Starting phenix.real_space_refine on Fri Sep 27 06:31:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/09_2024/7tz6_26203_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/09_2024/7tz6_26203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/09_2024/7tz6_26203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/09_2024/7tz6_26203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/09_2024/7tz6_26203_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz6_26203/09_2024/7tz6_26203_trim.cif" } resolution = 2.88 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= -0.015 sd= 0.691 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: 8 Type Number sf(0) Gaussians Fe 10 7.16 5 S 158 5.16 5 Cl 2 4.86 5 C 20972 2.51 5 N 5636 2.21 5 O 5958 1.98 5 F 6 1.80 5 H 32164 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 64906 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6812 Classifications: {'peptide': 446} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "B" Number of atoms: 6323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6323 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain: "C" Number of atoms: 6067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3786 Classifications: {'peptide': 241} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 218} Chain: "E" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3021 Classifications: {'peptide': 196} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "F" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1816 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1264 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1077 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "I" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 272 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 988 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 863 Classifications: {'peptide': 52} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "N" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6812 Classifications: {'peptide': 446} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain: "O" Number of atoms: 6323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6323 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 17, 'TRANS': 405} Chain: "P" Number of atoms: 6067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 355} Chain: "Q" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3786 Classifications: {'peptide': 241} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 218} Chain: "R" Number of atoms: 3021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3021 Classifications: {'peptide': 196} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "S" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1816 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1264 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "U" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1077 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "V" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 272 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain: "W" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 988 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "X" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 863 Classifications: {'peptide': 52} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'HEM': 2, 'JHB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 117 Unusual residues: {'HEM': 2, 'JHB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25191 SG CYS E 139 122.361 121.952 52.002 1.00 56.81 S ATOM 25446 SG CYS E 158 124.544 119.437 53.483 1.00 57.46 S ATOM 57480 SG CYS R 139 102.287 117.546 113.686 1.00 56.45 S ATOM 57735 SG CYS R 158 100.694 120.531 112.346 1.00 33.75 S Time building chain proxies: 26.07, per 1000 atoms: 0.40 Number of scatterers: 64906 At special positions: 0 Unit cell: (176.748, 181.896, 145.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 10 26.01 Cl 2 17.00 S 158 16.00 F 6 9.00 O 5958 8.00 N 5636 7.00 C 20972 6.00 H 32164 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 160 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS R 144 " - pdb=" SG CYS R 160 " distance=2.03 Simple disulfide: pdb=" SG CYS U 24 " - pdb=" SG CYS U 68 " distance=2.02 Simple disulfide: pdb=" SG CYS U 40 " - pdb=" SG CYS U 54 " 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.84 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE2 FES E1001 " - pdb=" ND1 HIS E 161 " pdb="FE2 FES E1001 " - pdb=" ND1 HIS E 141 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 158 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 139 " pdb=" FES R1001 " pdb="FE2 FES R1001 " - pdb=" ND1 HIS R 161 " pdb="FE2 FES R1001 " - pdb=" ND1 HIS R 141 " pdb="FE1 FES R1001 " - pdb=" SG CYS R 158 " pdb="FE1 FES R1001 " - pdb=" SG CYS R 139 " Number of angles added : 6 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7700 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 19 sheets defined 58.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.581A pdb=" N TYR A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.793A pdb=" N LYS A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.602A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 141 Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.542A pdb=" N VAL A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.968A pdb=" N HIS A 289 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 290 " --> pdb=" O GLY A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 330 through 348 Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.612A pdb=" N VAL A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.610A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.614A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.683A pdb=" N VAL B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.684A pdb=" N GLU B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.073A pdb=" N LEU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.912A pdb=" N HIS B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.675A pdb=" N ILE B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.535A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 212 through 223 removed outlier: 3.715A pdb=" N LEU B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.849A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 4.439A pdb=" N GLY B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.607A pdb=" N GLY B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 removed outlier: 3.769A pdb=" N VAL B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 394 through 404 removed outlier: 3.631A pdb=" N VAL B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 419 removed outlier: 3.831A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 10 through 18 removed outlier: 3.780A pdb=" N VAL C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 32 through 52 removed outlier: 3.687A pdb=" N ILE C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 75 through 104 removed outlier: 3.922A pdb=" N ALA C 87 " --> pdb=" O HIS C 83 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 removed outlier: 3.772A pdb=" N THR C 108 " --> pdb=" O GLY C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 109 through 131 Processing helix chain 'C' and resid 136 through 150 removed outlier: 3.914A pdb=" N VAL C 145 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 171 through 204 Proline residue: C 186 - end of helix removed outlier: 3.609A pdb=" N VAL C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 203 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 246 removed outlier: 3.650A pdb=" N ILE C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS C 227 " --> pdb=" O TYR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.626A pdb=" N ASN C 255 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.507A pdb=" N ARG C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 removed outlier: 3.627A pdb=" N ILE C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 Proline residue: C 305 - end of helix removed outlier: 3.562A pdb=" N HIS C 308 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 317 removed outlier: 4.070A pdb=" N PHE C 317 " --> pdb=" O SER C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 314 through 317' Processing helix chain 'C' and resid 318 through 340 removed outlier: 3.924A pdb=" N GLY C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 37 through 40 removed outlier: 3.568A pdb=" N CYS D 40 " --> pdb=" O CYS D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 37 through 40' Processing