Starting phenix.real_space_refine on Tue Dec 31 05:23:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vsr_32114/12_2024/7vsr_32114_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vsr_32114/12_2024/7vsr_32114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vsr_32114/12_2024/7vsr_32114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vsr_32114/12_2024/7vsr_32114.map" model { file = "/net/cci-nas-00/data/ceres_data/7vsr_32114/12_2024/7vsr_32114_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vsr_32114/12_2024/7vsr_32114_trim.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 154 5.16 5 C 21400 2.51 5 N 5606 2.21 5 O 6222 1.98 5 H 32736 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66142 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "B" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "C" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4721 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "D" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4632 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "E" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4639 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "F" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "G" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "H" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4722 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "I" Number of atoms: 4721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4721 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 14, 'TRANS': 275} Chain: "J" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4632 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 14, 'TRANS': 269} Chain: "K" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4639 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "L" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4644 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain: "M" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4892 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 3 Chain: "N" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 4892 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain breaks: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 22.92, per 1000 atoms: 0.35 Number of scatterers: 66142 At special positions: 0 Unit cell: (160.5, 167.99, 125.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 154 16.00 P 18 15.00 Mg 6 11.99 O 6222 8.00 N 5606 7.00 C 21400 6.00 H 32736 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.85 Conformation dependent library (CDL) restraints added in 3.8 seconds 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 33 sheets defined 55.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.86 Creating SS restraints... Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.600A pdb=" N ALA A 173 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ASP A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 195 Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.636A pdb=" N ARG A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 3.516A pdb=" N ILE A 242 " --> pdb=" O TYR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 269 removed outlier: 3.775A pdb=" N GLU A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 removed outlier: 3.570A pdb=" N ALA A 284 " --> pdb=" O ILE A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.185A pdb=" N GLU A 298 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.660A pdb=" N ARG A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 348 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.516A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 395 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.831A pdb=" N CYS A 411 " --> pdb=" O HIS A 407 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 412' Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'B' and resid 169 through 175 removed outlier: 3.746A pdb=" N ALA B 173 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.563A pdb=" N ILE B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.673A pdb=" N ARG B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.716A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 343 through 348 Processing helix chain 'B' and resid 361 through 371 removed outlier: 3.607A pdb=" N ARG B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 371 " --> pdb=" O PHE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 395 removed outlier: 3.729A pdb=" N GLU B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.788A pdb=" N CYS B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 444 through 457 removed outlier: 3.852A pdb=" N GLN B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 3.783A pdb=" N ALA C 173 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 195 Processing helix chain 'C' and resid 206 through 220 removed outlier: 4.006A pdb=" N ARG C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 237 through 242 Processing helix chain 'C' and resid 257 through 269 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.616A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.177A pdb=" N ARG C 302 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.676A pdb=" N ARG C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 371 removed outlier: 3.556A pdb=" N ARG C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 395 Processing helix chain 'C' and resid 400 through 404 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 432 through 441 removed outlier: 3.520A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 457 removed outlier: 3.612A pdb=" N GLN C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 Processing helix chain 'D' and resid 206 through 220 Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.586A pdb=" N GLN D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 292 through 297 removed outlier: 4.114A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 343 through 350 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.809A pdb=" N ARG D 365 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 393 Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.553A pdb=" N CYS D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 407 through 412' Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.606A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 457 Processing helix chain 'E' and resid 180 through 195 removed outlier: 3.798A pdb=" N ILE E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 220 Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 257 through 269 removed outlier: 3.980A pdb=" N GLU E 268 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 291 Processing helix chain 'E' and resid 292 through 297 removed outlier: 4.419A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 297' Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 343 through 350 removed outlier: 3.573A pdb=" N ARG E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 370 Processing helix chain 'E' and resid 374 through 395 removed outlier: 3.642A pdb=" N GLU E 395 " --> pdb=" O GLU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 407 