Starting phenix.real_space_refine on Fri Apr 12 00:52:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/04_2024/8ihr_35453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/04_2024/8ihr_35453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/04_2024/8ihr_35453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/04_2024/8ihr_35453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/04_2024/8ihr_35453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/04_2024/8ihr_35453_updated.pdb" } resolution = 2.5 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= 0.065 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: 5 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 C 15184 2.51 5 N 4424 2.21 5 O 4528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 312": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "H GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Time building chain proxies: 13.11, per 1000 atoms: 0.54 Number of scatterers: 24224 At special positions: 0 Unit cell: (138.55, 138.55, 103.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 16 29.99 S 72 16.00 O 4528 8.00 N 4424 7.00 C 15184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.75 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 32 sheets defined 38.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.531A pdb=" N GLU A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP A 98 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.036A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 312 through 334 Proline residue: A 316 - end of helix removed outlier: 4.435A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.705A pdb=" N VAL A 361 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 362 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.676A pdb=" N HIS A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'B' and resid 94 through 100 removed outlier: 4.438A pdb=" N ASP B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.043A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.502A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 312 through 334 Proline residue: B 316 - end of helix removed outlier: 4.420A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 367 through 382 removed outlier: 4.700A pdb=" N HIS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'C' and resid 94 through 100 removed outlier: 4.440A pdb=" N ASP C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 120 removed outlier: 4.043A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 142 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.503A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 312 through 334 Proline residue: C 316 - end of helix removed outlier: 4.420A pdb=" N ALA C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 325 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 367 through 382 removed outlier: 4.700A pdb=" N HIS C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'D' and resid 94 through 100 removed outlier: 4.439A pdb=" N ASP D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 120 removed outlier: 4.044A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 231 through 243 removed outlier: 3.502A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 312 through 334 Proline residue: D 316 - end of helix removed outlier: 4.419A pdb=" N ALA D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE D 325 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.700A pdb=" N HIS D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'E' and resid 94 through 100 removed outlier: 5.452A pdb=" N ASP E 98 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 277 through 286 Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.985A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 334 Proline residue: E 316 - end of helix removed outlier: 4.531A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER E 326 " --> pdb=" O GLY E 322 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 367 through 382 removed outlier: 3.537A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'F' and resid 94 through 100 removed outlier: 5.450A pdb=" N ASP F 98 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 119 removed outlier: 4.164A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 231 through 243 Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 277 through 286 Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.991A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 334 Proline residue: F 316 - end of helix removed outlier: 4.528A pdb=" N ALA F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE F 325 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N SER F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.539A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'G' and resid 94 through 100 removed outlier: 5.450A pdb=" N ASP G 98 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG G 100 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 119 removed outlier: 4.164A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 142 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 191 through 203 Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 277 through 286 Processing helix chain 'G' and resid 294 through 305 removed outlier: 3.985A pdb=" N ALA G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 334 Proline residue: G 316 - end of helix removed outlier: 4.528A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE G 325 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 367 through 382 removed outlier: 3.537A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 Processing helix chain 'H' and resid 94 through 100 removed outlier: 5.451A pdb=" N ASP H 98 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG H 100 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 172 through 178 Processing helix chain 'H' and resid 191 through 203 Processing helix chain 'H' and resid 231 through 243 