helix chain 'D' and resid 47 through 52 removed outlier: 3.884A pdb=" N LEU D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 52' Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 97 through 104 Processing helix chain 'D' and resid 123 through 132 removed outlier: 3.673A pdb=" N VAL D 127 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 195 Processing helix chain 'D' and resid 197 through 232 removed outlier: 3.531A pdb=" N LYS D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) Proline residue: D 217 - end of helix removed outlier: 4.695A pdb=" N VAL D 229 " --> pdb=" O HIS D 225 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU D 230 " --> pdb=" O LYS D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.632A pdb=" N LEU E 19 " --> pdb=" O PRO E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 62 removed outlier: 4.709A pdb=" N GLU E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'F' and resid 7 through 25 removed outlier: 3.889A pdb=" N GLY F 25 " --> pdb=" O TYR F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 33 through 37 removed outlier: 3.606A pdb=" N ILE F 37 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 49 Processing helix chain 'F' and resid 51 through 72 Processing helix chain 'F' and resid 76 through 80 removed outlier: 3.674A pdb=" N TRP F 80 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 110 removed outlier: 3.504A pdb=" N LEU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 71 removed outlier: 4.630A pdb=" N LEU G 46 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Proline residue: G 50 - end of helix removed outlier: 3.506A pdb=" N ARG G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 removed outlier: 4.372A pdb=" N THR H 19 " --> pdb=" O ASP H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 47 removed outlier: 3.564A pdb=" N VAL H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 77 removed outlier: 3.643A pdb=" N ALA H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N CYS H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA H 70 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS H 71 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS H 72 " --> pdb=" O CYS H 68 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN H 75 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 13 Processing helix chain 'J' and resid 16 through 47 removed outlier: 3.511A pdb=" N PHE J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 60 removed outlier: 3.550A pdb=" N ILE J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N HIS J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS J 58 " --> pdb=" O HIS J 54 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 removed outlier: 4.038A pdb=" N PHE K 5 " --> pdb=" O LEU K 2 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU K 6 " --> pdb=" O THR K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2 through 6' Processing helix chain 'K' and resid 7 through 37 Proline residue: K 19 - end of helix Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'K' and resid 47 through 52 removed outlier: 3.605A pdb=" N GLY K 50 " --> pdb=" O TYR K 47 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE K 52 " --> pdb=" O ASN K 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 44 through 48 Processing helix chain 'N' and resid 54 through 63 removed outlier: 3.502A pdb=" N HIS N 61 " --> pdb=" O TYR N 57 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU N 62 " --> pdb=" O PHE N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 82 removed outlier: 3.673A pdb=" N MET N 82 " --> pdb=" O GLU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 119 Processing helix chain 'N' and resid 123 through 142 removed outlier: 3.922A pdb=" N ASP N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL N 133 " --> pdb=" O LYS N 129 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 158 Processing helix chain 'N' and resid 161 through 165 Processing helix chain 'N' and resid 170 through 175 removed outlier: 3.646A pdb=" N ARG N 175 " --> pdb=" O SER N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 190 Processing helix chain 'N' and resid 191 through 193 No H-bonds generated for 'chain 'N' and resid 191 through 193' Processing helix chain 'N' and resid 204 through 216 Processing helix chain 'N' and resid 265 through 278 removed outlier: 4.296A pdb=" N ALA N 269 " --> pdb=" O PRO N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 290 removed outlier: 3.767A pdb=" N HIS N 289 " --> pdb=" O GLY N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 302 Processing helix chain 'N' and resid 330 through 349 removed outlier: 3.962A pdb=" N ALA N 349 " --> pdb=" O LEU N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 350 through 369 removed outlier: 3.624A pdb=" N VAL N 354 " --> pdb=" O THR N 350 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU N 369 " --> pdb=" O LEU N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 371 through 386 Processing helix chain 'N' and resid 391 through 402 removed outlier: 3.767A pdb=" N VAL N 402 " --> pdb=" O ARG N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 403 through 415 Processing helix chain 'N' and resid 433 through 440 Processing helix chain 'O' and resid 54 through 58 Processing helix chain 'O' and resid 64 through 71 Processing helix chain 'O' and resid 81 through 92 removed outlier: 3.780A pdb=" N VAL O 92 " --> pdb=" O GLY O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 129 Processing helix chain 'O' and resid 133 through 152 Proline residue: O 142 - end of helix removed outlier: 4.060A pdb=" N ARG O 145 " --> pdb=" O GLN O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 168 removed outlier: 3.852A pdb=" N HIS O 158 " --> pdb=" O ASN O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 174 Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 187 through 199 Processing helix chain 'O' and resid 200 through 202 No H-bonds generated for 'chain 'O' and resid 200 through 202' Processing helix chain 'O' and resid 212 through 224 Processing helix chain 'O' and resid 266 through 280 removed outlier: 3.924A pdb=" N ASN O 270 " --> pdb=" O SER O 266 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 302 removed outlier: 4.342A pdb=" N GLY O 302 " --> pdb=" O ALA O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 332 through 349 Processing helix chain 'O' and resid 353 through 371 removed outlier: 3.519A pdb=" N VAL O 357 " --> pdb=" O SER O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 374 through 389 Processing helix chain 'O' and resid 394 through 404 Processing helix chain 'O' and resid 406 through 420 Processing helix chain 'O' and resid 435 through 439 Processing helix chain 'P' and resid 3 through 8 Processing helix chain 'P' and resid 10 through 19 removed outlier: 3.996A pdb=" N VAL P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 31 Processing helix chain 'P' and resid 32 through 53 removed outlier: 3.528A pdb=" N GLY P 38 " --> pdb=" O GLY P 34 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 72 removed outlier: 3.663A pdb=" N VAL P 66 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR P 67 " --> pdb=" O PHE P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 104 removed outlier: 3.634A pdb=" N SER P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 108 Processing helix chain 'P' and resid 109 through 131 Processing helix chain 'P' and resid 136 through 149 Processing helix chain 'P' and resid 150 through 153 Processing helix chain 'P' and resid 156 through 166 Processing helix chain 'P' and resid 171 through 204 Proline residue: P 186 - end of helix removed outlier: 3.760A pdb=" N GLU P 202 " --> pdb=" O LEU P 198 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR P 203 " --> pdb=" O PHE P 199 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 246 removed outlier: 6.956A pdb=" N THR P 225 " --> pdb=" O HIS P 221 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 257 removed outlier: 3.514A pdb=" N ASN P 255 " --> pdb=" O ASP P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 273 No H-bonds generated for 'chain 'P' and resid 271 through 273' Processing helix chain 'P' and resid 274 through 283 Processing helix chain 'P' and resid 286 through 300 removed outlier: 3.852A pdb=" N ILE P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 308 Proline residue: P 305 - end of helix removed outlier: 3.763A pdb=" N HIS P 308 " --> pdb=" O PRO P 305 " (cutoff:3.500A) Processing helix chain 'P' and resid 314 through 317 removed outlier: 4.190A pdb=" N PHE P 317 " --> pdb=" O