through 412 removed outlier: 3.726A pdb=" N CYS E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 407 through 412' Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'E' and resid 432 through 442 Processing helix chain 'E' and resid 444 through 457 removed outlier: 3.609A pdb=" N GLN E 448 " --> pdb=" O ASP E 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 195 Processing helix chain 'F' and resid 206 through 220 Processing helix chain 'F' and resid 237 through 242 Processing helix chain 'F' and resid 258 through 269 removed outlier: 3.676A pdb=" N GLU F 268 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 291 Processing helix chain 'F' and resid 292 through 297 removed outlier: 4.310A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 343 through 350 removed outlier: 3.915A pdb=" N ARG F 349 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 371 Processing helix chain 'F' and resid 374 through 395 removed outlier: 3.585A pdb=" N GLU F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 404 Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 421 through 432 removed outlier: 4.020A pdb=" N GLU F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE F 428 " --> pdb=" O TRP F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 441 Processing helix chain 'F' and resid 444 through 457 removed outlier: 3.625A pdb=" N GLN F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 455 " --> pdb=" O TRP F 451 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 177 removed outlier: 3.527A pdb=" N ALA G 173 " --> pdb=" O CYS G 169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP G 176 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU G 177 " --> pdb=" O ALA G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 195 Processing helix chain 'G' and resid 206 through 220 removed outlier: 3.667A pdb=" N ARG G 212 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 242 removed outlier: 3.503A pdb=" N ILE G 242 " --> pdb=" O TYR G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 269 removed outlier: 3.776A pdb=" N GLU G 268 " --> pdb=" O GLN G 264 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN G 269 " --> pdb=" O GLN G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 284 removed outlier: 3.561A pdb=" N ALA G 284 " --> pdb=" O ILE G 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 281 through 284' Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 293 through 298 removed outlier: 4.153A pdb=" N GLU G 298 " --> pdb=" O MET G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 307 Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 343 through 350 removed outlier: 3.666A pdb=" N ARG G 347 " --> pdb=" O ASP G 343 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG G 348 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG G 349 " --> pdb=" O ALA G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 371 Processing helix chain 'G' and resid 374 through 395 Processing helix chain 'G' and resid 400 through 404 Processing helix chain 'G' and resid 407 through 412 removed outlier: 4.007A pdb=" N CYS G 411 " --> pdb=" O HIS G 407 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS G 412 " --> pdb=" O SER G 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 407 through 412' Processing helix chain 'G' and resid 421 through 432 Processing helix chain 'G' and resid 432 through 441 removed outlier: 3.564A pdb=" N LEU G 436 " --> pdb=" O ASP G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 457 Processing helix chain 'H' and resid 169 through 175 removed outlier: 3.549A pdb=" N ALA H 173 " --> pdb=" O CYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 195 Processing helix chain 'H' and resid 206 through 220 removed outlier: 3.819A pdb=" N ARG H 212 " --> pdb=" O THR H 208 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 225 No H-bonds generated for 'chain 'H' and resid 223 through 225' Processing helix chain 'H' and resid 237 through 242 Processing helix chain 'H' and resid 257 through 269 removed outlier: 3.743A pdb=" N GLU H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN H 269 " --> pdb=" O GLN H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 291 Processing helix chain 'H' and resid 292 through 297 removed outlier: 3.662A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 307 Processing helix chain 'H' and resid 343 through 350 removed outlier: 3.509A pdb=" N ARG H 349 " --> pdb=" O ALA H 345 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE H 350 " --> pdb=" O LEU H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 371 removed outlier: 3.649A pdb=" N ARG H 365 " --> pdb=" O THR H 361 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 371 " --> pdb=" O PHE H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 395 removed outlier: 3.530A pdb=" N GLU H 395 " --> pdb=" O GLU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 404 Processing helix chain 'H' and resid 407 through 412 removed outlier: 3.803A pdb=" N CYS H 412 " --> pdb=" O SER H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 432 Processing helix chain 'H' and resid 432 through 442 removed outlier: 3.518A pdb=" N LEU H 436 " --> pdb=" O ASP H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 457 Processing helix chain 'I' and resid 169 through 175 removed outlier: 3.724A pdb=" N ALA I 173 " --> pdb=" O CYS I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 195 Processing helix chain 'I' and resid 206 through 220 removed outlier: 3.967A pdb=" N ARG I 212 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG I 213 " --> pdb=" O PHE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'I' and resid 237 through 242 Processing helix chain 'I' and resid 257 through 269 Processing helix chain 'I' and resid 281 through 284 Processing helix chain 'I' and resid 285 through 291 Processing helix chain 'I' and resid 292 through 297 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 343 through 350 removed outlier: 3.747A pdb=" N ARG I 349 " --> pdb=" O ALA I 345 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE I 350 " --> pdb=" O LEU I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 371 removed outlier: 3.629A pdb=" N ARG I 365 " --> pdb=" O THR I 361 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 395 Processing helix chain 'I' and resid 400 through 404 Processing helix chain 'I' and resid 407 through 412 Processing helix chain 'I' and resid 421 through 432 Processing helix chain 'I' and resid 432 through 441 removed outlier: 3.582A pdb=" N LEU I 436 " --> pdb=" O ASP I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 457 Processing helix chain 'J' and resid 180 through 195 Processing helix chain 'J' and resid 206 through 220 Processing helix chain 'J' and resid 237 through 242 Processing helix chain 'J' and resid 257 through 269 Processing helix chain 'J' and resid 281 through 284 removed outlier: 3.540A pdb=" N ALA J 284 " --> pdb=" O ILE J 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 281 through 284' Processing helix chain 'J' and resid 285 through 291 Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.638A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 