Processing helix chain 'H' and resid 255 through 264 Processing helix chain 'H' and resid 277 through 286 Processing helix chain 'H' and resid 294 through 305 removed outlier: 3.993A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 333 Proline residue: H 316 - end of helix removed outlier: 4.527A pdb=" N ALA H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE H 325 " --> pdb=" O ILE H 321 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER H 326 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLN H 327 " --> pdb=" O ALA H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 363 removed outlier: 4.027A pdb=" N GLU H 362 " --> pdb=" O TYR H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 382 removed outlier: 3.540A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA H 378 " --> pdb=" O ALA H 374 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 413 Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.361A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.571A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 420 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 149 through 152 removed outlier: 7.082A pdb=" N TRP A 79 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 125 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP A 81 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP A 127 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.561A pdb=" N SER A 268 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP A 289 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.364A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.571A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS B 420 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 149 through 152 removed outlier: 7.082A pdb=" N TRP B 79 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 125 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 81 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP B 127 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 249 through 251 removed outlier: 6.559A pdb=" N SER B 268 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP B 289 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.363A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.570A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS C 420 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 149 through 152 removed outlier: 7.084A pdb=" N TRP C 79 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL C 125 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP C 81 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASP C 127 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 249 through 251 removed outlier: 6.559A pdb=" N SER C 268 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP C 289 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.364A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.565A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS D 420 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 149 through 152 removed outlier: 7.084A pdb=" N TRP D 79 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL D 125 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP D 81 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 127 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 249 through 251 removed outlier: 6.560A pdb=" N SER D 268 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP D 289 " --> pdb=" O ILE D 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.644A pdb=" N GLN E 53 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA E 47 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.583A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 149 through 152 removed outlier: 7.096A pdb=" N TRP E 79 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL E 125 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP E 81 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP E 127 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 249 through 251 removed outlier: 6.636A pdb=" N SER E 268 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP E 289 " --> pdb=" O ILE E 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.638A pdb=" N GLN F 53 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA F 47 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.581A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 149 through 152 removed outlier: 7.095A pdb=" N TRP F 79 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL F 125 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP F 81 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP F 127 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 249 through 251 removed outlier: 6.633A pdb=" N SER F 268 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP F 289 " --> pdb=" O ILE F 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.645A pdb=" N GLN G 53 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA G 47 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.583A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 149 through 152 removed outlier: 7.098A pdb=" N TRP G 79 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL G 125 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP G 81 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP G 127 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 249 through 251 removed outlier: 6.635A pdb=" N SER G 268 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP G 289 " --> pdb=" O ILE G 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 66 through 70 removed outlier: 3.647A pdb=" N GLN H 53 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA H 47 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.582A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 149 through 152 removed outlier: 7.096A pdb=" N TRP H 79 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL H 125 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP H 81 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP H 127 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 249 through 251 removed outlier: 6.638A pdb=" N SER H 268 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP H 289 " --> pdb=" O ILE H 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF 900 hydrogen bonds defined for protein. 