SER P 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 314 through 317' Processing helix chain 'P' and resid 318 through 340 Processing helix chain 'P' and resid 346 through 364 removed outlier: 3.605A pdb=" N PHE P 359 " --> pdb=" O SER P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 377 Processing helix chain 'Q' and resid 22 through 36 Processing helix chain 'Q' and resid 37 through 40 Processing helix chain 'Q' and resid 47 through 52 Processing helix chain 'Q' and resid 57 through 67 Processing helix chain 'Q' and resid 97 through 105 Processing helix chain 'Q' and resid 122 through 132 Processing helix chain 'Q' and resid 178 through 195 Processing helix chain 'Q' and resid 197 through 232 Proline residue: Q 217 - end of helix removed outlier: 4.469A pdb=" N VAL Q 229 " --> pdb=" O HIS Q 225 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU Q 230 " --> pdb=" O LYS Q 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 19 removed outlier: 3.896A pdb=" N LEU R 19 " --> pdb=" O PRO R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 62 removed outlier: 3.950A pdb=" N MET R 62 " --> pdb=" O PHE R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 81 No H-bonds generated for 'chain 'R' and resid 79 through 81' Processing helix chain 'R' and resid 102 through 111 Processing helix chain 'R' and resid 113 through 117 Processing helix chain 'R' and resid 122 through 126 Processing helix chain 'S' and resid 7 through 25 removed outlier: 3.692A pdb=" N TRP S 12 " --> pdb=" O ALA S 8 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY S 25 " --> pdb=" O TYR S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 30 Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.586A pdb=" N ILE S 37 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 49 Processing helix chain 'S' and resid 51 through 72 Processing helix chain 'S' and resid 76 through 80 Processing helix chain 'S' and resid 82 through 86 removed outlier: 3.613A pdb=" N ASP S 86 " --> pdb=" O TYR S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 108 Processing helix chain 'T' and resid 20 through 23 removed outlier: 3.800A pdb=" N GLN T 23 " --> pdb=" O PRO T 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 20 through 23' Processing helix chain 'T' and resid 32 through 71 removed outlier: 4.755A pdb=" N LEU T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG T 47 " --> pdb=" O ALA T 43 " (cutoff:3.500A) Proline residue: T 50 - end of helix removed outlier: 3.813A pdb=" N ARG T 71 " --> pdb=" O GLU T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 15 through 25 removed outlier: 3.866A pdb=" N THR U 19 " --> pdb=" O ASP U 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN U 23 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU U 25 " --> pdb=" O ARG U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 27 through 47 removed outlier: 4.027A pdb=" N LYS U 32 " --> pdb=" O GLU U 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER U 46 " --> pdb=" O GLU U 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG U 47 " --> pdb=" O ARG U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 74 removed outlier: 3.569A pdb=" N PHE U 61 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS U 67 " --> pdb=" O HIS U 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS U 71 " --> pdb=" O HIS U 67 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS U 72 " --> pdb=" O CYS U 68 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 13 Processing helix chain 'W' and resid 16 through 47 Processing helix chain 'W' and resid 51 through 54 Processing helix chain 'W' and resid 55 through 60 removed outlier: 4.079A pdb=" N TYR W 59 " --> pdb=" O ILE W 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 6 removed outlier: 3.720A pdb=" N PHE X 5 " --> pdb=" O LEU X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 37 Proline residue: X 19 - end of helix Processing helix chain 'X' and resid 38 through 43 Processing helix chain 'X' and resid 46 through 52 removed outlier: 3.500A pdb=" N GLY X 50 " --> pdb=" O TYR X 47 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.595A pdb=" N ARG A 24 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA A 199 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 26 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLY A 201 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU A 28 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.760A pdb=" N VAL G 13 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 28 removed outlier: 3.587A pdb=" N VAL B 34 " --> pdb=" O MET B 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.758A pdb=" N ILE B 244 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLY B 428 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU B 246 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 24 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 72 Processing sheet with id=AA7, first strand: chain 'E' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AA9, first strand: chain 'E' and resid 147 through 148 removed outlier: 6.913A pdb=" N HIS E 164 " --> pdb=" O ARG E 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 15 through 18 removed outlier: 6.615A pdb=" N ARG N 24 " --> pdb=" O LEU N 197 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA N 199 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA N 26 " --> pdb=" O ALA N 199 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLY N 201 " --> pdb=" O ALA N 26 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU N 28 " --> pdb=" O GLY N 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 279 through 281 removed outlier: 3.610A pdb=" N SER N 306 " --> pdb=" O VAL N 325 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL T 13 " --> pdb=" O ARG N 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 25 through 28 removed outlier: 6.512A pdb=" N VAL O 34 " --> pdb=" O LEU O 206 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLY O 208 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA O 36 " --> pdb=" O GLY O 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'O' and resid 242 through 247 removed outlier: 6.242A pdb=" N GLY O 242 " --> pdb=" O MET O 424 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ALA O 426 " --> pdb=" O GLY O 242 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE O 244 " --> pdb=" O ALA O 426 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLY O 428 " --> pdb=" O ILE O 244 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU O 246 " --> pdb=" O GLY O 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 22 through 24 Processing sheet with id=AB6, first strand: chain 'Q' and resid 69 through 72 Processing sheet with id=AB7, first strand: chain 'Q' and resid 148 through 149 Processing sheet with id=AB8, first strand: chain 'R' and resid 74 through 77 Processing sheet with id=AB9, first strand: chain 'R' and resid 86 through 91 Processing sheet with id=AC1, first strand: chain 'R' and resid 147 through 148 removed outlier: 6.773A pdb=" N HIS R 164 " --> pdb=" O ARG R 172 " (cutoff:3.500A) 1821 hydrogen bonds defined for protein. 5169 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: 26.73 Time building geometry restraints manager: 16.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.11: 32118 1.11 - 1.38: 13249 1.38 - 1.65: 20107 1.65 - 1.93: 244 1.93 - 2.20: 32 Bond restraints: 65750 Sorted by residual: bond pdb=" C TYR C 256 " pdb=" N THR C 257 " ideal model delta sigma weight residual 1.331 1.384 -0.053 2.07e-02 2.33e+03 6.56e+00 bond pdb=" C2 JHB C1003 " pdb="CL JHB C1003 " ideal model delta sigma weight residual 1.729 1.779 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C2 JHB P1003 " pdb="CL JHB P1003 " ideal model delta sigma weight residual 1.729 1.778 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C7 JHB P1003 " pdb=" C8 JHB P1003 " ideal model delta sigma weight residual 1.367 1.406 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" CB ILE C 146 " pdb=" CG2 ILE C 146 " ideal model delta sigma weight residual 1.521 1.585 -0.064 3.30e-02 9.18e+02 3.71e+00 ... (remaining 65745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 115688 1.85 - 3.70: 2584 3.70 - 5.55: 383 5.55 - 7.40: 32 7.40 - 9.25: 7 Bond angle restraints: 118694 Sorted by residual: angle pdb=" N ALA O 171 " pdb=" CA ALA O 171 " pdb=" C ALA O 171 " ideal model delta sigma weight residual 110.80 120.05 -9.25 2.13e+00 2.20e-01 1.89e+01 angle pdb=" N PRO X 46 " pdb=" CA PRO X 46 " pdb=" C PRO X 46 " ideal model delta sigma weight residual 112.47 120.35 -7.88 2.06e+00 2.36e-01 1.46e+01 angle pdb=" N ALA G 49 " pdb=" CA ALA G 49 " pdb=" C ALA G 49 " ideal model delta sigma weight residual 109.81 117.58 -7.77 2.21e+00 2.05e-01 1.24e+01 angle pdb=" C ASN O 170 " pdb=" N ALA O 171 " pdb=" CA ALA O 171 " ideal model delta sigma weight residual 121.54 128.17 -6.63 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA CYS U 68 " pdb=" CB CYS U 68 " pdb=" SG CYS U 68 " ideal model delta sigma weight residual 114.40 106.60 7.80 2.30e+00 1.89e-01 1.15e+01 ... (remaining 118689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 28468 17.83 - 35.67: 1824 35.67 - 53.50: 489 53.50 - 71.33: 176 71.33 - 89.16: 39 Dihedral angle restraints: 30996 sinusoidal: 16696 harmonic: 14300 Sorted by residual: dihedral pdb=" CB CYS H 24 " pdb=" SG CYS H 24 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 150.23 -57.23 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" CA LEU R 69 " pdb=" C LEU R 69 " pdb=" N ALA R 70 " pdb=" CA ALA R 70 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN O 153 " pdb=" C GLN O 153 " pdb=" N ASN O 154 " pdb=" CA ASN O 154 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 30993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3728 0.047 - 0.095: 1002 0.095 - 0.142: 239 0.142 - 0.190: 22 0.190 - 0.237: 1 Chirality restraints: 4992 Sorted by residual: chirality pdb=" CA PRO X 46 " pdb=" N PRO X 46 " pdb=" C PRO X 46 " pdb=" CB PRO X 46 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO N 260 " pdb=" N PRO N 260 " pdb=" C PRO N 260 " pdb=" CB PRO N 260 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA VAL V 72 " pdb=" N VAL V 72 " pdb=" C VAL V 72 " pdb=" CB VAL V 72 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 4989 not shown) Planarity restraints: 9726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC Q1001 " -0.013 2.00e-02 2.50e+03 3.40e-02 2.60e+01 pdb=" C2C HEC Q1001 " 0.091 2.00e-02 2.50e+03 pdb=" C3C HEC Q1001 " 0.003 2.00e-02 2.50e+03 pdb=" C4C HEC Q1001 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HEC Q1001 " -0.025 2.00e-02 2.50e+03 pdb=" CHC HEC Q1001 " -0.020 2.00e-02 2.50e+03 pdb=" CHD HEC Q1001 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HEC Q1001 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC Q1001 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP P 272 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C TRP P 272 " -0.065 2.00e-02 2.50e+03 pdb=" O TRP P 272 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR P 273 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE W 20 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C PHE W 20 " 0.061 2.00e-02 2.50e+03 pdb=" O PHE W 20 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA W 21 " -0.021 2.00e-02 2.50e+03 ... (remaining 9723 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 9083 2.28 - 2.86: 143037 2.86 - 3.44: 161288 3.44 - 4.02: 222039 4.02 - 4.60: 345928 Nonbonded interactions: 881375 Sorted by model distance: nonbonded pdb="HE21 GLN N 32 " pdb=" OE2 GLU O 373 " model vdw 1.704 2.450 nonbonded pdb=" OE1 GLU N 429 " pdb=" H GLY T 5 " model vdw 1.707 2.450 nonbonded pdb=" HE ARG Q 28 " pdb=" OD2 ASP Q 185 " model vdw 1.712 2.450 nonbonded pdb=" OD2 ASP A 246 " pdb=" H VAL G 10 " model vdw 1.715 2.450 nonbonded pdb=" OD2 ASP Q 72 " pdb=" HE ARG Q 83 " model vdw 1.722 2.450 ... (remaining 881370 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 'A' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 510.860 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: 0.880 Extract box with map and model: 2.090 Check model and map are aligned: 0.380 Set scattering table: 0.500 Process input model: 139.360 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 669.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 : 0.005 0.077 33586 Z= 0.346 Angle : 0.766 9.249 45694 Z= 0.412 Chirality : 0.045 0.237 4992 Planarity : 0.006 0.067 5834 Dihedral : 12.160 89.163 12172 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 0.26 % Allowed : 3.86 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.13), residues: 4082 helix: 0.83 (0.11), residues: 1996 sheet: -0.38 (0.24), residues: 414 loop : -0.05 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 77 HIS 0.011 0.002 HIS P 97 PHE 0.021 0.002 PHE B 199 TYR 0.019 0.002 TYR N 223 ARG 0.007 0.001 ARG W 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 767 time to evaluate : 4.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7288 (mm-40) cc_final: 0.6937 (tp40) REVERT: A 61 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8685 (m-70) REVERT: A 381 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.7226 (mtt-85) REVERT: B 351 ASN cc_start: 0.7798 (m-40) cc_final: 0.6998 (p0) REVERT: B 421 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7710 (ttm110) REVERT: C 11 MET cc_start: 0.6613 (mtt) cc_final: 0.6389 (mtp) REVERT: C 162 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7242 (mm-30) REVERT: C 171 ASP cc_start: 0.8269 (t0) cc_final: 0.7826 (m-30) REVERT: C 190 MET cc_start: 0.8034 (ttp) cc_final: 0.7833 (ttp) REVERT: C 240 MET cc_start: 0.8406 (mmt) cc_final: 0.8064 (mmm) REVERT: C 254 ASP cc_start: 0.8363 (m-30) cc_final: 0.7912 (m-30) REVERT: D 93 LYS cc_start: 0.9079 (mttt) cc_final: 0.8839 (mttm) REVERT: D 214 LEU cc_start: 0.8441 (tp) cc_final: 0.8217 (tp) REVERT: F 39 GLU cc_start: 0.7793 (tt0) cc_final: 0.7350 (tt0) REVERT: F 45 GLU cc_start: 0.7718 (tp30) cc_final: 0.7170 (tp30) REVERT: F 69 SER cc_start: 0.9123 (t) cc_final: 0.8830 (m) REVERT: F 95 LYS cc_start: 0.8467 (tppt) cc_final: 0.8266 (ttmp) REVERT: F 96 GLU cc_start: 0.7587 (tp30) cc_final: 0.7339 (mp0) REVERT: H 23 GLN cc_start: 0.8025 (tp40) cc_final: 0.7817 (tt0) REVERT: J 40 ASP cc_start: 0.8445 (m-30) cc_final: 0.8188 (m-30) REVERT: J 58 LYS cc_start: 0.8348 (ttmm) cc_final: 0.8140 (tmtt) REVERT: K 39 ARG cc_start: 0.7442 (mtp85) cc_final: 0.6596 (pmt170) REVERT: N 34 THR cc_start: 0.9295 (p) cc_final: 0.9089 (t) REVERT: N 69 ASN cc_start: 0.7913 (m-40) cc_final: 0.7619 (m-40) REVERT: N 181 ASP cc_start: 0.7922 (m-30) cc_final: 0.7649 (m-30) REVERT: N 266 ASP cc_start: 0.7995 (m-30) cc_final: 0.7781 (m-30) REVERT: O 41 TYR cc_start: 0.7854 (m-80) cc_final: 0.7588 (m-80) REVERT: O 84 LYS cc_start: 0.8371 (tttt) cc_final: 0.7861 (tmtm) REVERT: O 90 GLU cc_start: 0.8457 (tp30) cc_final: 0.8212 (tp30) REVERT: O 189 VAL cc_start: 0.8013 (t) cc_final: 0.7539 (m) REVERT: O 193 ASP cc_start: 0.8317 (m-30) cc_final: 0.8030 (m-30) REVERT: P 12 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7902 (mtmm) REVERT: P 162 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7909 (tt0) REVERT: P 252 ASP cc_start: 0.7362 (t70) cc_final: 0.6938 (t70) REVERT: P 263 ASN cc_start: 0.7469 (t0) cc_final: 0.7247 (m-40) REVERT: P 331 ASP cc_start: 0.8724 (t70) cc_final: 0.8147 (t0) REVERT: Q 62 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7759 (tttt) REVERT: Q 160 MET cc_start: 0.9168 (ttp) cc_final: 0.8832 (ttp) REVERT: R 12 ASP cc_start: 0.8152 (t70) cc_final: 0.7528 (t0) REVERT: R 20 ASP cc_start: 0.8415 (m-30) cc_final: 0.8135 (m-30) REVERT: S 110 LYS cc_start: 0.8133 (mttp) cc_final: 0.6994 (mmtm) REVERT: T 9 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7759 (ttm170) REVERT: T 24 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.6024 (tpt170) REVERT: X 44 TRP cc_start: 0.6925 (m-10) cc_final: 0.6499 (m100) outliers start: 9 outliers final: 4 residues processed: 773 average time/residue: 2.5995 time to fit residues: 2390.6390 Evaluate side-chains 476 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 471 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain W residue 46 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 206 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN A 252 HIS B 349 GLN C 8 HIS G 3 GLN N 9 GLN N 189 HIS N 252 HIS N 435 ASN O 349 GLN O 412 ASN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 159 ASN T 36 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33586 Z= 0.239 Angle : 0.599 16.055 45694 Z= 0.298 Chirality : 0.040 0.157 4992 Planarity : 0.005 0.068 5834 Dihedral : 6.927 89.550 4605 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer: Outliers : 1.67 % Allowed : 11.79 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.13), residues: 4082 helix: 1.98 (0.11), residues: 2018 sheet: -0.09 (0.24), residues: 406 loop : 0.11 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 141 HIS 0.010 0.001 HIS P 201 PHE 0.018 0.001 PHE B 122 TYR 0.020 0.001 TYR N 4 ARG 0.012 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 489 