343 through 350 removed outlier: 3.516A pdb=" N ARG J 347 " --> pdb=" O ASP J 343 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG J 349 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 371 removed outlier: 3.514A pdb=" N ARG J 365 " --> pdb=" O THR J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 395 removed outlier: 4.026A pdb=" N GLU J 395 " --> pdb=" O GLU J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 404 Processing helix chain 'J' and resid 407 through 412 removed outlier: 3.524A pdb=" N CYS J 412 " --> pdb=" O SER J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 421 through 432 Processing helix chain 'J' and resid 432 through 441 Processing helix chain 'J' and resid 444 through 457 Processing helix chain 'K' and resid 180 through 195 Processing helix chain 'K' and resid 206 through 220 Processing helix chain 'K' and resid 237 through 242 Processing helix chain 'K' and resid 257 through 269 removed outlier: 3.805A pdb=" N GLU K 268 " --> pdb=" O GLN K 264 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN K 269 " --> pdb=" O GLN K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 284 removed outlier: 3.515A pdb=" N ALA K 284 " --> pdb=" O ILE K 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 281 through 284' Processing helix chain 'K' and resid 285 through 291 removed outlier: 3.519A pdb=" N VAL K 289 " --> pdb=" O ASN K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 297 removed outlier: 4.114A pdb=" N LEU K 296 " --> pdb=" O GLU K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 307 Processing helix chain 'K' and resid 343 through 350 removed outlier: 3.599A pdb=" N ARG K 347 " --> pdb=" O ASP K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 371 removed outlier: 3.553A pdb=" N ARG K 365 " --> pdb=" O THR K 361 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS K 371 " --> pdb=" O PHE K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 395 removed outlier: 3.632A pdb=" N GLU K 395 " --> pdb=" O GLU K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 404 Processing helix chain 'K' and resid 407 through 412 removed outlier: 3.546A pdb=" N CYS K 411 " --> pdb=" O HIS K 407 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS K 412 " --> pdb=" O SER K 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 407 through 412' Processing helix chain 'K' and resid 421 through 432 Processing helix chain 'K' and resid 432 through 442 removed outlier: 3.534A pdb=" N LEU K 436 " --> pdb=" O ASP K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 457 Processing helix chain 'L' and resid 180 through 195 Processing helix chain 'L' and resid 206 through 220 Processing helix chain 'L' and resid 237 through 242 Processing helix chain 'L' and resid 258 through 269 removed outlier: 3.652A pdb=" N GLU L 268 " --> pdb=" O GLN L 264 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 284 Processing helix chain 'L' and resid 285 through 291 Processing helix chain 'L' and resid 292 through 297 removed outlier: 3.700A pdb=" N LEU L 296 " --> pdb=" O GLU L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 307 Processing helix chain 'L' and resid 343 through 350 removed outlier: 3.540A pdb=" N ARG L 349 " --> pdb=" O ALA L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 371 removed outlier: 3.514A pdb=" N ARG L 365 " --> pdb=" O THR L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 395 removed outlier: 3.677A pdb=" N GLU L 395 " --> pdb=" O GLU L 391 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 404 Processing helix chain 'L' and resid 407 through 412 removed outlier: 3.549A pdb=" N CYS L 411 " --> pdb=" O HIS L 407 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS L 412 " --> pdb=" O SER L 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 407 through 412' Processing helix chain 'L' and resid 421 through 432 Processing helix chain 'L' and resid 432 through 441 Processing helix chain 'L' and resid 444 through 457 Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.596A pdb=" N ILE M 11 " --> pdb=" O PRO M 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR M 13 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET M 14 " --> pdb=" O ASN M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 57 removed outlier: 3.564A pdb=" N ILE M 41 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU M 51 " --> pdb=" O ASN M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 81 Processing helix chain 'M' and resid 85 through 99 Processing helix chain 'M' and resid 108 through 115 removed outlier: 3.782A pdb=" N PHE M 112 " --> pdb=" O THR M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 118 No H-bonds generated for 'chain 'M' and resid 116 through 118' Processing helix chain 'M' and resid 121 through 137 removed outlier: 3.727A pdb=" N LYS M 125 " --> pdb=" O THR M 121 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE M 126 " --> pdb=" O ARG M 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 175 removed outlier: 3.506A pdb=" N MET M 159 " --> pdb=" O ASN M 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG M 172 " --> pdb=" O TYR M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 228 removed outlier: 3.827A pdb=" N PHE M 227 " --> pdb=" O TYR M 223 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER M 228 " --> pdb=" O LYS M 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 223 through 228' Processing helix chain 'M' and resid 239 through 251 removed outlier: 4.010A pdb=" N GLN M 243 " --> pdb=" O GLN M 239 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN M 246 " --> pdb=" O TYR M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 310 Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.573A pdb=" N ILE N 11 " --> pdb=" O PRO N 7 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET N 14 " --> pdb=" O ASN N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 57 removed outlier: 3.540A pdb=" N ILE N 41 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU N 51 " --> pdb=" O ASN N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 81 Processing helix chain 'N' and resid 85 through 99 Processing helix chain 'N' and resid 108 through 115 removed outlier: 3.791A pdb=" N PHE N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 116 through 118 No H-bonds generated for 'chain 'N' and resid 116 through 118' Processing helix chain 'N' and resid 121 through 137 removed outlier: 3.762A pdb=" N LYS N 125 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE N 126 " --> pdb=" O ARG N 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL N 127 " --> pdb=" O TYR N 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 175 removed outlier: 3.552A pdb=" N ARG N 172 " --> pdb=" O TYR N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 228 removed outlier: 3.819A pdb=" N PHE N 227 " --> pdb=" O TYR N 223 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER N 228 " --> pdb=" O LYS N 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 223 through 228' Processing helix chain 'N' and resid 239 through 251 removed outlier: 4.017A pdb=" N GLN