2355 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: 8.27 Time building geometry restraints manager: 10.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4626 1.32 - 1.45: 6097 1.45 - 1.57: 13853 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24704 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX A 210 " pdb=" CX KCX A 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX G 210 " pdb=" CX KCX G 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" NZ KCX H 210 " pdb=" CX KCX H 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 24699 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.24: 733 106.24 - 113.18: 12950 113.18 - 120.12: 9041 120.12 - 127.07: 10495 127.07 - 134.01: 277 Bond angle restraints: 33496 Sorted by residual: angle pdb=" N VAL C 347 " pdb=" CA VAL C 347 " pdb=" C VAL C 347 " ideal model delta sigma weight residual 111.67 101.21 10.46 9.50e-01 1.11e+00 1.21e+02 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 111.67 101.42 10.25 9.50e-01 1.11e+00 1.16e+02 angle pdb=" N GLY C 346 " pdb=" CA GLY C 346 " pdb=" C GLY C 346 " ideal model delta sigma weight residual 113.18 102.11 11.07 2.37e+00 1.78e-01 2.18e+01 angle pdb=" C GLN C 345 " pdb=" CA GLN C 345 " pdb=" CB GLN C 345 " ideal model delta sigma weight residual 109.72 117.46 -7.74 1.66e+00 3.63e-01 2.17e+01 angle pdb=" C GLN B 345 " pdb=" CA GLN B 345 " pdb=" CB GLN B 345 " ideal model delta sigma weight residual 109.72 117.43 -7.71 1.66e+00 3.63e-01 2.16e+01 ... (remaining 33491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 12882 17.58 - 35.16: 1251 35.16 - 52.74: 368 52.74 - 70.33: 86 70.33 - 87.91: 29 Dihedral angle restraints: 14616 sinusoidal: 5656 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN D 345 " pdb=" C GLN D 345 " pdb=" N GLY D 346 " pdb=" CA GLY D 346 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY F 272 " pdb=" C GLY F 272 " pdb=" N THR F 273 " pdb=" CA THR F 273 " ideal model delta harmonic sigma weight residual 180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2988 0.057 - 0.114: 610 0.114 - 0.171: 68 0.171 - 0.229: 6 0.229 - 0.286: 8 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CA VAL G 347 " pdb=" N VAL G 347 " pdb=" C VAL G 347 " pdb=" CB VAL G 347 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL E 347 " pdb=" N VAL E 347 " pdb=" C VAL E 347 " pdb=" CB VAL E 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA VAL H 347 " pdb=" N VAL H 347 " pdb=" C VAL H 347 " pdb=" CB VAL H 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3677 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 55 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO G 56 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 56 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 56 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 374 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.05e+00 pdb=" C ALA E 374 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA E 374 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 375 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 374 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C ALA G 374 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA G 374 " -0.017 2.00e-02 2.50e+03 pdb=" N THR G 375 " -0.016 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 412 2.69 - 3.24: 22041 3.24 - 3.80: 37679 3.80 - 4.35: 54855 4.35 - 4.90: 88642 Nonbonded interactions: 203629 Sorted by model distance: nonbonded pdb=" OQ2 KCX E 210 " pdb="ZN ZN E 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX F 210 " pdb="ZN ZN F 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX G 210 " pdb="ZN ZN G 501 " model vdw 2.139 2.230 nonbonded pdb=" OQ2 KCX H 210 " pdb="ZN ZN H 501 " model vdw 2.139 2.230 nonbonded pdb=" N GLN H 327 " pdb=" OE1 GLN H 327 " model vdw 2.216 2.520 ... (remaining 203624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 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: 0.040 Extract box with map and model: 11.390 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 70.390 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24704 Z= 0.239 Angle : 0.669 11.066 33496 Z= 0.401 Chirality : 0.048 0.286 3680 Planarity : 0.005 0.068 4464 Dihedral : 15.866 87.908 8912 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.70 % Allowed : 15.72 % Favored : 83.58 % 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: -0.52 (0.14), residues: 3136 helix: 0.21 (0.14), residues: 1344 sheet: -0.05 (0.24), residues: 400 loop : -0.90 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.012 0.001 PHE D 294 TYR 0.008 0.001 TYR A 95 ARG 0.006 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 2.787 Fit side-chains REVERT: E 55 LEU cc_start: 0.8051 (mm) cc_final: 0.7754 (mp) REVERT: E 331 LYS cc_start: 0.8278 (tptt) cc_final: 0.8011 (tttm) REVERT: F 55 LEU cc_start: 0.8062 (mm) cc_final: 0.7747 (mp) REVERT: F 277 ASP cc_start: 0.7809 (m-30) cc_final: 0.7472 (m-30) REVERT: G 55 LEU cc_start: 0.8039 (mm) cc_final: 0.7728 (mp) REVERT: G 277 ASP cc_start: 0.7718 (m-30) cc_final: 0.7409 (m-30) REVERT: H 55 LEU cc_start: 0.8062 (mm) cc_final: 0.7746 (mp) REVERT: H 331 LYS cc_start: 0.8376 (tttm) cc_final: 0.8017 (tptt) outliers start: 17 outliers final: 17 residues processed: 351 average time/residue: 1.5758 time to fit residues: 626.8541 Evaluate side-chains 339 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 322 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN B 335 ASN C 335 ASN D 335 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 24704 Z= 0.127 Angle : 0.481 7.282 33496 Z= 0.254 Chirality : 0.043 0.135 3680 Planarity : 0.004 0.046 4464 Dihedral : 5.232 52.369 3577 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.06 % Allowed : 14.44 % Favored : 83.50 % 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: -0.28 (0.15), residues: 3136 helix: 0.44 (0.14), residues: 1344 sheet: 0.11 (0.25), residues: 400 loop : -0.82 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 79 HIS 0.006 0.001 HIS C 251 PHE 0.012 0.001 PHE C 294 TYR 0.010 0.001 TYR C 95 ARG 0.004 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 324 time to evaluate : 2.777 Fit side-chains REVERT: A 419 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8632 (ttm) REVERT: B 419 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8624 (ttm) REVERT: C 419 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8640 (ttm) REVERT: D 419 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8623 (ttm) REVERT: E 55 LEU cc_start: 0.8108 (mm) cc_final: 0.7849 (mp) REVERT: F 55 LEU cc_start: 0.8114 (mm) cc_final: 0.7848 (mp) REVERT: G 55 LEU cc_start: 0.8090 (mm) cc_final: 0.7832 (mp) outliers start: 50 outliers final: 32 residues processed: 340 average time/residue: 1.6253 time to fit residues: 625.3863 Evaluate side-chains 355 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 319 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 353 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.0020 chunk 87 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 227 optimal weight: 9.9990 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 53 GLN A 335 ASN B 53 GLN B 335 ASN C 53 GLN C 335 ASN D 53 GLN D 335 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 24704 Z= 0.296 Angle : 0.604 8.965 33496 Z= 0.326 Chirality : 0.048 0.144 3680 Planarity : 0.005 0.048 4464 Dihedral : 5.491 55.981 3564 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.97 % Allowed : 15.14 % Favored : 81.89 % 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: -0.62 (0.14), residues: 3136 helix: 0.13 (0.14), residues: 1344 sheet: -0.15 (0.24), residues: 400 loop : -0.93 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 289 HIS 0.007 0.001 HIS D 271 PHE 0.016 0.002 PHE D 294 TYR 0.013 0.002 TYR C 95 ARG 0.004 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 324 time to evaluate : 2.641 Fit side-chains REVERT: A 155 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7628 (tmtm) REVERT: B 155 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7614 (tmtm) REVERT: C 155 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7635 (tmtm) REVERT: D 37 GLN cc_start: 0.7608 (mt0) cc_final: 0.7404 (mp10) REVERT: D 155 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7651 (tmtm) REVERT: E 155 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7333 (mmtt) REVERT: E 222 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7582 (mtm180) REVERT: F 155 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7323 (mmtt) REVERT: G 155 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7346 (mmtt) REVERT: G 222 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7556 (mtm180) REVERT: H 155 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7357 (mmtt) outliers start: 72 outliers final: 37 residues processed: 351 average time/residue: 1.6172 time to fit residues: 641.2960 Evaluate side-chains 367 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 320 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 255 THR Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 353 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 53 GLN B 53 GLN C 53 GLN C 335 ASN D 53 GLN D 93 GLN E 37 GLN E 53 GLN F 37 GLN F 53 GLN G 37 GLN G 53 GLN H 37 GLN H 53 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 24704 Z= 0.545 Angle : 0.777 10.367 33496 Z= 0.426 Chirality : 0.057 0.208 3680 Planarity : 0.007 0.055 4464 Dihedral : 5.981 59.542 3564 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.59 % Allowed : 15.72 % Favored : 80.69 % 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: -1.13 (0.14), residues: 3136 helix: -0.34 (0.14), residues: 1344 sheet: -0.44 (0.24), residues: 400 loop : -1.15 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP G 289 HIS 0.009 0.002 HIS D 271 PHE 0.020 0.003 PHE B 341 TYR 0.018 0.003 TYR A 369 ARG 0.007 0.001 ARG F 195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 313 time to evaluate : 2.681 Fit side-chains REVERT: A 37 GLN cc_start: 0.7655 (mt0) cc_final: 0.7453 (mp10) REVERT: A 155 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7684 (tmtm) REVERT: B 155 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7687 (tmtm) REVERT: C 155 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7687 (tmtm) REVERT: D 155 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7719 (tmtm) REVERT: E 98 ASP cc_start: 0.7751 (m-30) cc_final: 0.7296 (m-30) REVERT: E 155 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7366 (mmtt) REVERT: E 222 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7605 (mtm180) REVERT: F 155 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7355 (mmtt) REVERT: G 155 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7380 (mmtt) REVERT: G 222 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7576 (mtm180) REVERT: H 98 ASP cc_start: 0.7733 (m-30) cc_final: 0.7279 (m-30) REVERT: H 155 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7389 (mmtt) outliers start: 87 outliers final: 46 residues processed: 353 average time/residue: 1.2523 time to fit residues: 505.1168 Evaluate side-chains 362 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 306 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 155 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 155 LYS Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN C 53 GLN C 93 GLN D 37 GLN D 53 GLN D 93 GLN E 37 GLN E 53 GLN F 37 GLN F 53 GLN G 37 GLN G 53 GLN H 37 GLN H 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 24704 Z= 0.228 Angle : 0.570 