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6971 (tp40) REVERT: A 381 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7213 (mtt-85) REVERT: B 351 ASN cc_start: 0.7762 (m-40) cc_final: 0.6918 (p0) REVERT: B 421 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7795 (ttm110) REVERT: C 11 MET cc_start: 0.6592 (mtt) cc_final: 0.6340 (mtp) REVERT: C 162 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7187 (mm-30) REVERT: C 171 ASP cc_start: 0.8239 (t0) cc_final: 0.7745 (m-30) REVERT: C 254 ASP cc_start: 0.8422 (m-30) cc_final: 0.7920 (m-30) REVERT: C 260 ASN cc_start: 0.7969 (t0) cc_final: 0.7707 (t0) REVERT: D 214 LEU cc_start: 0.8370 (tp) cc_final: 0.8163 (tp) REVERT: E 119 ASP cc_start: 0.7415 (t0) cc_final: 0.7187 (t0) REVERT: E 122 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.6570 (m-70) REVERT: F 39 GLU cc_start: 0.7744 (tt0) cc_final: 0.7282 (tt0) REVERT: F 45 GLU cc_start: 0.7727 (tp30) cc_final: 0.7117 (tp30) REVERT: F 69 SER cc_start: 0.9114 (t) cc_final: 0.8792 (m) REVERT: J 48 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: J 58 LYS cc_start: 0.8342 (ttmm) cc_final: 0.8141 (tmtt) REVERT: K 39 ARG cc_start: 0.7539 (mtp85) cc_final: 0.6588 (pmt170) REVERT: N 20 ASP cc_start: 0.6983 (p0) cc_final: 0.6722 (m-30) REVERT: N 69 ASN cc_start: 0.7916 (m-40) cc_final: 0.7603 (m-40) REVERT: N 184 GLU cc_start: 0.8241 (tt0) cc_final: 0.8022 (tm-30) REVERT: N 290 LEU cc_start: 0.8596 (mt) cc_final: 0.8342 (mt) REVERT: O 84 LYS cc_start: 0.8376 (tttt) cc_final: 0.7889 (tptt) REVERT: O 189 VAL cc_start: 0.8109 (t) cc_final: 0.7673 (m) REVERT: O 193 ASP cc_start: 0.8394 (m-30) cc_final: 0.8092 (m-30) REVERT: P 4 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6931 (pp) REVERT: P 162 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7749 (tt0) REVERT: P 252 ASP cc_start: 0.7198 (t70) cc_final: 0.6977 (t70) REVERT: P 331 ASP cc_start: 0.8750 (t70) cc_final: 0.8233 (t0) REVERT: Q 62 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7724 (tttp) REVERT: S 84 GLU cc_start: 0.7881 (mp0) cc_final: 0.7625 (mp0) REVERT: S 85 GLU cc_start: 0.7681 (mp0) cc_final: 0.6888 (tm-30) REVERT: S 110 LYS cc_start: 0.8035 (mttp) cc_final: 0.6970 (mmtm) REVERT: T 9 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7776 (ttm170) REVERT: T 36 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.7867 (t0) REVERT: X 44 TRP cc_start: 0.7001 (m-10) cc_final: 0.6561 (m100) outliers start: 58 outliers final: 28 residues processed: 528 average time/residue: 2.1336 time to fit residues: 1379.4738 Evaluate side-chains 462 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 430 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain T residue 36 ASN Chi-restraints excluded: chain U residue 60 ASP Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 46 ILE Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 397 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 364 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN G 3 GLN N 9 GLN N 136 GLN N 173 ASN N 240 GLN N 430 GLN O 349 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 ASN Q 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 33586 Z= 0.375 Angle : 0.636 23.058 45694 Z= 0.313 Chirality : 0.042 0.164 4992 Planarity : 0.005 0.074 5834 Dihedral : 6.850 88.321 4603 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.19 % Allowed : 11.94 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.13), residues: 4082 helix: 1.93 (0.11), residues: 2028 sheet: -0.11 (0.24), residues: 410 loop : -0.09 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 91 HIS 0.010 0.001 HIS P 201 PHE 0.021 0.002 PHE P 128 TYR 0.020 0.002 TYR N 4 ARG 0.009 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 447 time to evaluate : 4.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6989 (tp40) REVERT: B 351 ASN cc_start: 0.7746 (m-40) cc_final: 0.6934 (p0) REVERT: B 421 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7796 (ttm110) REVERT: C 11 MET cc_start: 0.6615 (mtt) cc_final: 0.6380 (mtp) REVERT: C 20 ASP cc_start: 0.8418 (m-30) cc_final: 0.8131 (m-30) REVERT: C 171 ASP cc_start: 0.8258 (t0) cc_final: 0.7793 (m-30) REVERT: C 254 ASP cc_start: 0.8411 (m-30) cc_final: 0.7893 (m-30) REVERT: D 44 ASP cc_start: 0.8474 (m-30) cc_final: 0.8272 (m-30) REVERT: D 93 LYS cc_start: 0.9028 (mttp) cc_final: 0.8814 (mttp) REVERT: E 119 ASP cc_start: 0.7462 (t0) cc_final: 0.7240 (t0) REVERT: E 122 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.6585 (m-70) REVERT: F 39 GLU cc_start: 0.7803 (tt0) cc_final: 0.7279 (tt0) REVERT: F 45 GLU cc_start: 0.7779 (tp30) cc_final: 0.7085 (tp30) REVERT: F 69 SER cc_start: 0.9114 (t) cc_final: 0.8801 (m) REVERT: F 96 GLU cc_start: 0.7725 (tp30) cc_final: 0.7397 (mm-30) REVERT: J 48 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: K 39 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6602 (pmt170) REVERT: N 20 ASP cc_start: 0.7160 (p0) cc_final: 0.6795 (m-30) REVERT: N 181 ASP cc_start: 0.7952 (m-30) cc_final: 0.7686 (m-30) REVERT: N 184 GLU cc_start: 0.8271 (tt0) cc_final: 0.8069 (tm-30) REVERT: O 84 LYS cc_start: 0.8452 (tttt) cc_final: 0.7961 (tptt) REVERT: O 118 ILE cc_start: 0.8020 (mm) cc_final: 0.7801 (mt) REVERT: O 243 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: P 4 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7061 (pp) REVERT: P 200 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8537 (tm) REVERT: P 252 ASP cc_start: 0.7227 (t70) cc_final: 0.7017 (t70) REVERT: P 331 ASP cc_start: 0.8821 (t70) cc_final: 0.8342 (t0) REVERT: Q 62 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7775 (tttp) REVERT: S 85 GLU cc_start: 0.7763 (mp0) cc_final: 0.7046 (tm-30) REVERT: S 110 LYS cc_start: 0.7876 (mttp) cc_final: 0.6848 (mmtm) REVERT: T 36 ASN cc_start: 0.7664 (t0) cc_final: 0.7448 (t0) REVERT: U 57 GLU cc_start: 0.8401 (mp0) cc_final: 0.7487 (mp0) REVERT: W 37 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: W 48 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7082 (pm20) REVERT: X 44 TRP cc_start: 0.7042 (m-10) cc_final: 0.6612 (m100) outliers start: 76 outliers final: 38 residues processed: 497 average time/residue: 2.1444 time to fit residues: 1311.9352 Evaluate side-chains 460 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 415 time to evaluate : 3.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 210 ASP Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 115 ASP Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 255 ASN Chi-restraints excluded: chain Q residue 82 MET Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 37 GLN Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 0.4980 chunk 276 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 368 optimal weight: 2.9990 chunk 390 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN G 3 GLN G 6 HIS N 9 GLN N 136 GLN O 349 GLN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 255 ASN X 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33586 Z= 0.236 Angle : 0.563 13.503 45694 Z= 0.281 Chirality : 0.039 0.151 4992 Planarity : 0.005 0.077 5834 Dihedral : 6.745 89.971 4601 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.90 % Allowed : 13.18 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.13), residues: 4082 helix: 2.13 (0.11), residues: 2028 sheet: -0.03 (0.24), residues: 406 loop : -0.06 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 141 HIS 0.008 0.001 HIS P 201 PHE 0.016 0.001 PHE G 55 TYR 0.021 0.001 TYR N 4 ARG 0.012 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 443 time to evaluate : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7302 (mm-40) cc_final: 0.6987 (tp40) REVERT: B 28 ARG cc_start: 0.8298 (ttt180) cc_final: 0.8007 (ttt180) REVERT: B 120 MET cc_start: 0.8171 (mmm) cc_final: 0.7939 (mmm) REVERT: B 351 ASN cc_start: 0.7732 (m-40) cc_final: 0.6879 (p0) REVERT: B 421 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7773 (ttm110) REVERT: C 11 MET cc_start: 0.6579 (mtt) cc_final: 0.6370 (mtp) REVERT: C 162 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7299 (mm-30) REVERT: C 171 ASP cc_start: 0.8232 (t0) cc_final: 0.7751 (m-30) REVERT: C 254 ASP cc_start: 0.8388 (m-30) cc_final: 0.7850 (m-30) REVERT: D 93 LYS cc_start: 0.8994 (mttp) cc_final: 0.8793 (mttp) REVERT: E 119 ASP cc_start: 0.7432 (t0) cc_final: 0.7197 (t0) REVERT: E 122 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6545 (m-70) REVERT: F 39 GLU cc_start: 0.7783 (tt0) cc_final: 0.7252 (tt0) REVERT: F 45 GLU cc_start: 0.7765 (tp30) cc_final: 0.7034 (tp30) REVERT: F 69 SER cc_start: 0.9116 (t) cc_final: 