N 243 " --> pdb=" O GLN N 239 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN N 246 " --> pdb=" O TYR N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 310 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 231 removed outlier: 6.734A pdb=" N ASN A 228 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP A 279 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 230 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A 274 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 329 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE A 276 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 331 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 278 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASN A 333 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 197 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 247 Processing sheet with id=AA3, first strand: chain 'B' and resid 227 through 231 removed outlier: 6.594A pdb=" N ASN B 228 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP B 279 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 230 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR B 274 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 329 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 276 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 331 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE B 278 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASN B 333 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA6, first strand: chain 'C' and resid 227 through 231 removed outlier: 7.072A pdb=" N ASN C 196 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ILE C 353 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 198 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 243 through 247 Processing sheet with id=AA8, first strand: chain 'D' and resid 227 through 231 removed outlier: 6.423A pdb=" N ASN D 228 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP D 279 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 230 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N PHE D 276 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU D 331 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE D 278 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN D 333 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN D 196 " --> pdb=" O SER D 351 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D 353 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 198 " --> pdb=" O ILE D 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AB1, first strand: chain 'E' and resid 227 through 231 removed outlier: 6.629A pdb=" N ASN E 228 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ASP E 279 " --> pdb=" O ASN E 228 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL E 230 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR E 274 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE E 329 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE E 276 " --> pdb=" O ILE E 329 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU E 331 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 278 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER E 351 " --> pdb=" O ASN E 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 243 through 247 Processing sheet with id=AB3, first strand: chain 'E' and resid 308 through 309 Processing sheet with id=AB4, first strand: chain 'F' and resid 227 through 231 removed outlier: 6.731A pdb=" N ASN F 228 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASP F 279 " --> pdb=" O ASN F 228 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL F 230 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 243 through 247 Processing sheet with id=AB6, first strand: chain 'F' and resid 308 through 309 Processing sheet with id=AB7, first strand: chain 'G' and resid 227 through 231 removed outlier: 6.770A pdb=" N ASN G 228 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP G 279 " --> pdb=" O ASN G 228 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL G 230 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR G 274 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE G 329 " --> pdb=" O TYR G 274 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE G 276 " --> pdb=" O ILE G 329 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 331 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE G 278 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 197 " --> pdb=" O ILE G 328 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 243 through 247 Processing sheet with id=AB9, first strand: chain 'H' and resid 227 through 231 removed outlier: 6.691A pdb=" N ASN H 228 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ASP H 279 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL H 230 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR H 274 " --> pdb=" O TYR H 327 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE H 329 " --> pdb=" O TYR H 274 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE H 276 " --> pdb=" O ILE H 329 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU H 331 " --> pdb=" O PHE H 276 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE H 278 " --> pdb=" O LEU H 331 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN H 333 " --> pdb=" O ILE H 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 243 through 247 Processing sheet with id=AC2, first strand: chain 'I' and resid 227 through 231 removed outlier: 6.709A pdb=" N ASN I 228 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ASP I 279 " --> pdb=" O ASN I 228 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL I 230 " --> pdb=" O ASP I 279 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR I 274 " --> pdb=" O TYR I 327 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE I 329 " --> pdb=" O TYR I 274 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE I 276 " --> pdb=" O ILE I 329 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU I 331 " --> pdb=" O PHE I 276 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE I 278 " --> pdb=" O LEU I 331 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN I 333 " --> pdb=" O ILE I 278 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE I 197 " --> pdb=" O ILE I 328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 243 through 247 Processing sheet with id=AC4, first strand: chain 'J' and resid 227 through 231 removed outlier: 6.480A pdb=" N ASN J 228 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP J 279 " --> pdb=" O ASN J 228 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL J 230 " --> pdb=" O ASP J 279 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR J 274 " --> pdb=" O TYR J 327 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE J 329 " --> pdb=" O TYR J 274 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE J 276 " --> pdb=" O ILE J 329 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU J 331 " --> pdb=" O PHE J 276 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE J 278 " --> pdb=" O LEU J 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 243 through 247 removed