112 LEU Chi-restraints excluded: chain E residue 3174 TRP Chi-restraints excluded: chain E residue 3192 PHE Chi-restraints excluded: chain E residue 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 122 VAL Chi-restraints excluded: chain G residue 177 HIS Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 267 CYS Chi-restraints excluded: chain 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 184 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 165 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.120808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077846 restraints weight = 34611.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.080326 restraints weight = 20269.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.081908 restraints weight = 14854.105| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16677 Z= 0.119 Angle : 0.631 12.882 22722 Z= 0.302 Chirality : 0.043 0.304 2711 Planarity : 0.004 0.096 2852 Dihedral : 6.125 162.377 3051 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 3.27 % Allowed : 32.55 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 2074 helix: 2.53 (0.20), residues: 691 sheet: -0.54 (0.34), residues: 265 loop : -1.24 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E3287 HIS 0.003 0.001 HIS G 139 PHE 0.010 0.001 PHE G 151 TYR 0.020 0.001 TYR S 98 ARG 0.006 0.000 ARG S 152 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 10) link_NAG-ASN : angle 2.45218 ( 30) link_BETA1-4 : bond 0.00594 ( 13) link_BETA1-4 : angle 1.44285 ( 39) hydrogen bonds : bond 0.03290 ( 669) hydrogen bonds : angle 4.10439 ( 1920) metal coordination : bond 0.00422 ( 4) metal coordination : angle 3.12368 ( 6) SS BOND : bond 0.00168 ( 11) SS BOND : angle 1.07429 ( 22) link_BETA1-3 : bond 0.00912 ( 3) link_BETA1-3 : angle 1.90219 ( 9) link_NAG-THR : bond 0.00322 ( 2) link_NAG-THR : angle 3.17952 ( 4) covalent geometry : bond 0.00268 (16634) covalent geometry : angle 0.61774 (22612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6995.24 seconds wall clock time: 123 minutes 15.08 seconds (7395.08 seconds total)