0.8776 (m) REVERT: F 96 GLU cc_start: 0.7703 (tp30) cc_final: 0.7340 (mm-30) REVERT: J 36 ASP cc_start: 0.8390 (t70) cc_final: 0.8042 (t70) REVERT: J 48 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: J 58 LYS cc_start: 0.8376 (tmtt) cc_final: 0.7894 (mtmm) REVERT: K 39 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6597 (pmt170) REVERT: N 20 ASP cc_start: 0.7186 (p0) cc_final: 0.6839 (m-30) REVERT: N 28 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: N 181 ASP cc_start: 0.7914 (m-30) cc_final: 0.7663 (m-30) REVERT: O 84 LYS cc_start: 0.8445 (tttt) cc_final: 0.7966 (tptt) REVERT: O 90 GLU cc_start: 0.8421 (tp30) cc_final: 0.8102 (tp30) REVERT: O 118 ILE cc_start: 0.8012 (mm) cc_final: 0.7597 (tt) REVERT: O 243 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: P 4 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6968 (pp) REVERT: P 200 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8507 (tm) REVERT: P 213 SER cc_start: 0.8911 (p) cc_final: 0.8361 (t) REVERT: P 252 ASP cc_start: 0.7293 (t70) cc_final: 0.7084 (t70) REVERT: P 331 ASP cc_start: 0.8774 (t70) cc_final: 0.8346 (t70) REVERT: Q 62 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7764 (tttp) REVERT: S 85 GLU cc_start: 0.7720 (mp0) cc_final: 0.7020 (tm-30) REVERT: S 110 LYS cc_start: 0.7866 (mttp) cc_final: 0.6843 (mmtm) REVERT: U 56 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7177 (tm-30) REVERT: U 57 GLU cc_start: 0.8287 (mp0) cc_final: 0.7481 (mp0) REVERT: W 48 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: X 44 TRP cc_start: 0.7067 (m-10) cc_final: 0.6604 (m100) outliers start: 66 outliers final: 37 residues processed: 486 average time/residue: 2.1865 time to fit residues: 1316.6994 Evaluate side-chains 462 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 418 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 210 ASP Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain Q residue 82 MET Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain U residue 44 VAL Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 290 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 333 optimal weight: 0.8980 chunk 269 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 18 GLN A 240 GLN B 225 ASN C 16 ASN G 3 GLN G 6 HIS G 23 GLN N 136 GLN N 173 ASN O 349 GLN X 16 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33586 Z= 0.351 Angle : 0.612 17.982 45694 Z= 0.304 Chirality : 0.041 0.161 4992 Planarity : 0.005 0.088 5834 Dihedral : 6.866 89.845 4601 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.45 % Allowed : 13.58 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.13), residues: 4082 helix: 2.02 (0.11), residues: 2028 sheet: -0.06 (0.24), residues: 406 loop : -0.22 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 141 HIS 0.009 0.001 HIS P 97 PHE 0.013 0.002 PHE P 183 TYR 0.022 0.002 TYR N 4 ARG 0.012 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 433 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7336 (mm-40) cc_final: 0.7014 (tp40) REVERT: A 50 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: A 206 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7699 (ptm160) REVERT: B 28 ARG cc_start: 0.8312 (ttt180) cc_final: 0.8065 (ttt180) REVERT: B 120 MET cc_start: 0.8191 (mmm) cc_final: 0.7968 (mmm) REVERT: B 351 ASN cc_start: 0.7732 (m-40) cc_final: 0.6973 (p0) REVERT: B 421 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7792 (ttm110) REVERT: C 11 MET cc_start: 0.6630 (mtt) cc_final: 0.6395 (mtp) REVERT: C 162 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7283 (mm-30) REVERT: C 171 ASP cc_start: 0.8249 (t0) cc_final: 0.7761 (m-30) REVERT: C 254 ASP cc_start: 0.8405 (m-30) cc_final: 0.7846 (m-30) REVERT: D 204 MET cc_start: 0.8268 (mtp) cc_final: 0.8017 (mtp) REVERT: E 119 ASP cc_start: 0.7491 (t0) cc_final: 0.7252 (t0) REVERT: E 122 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.6568 (m-70) REVERT: F 39 GLU cc_start: 0.7790 (tt0) cc_final: 0.7267 (tt0) REVERT: F 45 GLU cc_start: 0.7803 (tp30) cc_final: 0.7391 (tp30) REVERT: F 69 SER cc_start: 0.9135 (t) cc_final: 0.8787 (m) REVERT: F 96 GLU cc_start: 0.7755 (tp30) cc_final: 0.7364 (mm-30) REVERT: J 48 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: J 58 LYS cc_start: 0.8390 (tmtt) cc_final: 0.7905 (mtmm) REVERT: K 39 ARG cc_start: 0.7610 (mtp85) cc_final: 0.6598 (pmt170) REVERT: N 20 ASP cc_start: 0.7132 (p0) cc_final: 0.6791 (m-30) REVERT: O 84 LYS cc_start: 0.8445 (tttt) cc_final: 0.7969 (tptt) REVERT: O 118 ILE cc_start: 0.8044 (mm) cc_final: 0.7655 (tt) REVERT: O 243 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: P 4 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.6934 (mt) REVERT: P 200 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8509 (tm) REVERT: P 331 ASP cc_start: 0.8868 (t70) cc_final: 0.8442 (t0) REVERT: Q 62 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7808 (tttp) REVERT: Q 212 MET cc_start: 0.8673 (tpp) cc_final: 0.8461 (tpp) REVERT: R 12 ASP cc_start: 0.8159 (t70) cc_final: 0.7478 (t0) REVERT: R 20 ASP cc_start: 0.8328 (m-30) cc_final: 0.8031 (m-30) REVERT: S 85 GLU cc_start: 0.7772 (mp0) cc_final: 0.7047 (tm-30) REVERT: S 110 LYS cc_start: 0.7846 (mttp) cc_final: 0.6821 (mmtm) REVERT: W 16 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6780 (mtt-85) REVERT: W 48 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: X 44 TRP cc_start: 0.7117 (m-10) cc_final: 0.6652 (m100) outliers start: 85 outliers final: 53 residues processed: 491 average time/residue: 2.0847 time to fit residues: 1265.3257 Evaluate side-chains 474 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 412 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 210 ASP Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 381 ARG Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 314 SER Chi-restraints excluded: chain Q residue 82 MET Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 ARG Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 390 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 173 ASN P 255 ASN P 341 GLN T 36 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 33586 Z= 0.403 Angle : 0.631 17.031 45694 Z= 0.316 Chirality : 0.042 0.165 4992 Planarity : 0.005 0.086 5834 Dihedral : 6.916 89.116 4601 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.57 % Allowed : 13.90 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.13), residues: 4082 helix: 1.90 (0.11), residues: 2024 sheet: -0.08 (0.25), residues: 406 loop : -0.37 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 91 HIS 0.009 0.001 HIS P 97 PHE 0.015 0.002 PHE G 55 TYR 0.020 0.002 TYR N 4 ARG 0.013 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 430 time to evaluate : 4.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.5498 (tt0) cc_final: 0.5246 (tt0) REVERT: A 9 GLN cc_start: 0.7341 (mm-40) cc_final: 0.7023 (tp40) REVERT: A 50 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: A 206 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7669 (ptm160) REVERT: B 28 ARG cc_start: 0.8322 (ttt180) cc_final: 0.8025 (ttt180) REVERT: B 120 MET cc_start: 0.8193 (mmm) cc_final: 0.7970 (mmm) REVERT: B 351 ASN cc_start: 0.7749 (m-40) cc_final: 0.7008 (p0) REVERT: B 421 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7815 (ttm110) REVERT: C 11 MET cc_start: 0.6638 (mtt) cc_final: 0.6409 (mtp) REVERT: C 171 ASP cc_start: 0.8220 (t0) cc_final: 0.7754 (m-30) REVERT: C 254 ASP cc_start: 0.8380 (m-30) cc_final: 0.7807 (m-30) REVERT: D 99 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: E 122 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.6510 (m-70) REVERT: F 39 GLU cc_start: 0.7783 (tt0) cc_final: 0.7263 (tt0) REVERT: F 45 GLU cc_start: 0.7796 (tp30) cc_final: 0.7177 (tp30) REVERT: F 69 SER cc_start: 0.9143 (t) cc_final: 0.8799 (m) REVERT: F 96 GLU cc_start: 0.7793 (tp30) cc_final: 0.7332 (mm-30) REVERT: J 48 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: J 58 LYS cc_start: 0.8373 (tmtt) cc_final: 0.7884 (mttp) REVERT: K 39 ARG cc_start: 0.7627 (mtp85) cc_final: 0.6673 (pmt170) REVERT: N 20 ASP cc_start: 0.7129 (p0) cc_final: 0.6755 (m-30) REVERT: N 117 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (t) REVERT: O 84 LYS cc_start: 0.8456 (tttt) cc_final: 0.7962 (tptt) REVERT: O 118 ILE cc_start: 0.8050 (mm) cc_final: 0.7695 (tt) REVERT: O 243 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7736 (pt0) REVERT: P 200 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8533 (tm) REVERT: P 331 ASP cc_start: 0.8912 (t70) cc_final: 0.8491 (t0) REVERT: Q 62 