outlier: 3.594A pdb=" N GLY J 244 " --> pdb=" O LYS J 255 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 227 through 231 removed outlier: 6.595A pdb=" N ASN K 228 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ASP K 279 " --> pdb=" O ASN K 228 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL K 230 " --> pdb=" O ASP K 279 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR K 274 " --> pdb=" O TYR K 327 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE K 329 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE K 276 " --> pdb=" O ILE K 329 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU K 331 " --> pdb=" O PHE K 276 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE K 278 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 243 through 247 Processing sheet with id=AC8, first strand: chain 'L' and resid 227 through 231 removed outlier: 6.643A pdb=" N ASN L 228 " --> pdb=" O ILE L 277 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP L 279 " --> pdb=" O ASN L 228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL L 230 " --> pdb=" O ASP L 279 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR L 274 " --> pdb=" O TYR L 327 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE L 329 " --> pdb=" O TYR L 274 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE L 276 " --> pdb=" O ILE L 329 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU L 331 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE L 278 " --> pdb=" O LEU L 331 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 243 through 247 Processing sheet with id=AD1, first strand: chain 'M' and resid 139 through 140 Processing sheet with id=AD2, first strand: chain 'M' and resid 179 through 181 removed outlier: 3.610A pdb=" N ILE M 207 " --> pdb=" O VAL M 218 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP M 282 " --> pdb=" O ILE M 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 184 through 185 removed outlier: 4.699A pdb=" N MET M 203 " --> pdb=" O LEU M 185 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 139 through 140 Processing sheet with id=AD5, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.611A pdb=" N ILE N 207 " --> pdb=" O VAL N 218 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP N 282 " --> pdb=" O ILE N 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 184 through 185 removed outlier: 4.688A pdb=" N MET N 203 " --> pdb=" O LEU N 185 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4185 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: 21.47 Time building geometry restraints manager: 15.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 32674 1.03 - 1.23: 289 1.23 - 1.43: 14404 1.43 - 1.62: 19297 1.62 - 1.82: 258 Bond restraints: 66922 Sorted by residual: bond pdb=" N3B GNP I1001 " pdb=" PG GNP I1001 " ideal model delta sigma weight residual 1.801 1.625 0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" N3B GNP H1001 " pdb=" PG GNP H1001 " ideal model delta sigma weight residual 1.801 1.626 0.175 2.00e-02 2.50e+03 7.69e+01 bond pdb=" N3B GNP C1001 " pdb=" PG GNP C1001 " ideal model delta sigma weight residual 1.801 1.627 0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" N3B GNP B1001 " pdb=" PG GNP B1001 " ideal model delta sigma weight residual 1.801 1.627 0.174 2.00e-02 2.50e+03 7.59e+01 bond pdb=" N3B GNP A1001 " pdb=" PG GNP A1001 " ideal model delta sigma weight residual 1.801 1.628 0.173 2.00e-02 2.50e+03 7.48e+01 ... (remaining 66917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 119293 1.95 - 3.89: 1285 3.89 - 5.84: 149 5.84 - 7.79: 14 7.79 - 9.74: 7 Bond angle restraints: 120748 Sorted by residual: angle pdb=" N VAL A 289 " pdb=" CA VAL A 289 " pdb=" C VAL A 289 " ideal model delta sigma weight residual 111.45 107.68 3.77 9.30e-01 1.16e+00 1.65e+01 angle pdb=" N LEU I 346 " pdb=" CA LEU I 346 " pdb=" C LEU I 346 " ideal model delta sigma weight residual 111.36 106.97 4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" CA GLY J 244 " pdb=" C GLY J 244 " pdb=" N TYR J 245 " ideal model delta sigma weight residual 114.67 119.14 -4.47 1.11e+00 8.12e-01 1.62e+01 angle pdb=" N GLY I 249 " pdb=" CA GLY I 249 " pdb=" C GLY I 249 " ideal model delta sigma weight residual 113.18 103.70 9.48 2.37e+00 1.78e-01 1.60e+01 angle pdb=" N ALA I 345 " pdb=" CA ALA I 345 " pdb=" C ALA I 345 " ideal model delta sigma weight residual 111.28 107.20 4.08 1.09e+00 8.42e-01 1.40e+01 ... (remaining 120743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 28567 17.60 - 35.19: 2315 35.19 - 52.79: 574 52.79 - 70.38: 123 70.38 - 87.98: 15 Dihedral angle restraints: 31594 sinusoidal: 17236 harmonic: 14358 Sorted by residual: dihedral pdb=" CA ASN B 285 " pdb=" C ASN B 285 " pdb=" N LEU B 286 " pdb=" CA LEU B 286 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ASN L 370 " pdb=" C ASN L 370 " pdb=" N LYS L 371 " pdb=" CA LYS L 371 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA K 335 " pdb=" C ALA K 335 " pdb=" N ASP K 336 " pdb=" CA ASP K 336 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 31591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3486 0.036 - 0.071: 912 0.071 - 0.107: 367 0.107 - 0.142: 106 0.142 - 0.178: 15 Chirality restraints: 4886 Sorted by residual: chirality pdb=" CA ARG I 283 " pdb=" N ARG I 283 " pdb=" C ARG I 283 " pdb=" CB ARG I 283 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ARG K 349 " pdb=" N ARG K 349 " pdb=" C ARG K 349 " pdb=" CB ARG K 349 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA TRP H 306 " pdb=" N TRP H 306 " pdb=" C TRP H 306 " pdb=" CB TRP H 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 4883 not shown) Planarity restraints: 9808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 287 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C SER B 287 " 0.056 2.00e-02 2.50e+03 pdb=" O SER B 287 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS B 288 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 287 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C SER C 287 " 0.052 2.00e-02 2.50e+03 pdb=" O SER C 287 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS C 288 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 450 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C LYS I 450 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS I 450 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP I 451 " 0.017 2.00e-02 2.50e+03 ... (remaining 9805 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 653 1.96 - 2.62: 84062 2.62 - 3.28: 203140 3.28 - 3.94: 243939 3.94 - 4.60: 396742 Nonbonded interactions: 928536 Sorted by model distance: nonbonded pdb=" O PHE B 441 " pdb="HH12 ARG M 122 " model vdw 1.305 2.450 nonbonded pdb=" O ILE H 242 " pdb=" H GLY H 257 " model vdw 1.410 2.450 nonbonded pdb=" O ILE E 242 " pdb=" H GLY E 257 " model vdw 1.413 2.450 nonbonded pdb=" H ASN H 248 " pdb=" O GLY H 251 " model vdw 1.419 2.450 nonbonded pdb=" O PHE H 441 " pdb="HH12 ARG N 122 " model vdw 1.425 2.450 ... (remaining 928531 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' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'B' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'C' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'D' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 254 or (resid 25 \ 5 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid \ 256 through 340 or (resid 341 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or n \ ame HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through 346 or (r \ esid 347 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'E' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 457)) selection = (chain 'F' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 254 or (resid 255 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 256 through 340 or (resid 341 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or \ name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or nam \ e HG23)) or resid 342 through 346 or (resid 347 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 348 throu \ gh 457)) selection = (chain 'G' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'H' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 406 or (resid 407 and (name \ N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD1 \ or name HD2 or name HE1)) or resid 408 through 457)) selection = (chain 'I' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 233 or (resid 234 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2 or name H or name H \ A or name HB2 or name HB3 or name HG2 or name HG3)) or resid 235 through 254 or \ (resid 255 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ or name H or name HA or name HB2 or name HB3 or nam \ e HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) \ or resid 256 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name \ HG12 or name HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through \ 346 or (resid 347 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE or name HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'J' and (resid 174 through 207 or (resid 208 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 209 through 254 or (resid 25 \ 5 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ3)) or resid \ 256 through 340 or (resid 341 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or n \ ame HG13 or name HG21 or name HG22 or name HG23)) or resid 342 through 346 or (r \ esid 347 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA or name \ HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or na \ me HH11 or name HH12)) or resid 348 through 457)) selection = (chain 'K' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 457)) selection = (chain 'L' and ((resid 174 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name H \ G or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23) \ ) or resid 175 through 207 or (resid 208 and (name N or name CA or name C or nam \ e O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name H \ G21 or name HG22 or name HG23)) or resid 209 through 233 or (resid 234 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1 o \ r name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3) \ ) or resid 235 through 254 or (resid 255 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE or name NZ or name H or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name \ HE2 or name HE3 or name HZ3)) or resid 256 through 340 or (resid 341 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2 or name HA or \ name HB or name HG11 or name HG12 or name HG13 or name HG21 or name HG22 or nam \ e HG23)) or resid 342 through 346 or (resid 347 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ r name HD2 or name HD3 or name HE or name HH11 or name HH12)) or resid 348 throu \ gh 457)) } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.810 Extract box with map and model: 1.800 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 99.010 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.200 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5820 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 0.176 34186 Z= 0.306 Angle : 0.725 9.735 46208 Z= 0.429 Chirality : 0.041 0.178 4886 Planarity : 0.005 0.089 5980 Dihedral : 13.560 87.976 13056 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.97 % Rotamer: Outliers : 1.90 % Allowed : 7.52 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.12), residues: 4000 helix: 0.08 (0.11), residues: 1716 sheet: 0.45 (0.23), residues: 520 loop : -0.48 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 306 HIS 0.008 0.001 HIS K 407 PHE 0.030 0.002 PHE E 252 TYR 0.022 0.002 TYR N 308 ARG 0.013 0.001 ARG K 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 906 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 837 time to evaluate : 4.082 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 214 LEU cc_start: 0.7999 (mt) cc_final: 0.7504 (tp) REVERT: C 230 VAL cc_start: 0.8309 (m) cc_final: 0.8083 (p) REVERT: C 286 LEU cc_start: 0.8207 (mt) cc_final: 0.7963 (mt) REVERT: C 297 MET cc_start: 0.8088 (ptm) cc_final: 0.7696 (ptm) REVERT: C 388 LEU cc_start: 0.8598 (tp) cc_final: 0.8156 (tt) REVERT: G 177 LEU cc_start: 0.6369 (mt) cc_final: 0.6155 (mp) REVERT: G 297 MET cc_start: 0.3298 (tmt) cc_final: 0.2509 (ppp) REVERT: I 388 LEU cc_start: 0.8645 (tp) cc_final: 0.8413 (tt) REVERT: M 58 LEU cc_start: 0.4785 (mt) cc_final: 0.4485 (mt) REVERT: N 304 ILE cc_start: 0.8791 (mt) cc_final: 0.8294 (mm) outliers start: 69 outliers final: 26 residues processed: 897 average time/residue: 0.9852 time to fit residues: 1349.8721 Evaluate side-chains 543 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 517 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 0.4980 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 363 optimal weight: 7.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 231 GLN B 234 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN G 264 GLN K 386 ASN L 449 GLN M 106 HIS ** M 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 142 GLN ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34186 Z= 0.271 Angle : 0.630 17.520 46208 Z= 0.341 Chirality : 0.040 0.162 4886 Planarity : 0.005 0.079 5980 Dihedral : 6.448 57.996 4644 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.08 % Rotamer: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.37 (0.13), residues: 4000 helix: 1.04 (0.12), residues: 1778 sheet: 0.63 (0.24), residues: 474 loop : -0.64 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 306 HIS 0.017 0.002 HIS K 407 PHE 0.042 0.002 PHE K 442 TYR 0.023 0.002 TYR M 123 ARG 0.008 0.001 ARG G 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 579 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 576 time to evaluate : 4.013 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: C 297 MET cc_start: 0.8259 (ptm) cc_final: 0.7707 (ptm) REVERT: K 294 MET cc_start: 0.5150 (ttp) cc_final: 0.3908 (ttp) REVERT: L 222 LYS cc_start: 0.5487 (tptp) cc_final: 0.5037 (mptt) REVERT: M 131 CYS cc_start: 0.8353 (m) cc_final: 0.7855 (m) REVERT: N 131 CYS cc_start: 0.8382 (m) cc_final: 0.7977 (m) outliers start: 3 outliers final: 2 residues processed: 579 average time/residue: 0.9891 