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7819 (tttp) REVERT: Q 86 LYS cc_start: 0.8283 (tptt) cc_final: 0.7994 (mtmt) REVERT: R 12 ASP cc_start: 0.8171 (t70) cc_final: 0.7634 (t0) REVERT: R 20 ASP cc_start: 0.8337 (m-30) cc_final: 0.8039 (m-30) REVERT: S 85 GLU cc_start: 0.7803 (mp0) cc_final: 0.7074 (tm-30) REVERT: S 103 GLU cc_start: 0.7998 (tp30) cc_final: 0.7682 (tt0) REVERT: S 110 LYS cc_start: 0.7737 (mttp) cc_final: 0.6728 (mmtm) REVERT: W 16 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6864 (mtt-85) REVERT: W 48 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: X 44 TRP cc_start: 0.7119 (m-10) cc_final: 0.6639 (m100) outliers start: 89 outliers final: 55 residues processed: 493 average time/residue: 2.0987 time to fit residues: 1281.1178 Evaluate side-chains 473 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 210 ASP Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 381 ARG Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 252 ASP Chi-restraints excluded: chain P residue 255 ASN Chi-restraints excluded: chain P residue 314 SER Chi-restraints excluded: chain Q residue 82 MET Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 ARG Chi-restraints excluded: chain W residue 48 GLU Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 329 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 389 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33586 Z= 0.306 Angle : 0.607 18.344 45694 Z= 0.299 Chirality : 0.040 0.176 4992 Planarity : 0.005 0.100 5834 Dihedral : 6.892 89.815 4601 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 14.53 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.13), residues: 4082 helix: 2.03 (0.11), residues: 2022 sheet: -0.00 (0.25), residues: 406 loop : -0.34 (0.16), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 141 HIS 0.008 0.001 HIS P 201 PHE 0.012 0.002 PHE U 61 TYR 0.019 0.002 TYR N 4 ARG 0.017 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 424 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7317 (mm-40) cc_final: 0.7003 (tp40) REVERT: A 50 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: A 206 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7657 (ptm160) REVERT: B 28 ARG cc_start: 0.8315 (ttt180) cc_final: 0.8076 (ttt180) REVERT: B 351 ASN cc_start: 0.7739 (m-40) cc_final: 0.7004 (p0) REVERT: B 421 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7823 (ttm110) REVERT: C 11 MET cc_start: 0.6629 (mtt) cc_final: 0.6405 (mtp) REVERT: C 171 ASP cc_start: 0.8193 (t0) cc_final: 0.7739 (m-30) REVERT: C 254 ASP cc_start: 0.8367 (m-30) cc_final: 0.7816 (m-30) REVERT: D 204 MET cc_start: 0.8249 (mtp) cc_final: 0.8045 (mtp) REVERT: E 122 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.6522 (m-70) REVERT: F 39 GLU cc_start: 0.7780 (tt0) cc_final: 0.7314 (tt0) REVERT: F 45 GLU cc_start: 0.7761 (tp30) cc_final: 0.7159 (tp30) REVERT: F 69 SER cc_start: 0.9134 (t) cc_final: 0.8786 (m) REVERT: F 96 GLU cc_start: 0.7771 (tp30) cc_final: 0.7325 (mm-30) REVERT: J 48 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: J 58 LYS cc_start: 0.8388 (tmtt) cc_final: 0.7895 (mttp) REVERT: K 39 ARG cc_start: 0.7626 (mtp85) cc_final: 0.6681 (pmt170) REVERT: N 20 ASP cc_start: 0.7115 (p0) cc_final: 0.6783 (m-30) REVERT: N 203 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8898 (pp) REVERT: O 84 LYS cc_start: 0.8443 (tttt) cc_final: 0.7963 (tptt) REVERT: O 118 ILE cc_start: 0.8007 (mm) cc_final: 0.7671 (tt) REVERT: O 243 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: P 200 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8518 (tm) REVERT: P 331 ASP cc_start: 0.8884 (t70) cc_final: 0.8523 (t70) REVERT: Q 62 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7809 (tttp) REVERT: S 85 GLU cc_start: 0.7773 (mp0) cc_final: 0.7050 (tm-30) REVERT: S 110 LYS cc_start: 0.7702 (mttp) cc_final: 0.6668 (mmtm) REVERT: U 36 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.6936 (mtp85) REVERT: W 16 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: W 48 GLU cc_start: 0.7643 (pm20) cc_final: 0.7356 (pm20) REVERT: X 44 TRP cc_start: 0.7127 (m-10) cc_final: 0.6648 (m100) outliers start: 82 outliers final: 53 residues processed: 484 average time/residue: 2.0964 time to fit residues: 1263.5508 Evaluate side-chains 469 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 408 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 381 ARG Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 180 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 243 GLU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain P residue 252 ASP Chi-restraints excluded: chain P residue 314 SER Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 ARG Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 306 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 173 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33586 Z= 0.259 Angle : 0.579 16.114 45694 Z= 0.289 Chirality : 0.039 0.166 4992 Planarity : 0.005 0.111 5834 Dihedral : 6.799 89.657 4601 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.85 % Allowed : 15.51 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.13), residues: 4082 helix: 2.13 (0.11), residues: 2024 sheet: 0.02 (0.25), residues: 406 loop : -0.29 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 141 HIS 0.008 0.001 HIS P 201 PHE 0.011 0.001 PHE U 61 TYR 0.018 0.001 TYR N 4 ARG 0.019 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 423 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7312 (mm-40) cc_final: 0.6941 (tp40) REVERT: A 50 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: A 206 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7646 (ptm160) REVERT: B 28 ARG cc_start: 0.8302 (ttt180) cc_final: 0.8067 (ttt180) REVERT: B 227 ARG cc_start: 0.7816 (mmm160) cc_final: 0.7347 (tpp-160) REVERT: B 351 ASN cc_start: 0.7735 (m-40) cc_final: 0.6976 (p0) REVERT: B 421 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7821 (ttm110) REVERT: C 11 MET cc_start: 0.6611 (mtt) cc_final: 0.6392 (mtp) REVERT: C 162 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7300 (mm-30) REVERT: C 171 ASP cc_start: 0.8234 (t0) cc_final: 0.7731 (m-30) REVERT: C 254 ASP cc_start: 0.8374 (m-30) cc_final: 0.7813 (m-30) REVERT: D 204 MET cc_start: 0.8233 (mtp) cc_final: 0.8021 (mtp) REVERT: E 122 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.6554 (m-70) REVERT: F 39 GLU cc_start: 0.7757 (tt0) cc_final: 0.7299 (tt0) REVERT: F 45 GLU cc_start: 0.7738 (tp30) cc_final: 0.7132 (tp30) REVERT: F 69 SER cc_start: 0.9116 (t) cc_final: 0.8753 (m) REVERT: F 96 GLU cc_start: 0.7757 (tp30) cc_final: 0.7318 (mm-30) REVERT: G 73 ASN cc_start: 0.8341 (t0) cc_final: 0.8009 (p0) REVERT: J 48 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: J 58 LYS cc_start: 0.8388 (tmtt) cc_final: 0.7893 (mttp) REVERT: K 39 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6667 (pmt170) REVERT: N 203 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8909 (pp) REVERT: N 381 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7668 (ttp-110) REVERT: O 84 LYS cc_start: 0.8461 (tttt) cc_final: 0.7967 (tptt) REVERT: O 118 ILE cc_start: 0.7987 (mm) cc_final: 0.7672 (tt) REVERT: P 200 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8503 (tm) REVERT: P 331 ASP cc_start: 0.8866 (t70) cc_final: 0.8502 (t70) REVERT: Q 62 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7800 (tttp) REVERT: S 85 GLU cc_start: 0.7768 (mp0) cc_final: 0.7051 (tm-30) REVERT: S 103 GLU cc_start: 0.7957 (tp30) cc_final: 0.7623 (tt0) REVERT: S 110 LYS cc_start: 0.7697 (mttp) cc_final: 0.6665 (mmtm) REVERT: W 16 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7086 (tpp80) REVERT: X 44 TRP cc_start: 0.7115 (m-10) cc_final: 0.6645 (m100) outliers start: 64 outliers final: 44 residues processed: 468 average time/residue: 2.0888 time to fit residues: 1208.3183 Evaluate side-chains 463 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 411 time to evaluate : 5.