time to fit residues: 878.7764 Evaluate side-chains 473 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 471 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 360 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN C 243 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN G 383 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 HIS ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34186 Z= 0.283 Angle : 0.612 14.275 46208 Z= 0.332 Chirality : 0.039 0.172 4886 Planarity : 0.005 0.057 5980 Dihedral : 6.638 55.971 4644 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.13), residues: 4000 helix: 0.94 (0.12), residues: 1786 sheet: 0.12 (0.22), residues: 516 loop : -0.77 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 306 HIS 0.009 0.002 HIS K 407 PHE 0.039 0.002 PHE C 377 TYR 0.033 0.002 TYR M 163 ARG 0.015 0.001 ARG K 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 512 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 4.156 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 293 VAL cc_start: 0.8929 (t) cc_final: 0.8672 (t) REVERT: D 278 ILE cc_start: 0.6783 (mp) cc_final: 0.6051 (mp) REVERT: I 235 SER cc_start: 0.8035 (m) cc_final: 0.7473 (m) REVERT: L 222 LYS cc_start: 0.5410 (tptp) cc_final: 0.5028 (mptt) REVERT: M 131 CYS cc_start: 0.8460 (m) cc_final: 0.7997 (m) REVERT: N 131 CYS cc_start: 0.8354 (m) cc_final: 0.7952 (m) REVERT: N 142 GLN cc_start: 0.7014 (mp-120) cc_final: 0.6808 (mp10) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.9790 time to fit residues: 768.3863 Evaluate side-chains 436 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 264 GLN M 146 HIS M 237 HIS M 279 ASN N 246 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34186 Z= 0.306 Angle : 0.631 13.575 46208 Z= 0.343 Chirality : 0.039 0.160 4886 Planarity : 0.005 0.083 5980 Dihedral : 6.886 56.737 4644 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.12), residues: 4000 helix: 0.59 (0.11), residues: 1778 sheet: -0.35 (0.22), residues: 516 loop : -1.00 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.008 0.002 HIS I 299 PHE 0.031 0.002 PHE N 166 TYR 0.023 0.002 TYR M 308 ARG 0.014 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 458 time to evaluate : 4.481 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 MET cc_start: 0.6105 (mmm) cc_final: 0.5334 (mmm) REVERT: C 385 MET cc_start: 0.8381 (ptp) cc_final: 0.7943 (ptm) REVERT: D 297 MET cc_start: 0.7296 (ptm) cc_final: 0.7092 (ptm) REVERT: I 280 GLU cc_start: 0.5046 (mm-30) cc_final: 0.4440 (mm-30) REVERT: J 286 LEU cc_start: 0.6926 (tp) cc_final: 0.6350 (tp) REVERT: L 222 LYS cc_start: 0.5606 (tptp) cc_final: 0.5341 (mptt) REVERT: M 131 CYS cc_start: 0.8467 (m) cc_final: 0.8102 (m) REVERT: M 159 MET cc_start: 0.7153 (mmm) cc_final: 0.6929 (mmm) REVERT: N 131 CYS cc_start: 0.8533 (m) cc_final: 0.8097 (m) REVERT: N 159 MET cc_start: 0.7622 (mmm) cc_final: 0.7269 (mmm) outliers start: 2 outliers final: 1 residues processed: 460 average time/residue: 0.9552 time to fit residues: 675.8096 Evaluate side-chains 393 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 329 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 386 ASN D 231 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 453 ASN N 3 GLN ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34186 Z= 0.307 Angle : 0.633 13.497 46208 Z= 0.345 Chirality : 0.039 0.156 4886 Planarity : 0.005 0.063 5980 Dihedral : 6.860 57.478 4644 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.63 (0.12), residues: 4000 helix: 0.38 (0.11), residues: 1778 sheet: -0.73 (0.21), residues: 548 loop : -1.09 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 306 HIS 0.010 0.002 HIS B 233 PHE 0.024 0.002 PHE M 166 TYR 0.025 0.002 TYR M 163 ARG 0.007 0.001 ARG J 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 429 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 429 time to evaluate : 4.084 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: 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: 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: 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: 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: 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: 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: 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: 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: C 293 VAL cc_start: 0.9069 (t) cc_final: 0.8627 (t) REVERT: C 294 MET cc_start: 0.6351 (mmm) cc_final: 0.5992 (mmm) REVERT: C 331 LEU cc_start: 0.7538 (mt) cc_final: 0.7293 (mt) REVERT: D 297 MET cc_start: 0.7876 (ptm) cc_final: 0.7522 (ptm) REVERT: H 295 MET cc_start: 0.5285 (mmm) cc_final: 0.4889 (mmm) REVERT: I 280 GLU cc_start: 0.4873 (mm-30) cc_final: 0.4505 (mm-30) REVERT: K 409 TYR cc_start: 0.6268 (m-80) cc_final: 0.5972 (m-80) REVERT: M 131 CYS cc_start: 0.8638 (m) cc_final: 0.8197 (m) REVERT: N 131 CYS cc_start: 0.8404 (m) cc_final: 0.7985 (m) outliers start: 0 outliers final: 0 residues processed: 429 average time/residue: 0.9660 time to fit residues: 639.6726 Evaluate side-chains 370 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 2.9990 chunk 348 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 387 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 269 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34186 Z= 0.217 Angle : 0.555 13.369 46208 Z= 0.299 Chirality : 0.039 0.152 4886 Planarity : 0.005 0.086 5980 Dihedral : 6.643 59.696 4644 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.13), residues: 4000 helix: 0.65 (0.12), residues: 1788 sheet: -0.73 (0.20), residues: 582 loop : -0.93 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 249 HIS 0.008 0.001 HIS K 233 PHE 0.024 0.002 PHE I 232 TYR 0.028 0.002 TYR N 163 ARG 0.005 0.001 ARG K 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 5.276 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: 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: 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: 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: 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: 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: 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: 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: 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: K 409 TYR cc_start: 0.6245 (m-80) cc_final: 0.5959 (m-80) REVERT: M 14 MET cc_start: 0.6181 (mmp) cc_final: 0.5956 (mmp) REVERT: M 131 CYS cc_start: 0.8540 (m) cc_final: 0.8119 (m) REVERT: M 159 MET cc_start: 0.7208 (mmm) cc_final: 0.6804 (mmm) REVERT: N 131 CYS cc_start: 0.8406 (m) cc_final: 0.7991 (m) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.9980 time to fit residues: 656.0353 Evaluate side-chains 359 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 216 optimal weight: 8.9990 chunk 385 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34186 Z= 0.188 Angle : 0.530 17.857 46208 Z= 0.282 Chirality : 0.038 0.151 4886 Planarity : 0.004 0.077 5980 Dihedral : 6.466 62.116 4644 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.03 % Allowed : 0.72 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.13), residues: 4000 helix: 0.85 (0.12), residues: 1792 sheet: -0.65 (0.21), residues: 582 loop : -0.81 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 424 HIS 0.007 0.001 HIS B 233 PHE 0.053 0.002 PHE I 232 TYR 0.025 0.001 TYR N 163 ARG 0.004 0.000 ARG J 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 4.338 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: 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: 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: 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: 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: 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: 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: 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: 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: C 293 VAL cc_start: 0.9166 (t) cc_final: 0.8872 (t) REVERT: C 294 MET cc_start: 0.6236 (mmm) cc_final: 0.5946 (mmm) REVERT: C 388 LEU cc_start: 0.8770 (tt) cc_final: 0.8567 (tt) REVERT: D 297 MET cc_start: 0.7831 (ptm) cc_final: 0.7288 (ptm) REVERT: F 286 LEU cc_start: 0.6118 (tt) cc_final: 0.5872 (tt) REVERT: H 297 MET cc_start: 0.7361 (ppp) cc_final: 0.7003 (ppp) REVERT: M 131 CYS cc_start: 0.8456 (m) cc_final: 0.8069 (m) REVERT: M 159 MET cc_start: 0.7263 (mmm) cc_final: 0.6843 (mmm) REVERT: N 131 CYS cc_start: 0.8365 (m) cc_final: 0.7957 (m) outliers start: 1 outliers final: 1 residues processed: 414 average time/residue: 0.9411 time to fit residues: 605.4443 Evaluate side-chains 364 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN D 231 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** H 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34186 Z= 0.311 Angle : 0.633 14.898 46208 Z= 0.348 Chirality : 0.039 0.161 4886 Planarity : 0.005 0.074 5980 Dihedral : 6.879 67.264 4644 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.06 % Allowed : 0.85 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.13), residues: 4000 helix: 0.34 (0.11), residues: 1782 sheet: -1.08 (0.20), residues: 590 loop : -0.97 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 306 HIS 0.010 0.002 HIS B 233 PHE 0.029 0.002 PHE M 166 TYR 0.029 0.002 TYR N 163 ARG 0.008 0.001 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 392 time to evaluate : 4.067 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: D 297 MET cc_start: 0.8162 (ptm) cc_final: 0.7715 (ptm) REVERT: F 286 LEU cc_start: 0.6490 (tt) cc_final: 0.6154 (tt) REVERT: H 297 MET cc_start: 0.7561 (ppp) cc_final: 0.7206 (ppp) REVERT: I 350 PHE cc_start: 0.6206 (m-80) cc_final: 0.5957 (m-80) REVERT: M 131 CYS cc_start: 0.8626 (m) cc_final: 0.8226 (m) REVERT: N 131 CYS cc_start: 0.8574 (m) cc_final: 0.8235 (m) outliers start: 2 outliers final: 1 residues processed: 394 average time/residue: 0.9591 time to fit residues: 586.6769 Evaluate side-chains 340 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 10.0000 chunk 369 optimal weight: 0.9990 chunk 336 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 156 optimal weight: 0.0370 chunk 282 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 453 ASN H 228 ASN ** I 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34186 Z= 0.190 Angle : 0.541 15.051 46208 Z= 0.290 Chirality : 0.039 0.150 4886 Planarity : 0.005 0.093 5980 Dihedral : 6.484 58.295 4644 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.13), residues: 4000 helix: 0.67 (0.12), residues: 1794 sheet: -0.92 (0.20), residues: 598 loop : -0.81 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 424 HIS 0.007 0.001 HIS K 407 PHE 0.037 0.002 PHE F 241 TYR 0.028 0.001 TYR N 163 ARG 0.005 0.000 ARG J 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 399 time to evaluate : 4.146 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 293 VAL cc_start: 0.9132 (t) cc_final: 0.8512 (t) REVERT: F 286 LEU cc_start: 0.6355 (tt) cc_final: 0.6070 (tt) REVERT: H 297 MET cc_start: 0.7574 (ppp) cc_final: 0.6943 (ppp) REVERT: M 131 CYS cc_start: 0.8614 (m) cc_final: 0.8191 (m) REVERT: M 159 MET cc_start: 0.7494 (mmm) cc_final: 0.7025 (mmm) REVERT: N 131 CYS cc_start: 0.8549 (m) cc_final: 0.8174 (m) outliers start: 1 outliers final: 1 residues processed: 400 average time/residue: 0.9888 time to fit residues: 620.1360 Evaluate side-chains 348 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 347 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 231 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 398 optimal weight: 4.9990 chunk 366 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34186 Z= 0.247 Angle : 0.575 14.559 46208 Z= 0.311 Chirality : 0.038 0.153 4886 Planarity : 0.005 0.114 5980 Dihedral : 6.574 63.662 4644 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.13), residues: 4000 helix: 0.56 (0.12), residues: 1790 sheet: -1.08 (0.21), residues: 580 loop : -0.89 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 424 HIS 0.007 0.001 HIS B 233 PHE 0.033 0.002 PHE F 241 TYR 0.030 0.002 TYR N 163 ARG 0.015 0.001 ARG C 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue THR 208 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 388 time to evaluate : 4.101 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: D 281 ILE cc_start: 0.6834 (tt) cc_final: 0.6546 (tt) REVERT: D 297 MET cc_start: 0.8053 (ptm) cc_final: 0.7690 (ptm) REVERT: F 286 LEU cc_start: 0.6388 (tt) cc_final: 0.6029 (tt) REVERT: M 131 CYS cc_start: 0.8557 (m) cc_final: 0.8176 (m) REVERT: M 245 MET cc_start: 0.7090 (tpp) cc_final: 0.6766 (tpp) REVERT: N 131 CYS cc_start: 0.8551 (m) cc_final: 0.8182 (m) outliers start: 1 outliers final: 1 residues processed: 389 average time/residue: 0.9868 time to fit residues: 597.9967 Evaluate side-chains 344 residues out of total 3630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 343 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 10.0000 chunk 338 optimal weight: 0.0070 chunk 97 optimal weight: 6.9990 chunk 292 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 326 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 228 ASN ** I 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 HIS ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.053903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.042127 restraints weight = 887033.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.044062 restraints weight = 538467.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.045479 restraints weight = 359990.629| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34186 Z= 0.268 Angle : 0.601 14.595 46208 Z= 0.327 Chirality : 0.039 0.155 4886 Planarity : 0.006 0.155 5980 Dihedral : 6.671 60.911 4644 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.13), residues: 4000 helix: 0.36 (0.12), residues: 1794 sheet: -1.18 (0.21), residues: 580 loop : -1.03 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 424 HIS 0.006 0.001 HIS K 407 PHE 0.027 0.002 PHE F 241 TYR 0.030 0.002 TYR N 163 ARG 0.024 0.001 ARG C 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12373.91 seconds wall clock time: 215 minutes 27.52 seconds (12927.52 seconds total)