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 381 ARG Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 200 LEU Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 16 ARG Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 3.9990 chunk 373 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 362 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 327 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 173 ASN R 108 GLN T 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33586 Z= 0.239 Angle : 0.569 15.315 45694 Z= 0.285 Chirality : 0.039 0.154 4992 Planarity : 0.005 0.088 5834 Dihedral : 6.706 89.995 4601 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.85 % Allowed : 15.60 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.13), residues: 4082 helix: 2.25 (0.11), residues: 2026 sheet: 0.03 (0.25), residues: 406 loop : -0.26 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 132 HIS 0.007 0.001 HIS W 45 PHE 0.017 0.001 PHE G 55 TYR 0.018 0.001 TYR N 4 ARG 0.014 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 417 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6929 (tp40) REVERT: A 50 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: A 206 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7626 (ptm160) REVERT: B 28 ARG cc_start: 0.8298 (ttt180) cc_final: 0.8070 (ttt180) REVERT: B 227 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7442 (tpp-160) REVERT: B 351 ASN cc_start: 0.7732 (m-40) cc_final: 0.6968 (p0) REVERT: B 421 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7818 (ttm110) REVERT: C 11 MET cc_start: 0.6613 (mtt) cc_final: 0.6396 (mtp) REVERT: C 162 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7294 (mm-30) REVERT: C 171 ASP cc_start: 0.8208 (t0) cc_final: 0.7708 (m-30) REVERT: C 254 ASP cc_start: 0.8351 (m-30) cc_final: 0.7811 (m-30) REVERT: D 204 MET cc_start: 0.8226 (mtp) cc_final: 0.7915 (mtp) REVERT: E 122 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.6545 (m-70) REVERT: F 39 GLU cc_start: 0.7727 (tt0) cc_final: 0.7203 (tt0) REVERT: F 45 GLU cc_start: 0.7721 (tp30) cc_final: 0.7417 (tp30) REVERT: F 69 SER cc_start: 0.9107 (t) cc_final: 0.8754 (m) REVERT: F 96 GLU cc_start: 0.7759 (tp30) cc_final: 0.7352 (mm-30) REVERT: G 73 ASN cc_start: 0.8355 (t0) cc_final: 0.8001 (p0) REVERT: J 48 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: J 58 LYS cc_start: 0.8390 (tmtt) cc_final: 0.7887 (mttp) REVERT: K 39 ARG cc_start: 0.7599 (mtp85) cc_final: 0.6650 (pmt170) REVERT: N 203 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8874 (pp) REVERT: N 381 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7626 (ttp-110) REVERT: O 84 LYS cc_start: 0.8470 (tttt) cc_final: 0.7985 (tptt) REVERT: O 118 ILE cc_start: 0.7960 (mm) cc_final: 0.7656 (tt) REVERT: O 120 MET cc_start: 0.8180 (ttp) cc_final: 0.7958 (ttm) REVERT: P 331 ASP cc_start: 0.8802 (t70) cc_final: 0.8437 (t70) REVERT: Q 62 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7793 (tttp) REVERT: S 85 GLU cc_start: 0.7766 (mp0) cc_final: 0.7055 (tm-30) REVERT: S 110 LYS cc_start: 0.7680 (mttp) cc_final: 0.6691 (mmtm) REVERT: U 36 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.6949 (mtp85) REVERT: X 44 TRP cc_start: 0.7115 (m-10) cc_final: 0.6645 (m100) outliers start: 64 outliers final: 47 residues processed: 460 average time/residue: 2.2183 time to fit residues: 1271.1802 Evaluate side-chains 456 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 403 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 122 HIS Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 76 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 203 LEU Chi-restraints excluded: chain N residue 348 SER Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 381 ARG Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain O residue 347 ILE Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 146 ILE Chi-restraints excluded: chain P residue 184 ILE Chi-restraints excluded: chain P residue 252 ASP Chi-restraints excluded: chain P residue 255 ASN Chi-restraints excluded: chain P residue 314 SER Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain X residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 383 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 402 optimal weight: 4.9990 chunk 370 optimal weight: 0.9980 chunk 320 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 247 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 165 GLN N 173 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33586 Z= 0.183 Angle : 0.541 12.724 45694 Z= 0.271 Chirality : 0.038 0.149 4992 Planarity : 0.004 0.082 5834 Dihedral : 6.568 88.156 4601 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.44 % Allowed : 16.12 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.13), residues: 4082 helix: 2.43 (0.11), residues: 2030 sheet: 0.11 (0.25), residues: 406 loop : -0.16 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 91 HIS 0.012 0.001 HIS W 45 PHE 0.012 0.001 PHE A 324 TYR 0.017 0.001 TYR N 4 ARG 0.014 0.000 ARG B 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8164 Ramachandran restraints generated. 4082 Oldfield, 0 Emsley, 4082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 423 time to evaluate : 4.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6911 (tp40) REVERT: A 206 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7571 (ptm160) REVERT: B 28 ARG cc_start: 0.8290 (ttt180) cc_final: 0.8069 (ttt180) REVERT: B 227 ARG cc_start: 0.7707 (mmm160) cc_final: 0.7413 (tpp-160) REVERT: B 351 ASN cc_start: 0.7737 (m-40) cc_final: 0.6850 (p0) REVERT: B 421 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7789 (ttm110) REVERT: C 162 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7291 (mm-30) REVERT: C 171 ASP cc_start: 0.8190 (t0) cc_final: 0.7696 (m-30) REVERT: C 254 ASP cc_start: 0.8346 (m-30) cc_final: 0.7853 (m-30) REVERT: D 204 MET cc_start: 0.8225 (mtp) cc_final: 0.7934 (mtp) REVERT: E 119 ASP cc_start: 0.7452 (t0) cc_final: 0.7204 (t0) REVERT: F 39 GLU cc_start: 0.7725 (tt0) cc_final: 0.7182 (tt0) REVERT: F 45 GLU cc_start: 0.7681 (tp30) cc_final: 0.7373 (tp30) REVERT: F 69 SER cc_start: 0.9089 (t) cc_final: 0.8726 (m) REVERT: G 73 ASN cc_start: 0.8362 (t0) cc_final: 0.7993 (p0) REVERT: J 48 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: J 58 LYS cc_start: 0.8377 (tmtt) cc_final: 0.7854 (mtmm) REVERT: K 39 ARG cc_start: 0.7561 (mtp85) cc_final: 0.6659 (pmt170) REVERT: N 124 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7536 (t0) REVERT: O 90 GLU cc_start: 0.8336 (tp30) cc_final: 0.7950 (tp30) REVERT: O 118 ILE cc_start: 0.7925 (mm) cc_final: 0.7645 (tt) REVERT: P 331 ASP cc_start: 0.8761 (t70) cc_final: 0.8412 (t70) REVERT: Q 62 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7779 (tttp) REVERT: S 85 GLU cc_start: 0.7733 (mp0) cc_final: 0.7117 (tm-30) REVERT: S 110 LYS cc_start: 0.7663 (mttp) cc_final: 0.6682 (mmtm) REVERT: U 36 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.6928 (mtp85) REVERT: X 44 TRP cc_start: 0.7107 (m-10) cc_final: 0.6646 (m100) outliers start: 50 outliers final: 33 residues processed: 458 average time/residue: 2.1321 time to fit residues: 1217.7753 Evaluate side-chains 444 residues out of total 3468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 408 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain C residue 70 CYS Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain G residue 6 HIS Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 48 GLU Chi-restraints excluded: chain N residue 124 ASP Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 350 THR Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 403 ASP Chi-restraints excluded: chain O residue 82 SER Chi-restraints excluded: chain O residue 193 ASP Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain O residue 400 GLN Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 252 ASP Chi-restraints excluded: chain Q residue 125 ASP Chi-restraints excluded: chain Q residue 208 MET Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain U residue 68 CYS Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 69 SER Chi-restraints excluded: chain W residue 4 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 329 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN G 3 GLN G 6 HIS N 136 GLN N 173 ASN P 255 ASN T 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.131296 restraints weight = 140584.612| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.99 r_work: 0.3560 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33586 Z= 0.205 Angle : 0.545 13.266 45694 Z= 0.271 Chirality : 0.038 0.148 4992 Planarity : 0.004 0.074 5834 Dihedral : 6.511 88.305 4601 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.27 % Allowed : 16.38 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.13), residues: 4082 helix: 2.49 (0.11), residues: 2028 sheet: 0.15 (0.25), residues: 406 loop : -0.12 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 91 HIS 0.006 0.001 HIS P 201 PHE 0.012 0.001 PHE A 324 TYR 0.016 0.001 TYR N 4 ARG 0.012 0.000 ARG B 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22054.50 seconds wall clock time: 375 minutes 42.74 seconds (22542.74 seconds total)