8.378 33496 Z= 0.308 Chirality : 0.046 0.138 3680 Planarity : 0.005 0.054 4464 Dihedral : 5.357 56.024 3561 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.22 % Allowed : 16.63 % Favored : 80.16 % 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: -0.84 (0.14), residues: 3136 helix: -0.06 (0.14), residues: 1344 sheet: -0.33 (0.24), residues: 400 loop : -1.01 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.012 0.002 PHE B 294 TYR 0.012 0.002 TYR A 95 ARG 0.003 0.000 ARG G 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 2.572 Fit side-chains REVERT: A 419 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8743 (ttm) REVERT: B 419 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8735 (ttm) REVERT: C 419 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8750 (ttm) REVERT: D 419 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8730 (ttm) REVERT: E 98 ASP cc_start: 0.7673 (m-30) cc_final: 0.7206 (m-30) REVERT: E 155 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7318 (mmtt) REVERT: E 222 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7509 (mtm180) REVERT: F 155 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7307 (mmtt) REVERT: F 298 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7718 (mtt180) REVERT: G 155 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7331 (mmtt) REVERT: G 222 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7499 (mtm180) REVERT: H 98 ASP cc_start: 0.7656 (m-30) cc_final: 0.7189 (m-30) REVERT: H 155 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7341 (mmtt) outliers start: 78 outliers final: 41 residues processed: 348 average time/residue: 1.5237 time to fit residues: 603.4843 Evaluate side-chains 366 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 314 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 222 ARG Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 222 ARG Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 353 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 53 GLN B 53 GLN B 93 GLN C 53 GLN C 93 GLN D 53 GLN D 93 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 24704 Z= 0.301 Angle : 0.623 9.077 33496 Z= 0.338 Chirality : 0.048 0.179 3680 Planarity : 0.005 0.054 4464 Dihedral : 5.496 55.737 3561 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.22 % Allowed : 16.21 % Favored : 80.57 % 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: -0.90 (0.14), residues: 3136 helix: -0.10 (0.14), residues: 1344 sheet: -0.39 (0.24), residues: 400 loop : -1.05 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 289 HIS 0.007 0.001 HIS A 251 PHE 0.015 0.002 PHE C 294 TYR 0.013 0.002 TYR A 95 ARG 0.003 0.000 ARG H 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 315 time to evaluate : 3.106 Fit side-chains REVERT: A 37 GLN cc_start: 0.7716 (mt0) cc_final: 0.7451 (mp10) REVERT: B 419 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8724 (ttm) REVERT: C 419 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8744 (ttm) REVERT: D 419 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8720 (ttm) REVERT: E 98 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: E 155 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7331 (mmtt) REVERT: F 155 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7321 (mmtt) REVERT: G 155 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7345 (mmtt) REVERT: H 98 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: H 155 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7357 (mmtt) REVERT: H 298 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7714 (mtt180) outliers start: 78 outliers final: 46 residues processed: 351 average time/residue: 1.5927 time to fit residues: 633.0582 Evaluate side-chains 366 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 310 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain D residue 419 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 0.1980 chunk 254 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 300 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 53 GLN B 93 GLN C 53 GLN C 93 GLN D 37 GLN D 53 GLN D 93 GLN E 37 GLN E 53 GLN F 37 GLN F 53 GLN G 37 GLN G 53 GLN H 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24704 Z= 0.180 Angle : 0.541 7.929 33496 Z= 0.289 Chirality : 0.045 0.156 3680 Planarity : 0.005 0.052 4464 Dihedral : 5.157 51.194 3561 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.81 % Allowed : 16.67 % Favored : 80.53 % 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: -0.65 (0.14), residues: 3136 helix: 0.10 (0.14), residues: 1344 sheet: -0.26 (0.24), residues: 400 loop : -0.91 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 289 HIS 0.007 0.001 HIS A 251 PHE 0.012 0.002 PHE C 294 TYR 0.010 0.001 TYR A 95 ARG 0.003 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 318 time to evaluate : 3.037 Fit side-chains REVERT: A 419 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8741 (ttm) REVERT: E 98 ASP cc_start: 0.7629 (m-30) cc_final: 0.7162 (m-30) REVERT: E 155 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7303 (mmtt) REVERT: F 155 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7295 (mmtt) REVERT: G 155 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7318 (mmtt) REVERT: H 98 ASP cc_start: 0.7613 (m-30) cc_final: 0.7146 (m-30) REVERT: H 155 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7331 (mmtt) outliers start: 68 outliers final: 40 residues processed: 350 average time/residue: 1.6263 time to fit residues: 644.9476 Evaluate side-chains 364 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 319 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 236 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 37 GLN B 53 GLN B 93 GLN C 37 GLN C 53 GLN C 93 GLN D 53 GLN D 93 GLN E 37 GLN E 53 GLN F 37 GLN F 53 GLN G 37 GLN G 53 GLN H 37 GLN H 53 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24704 Z= 0.264 Angle : 0.601 8.770 33496 Z= 0.323 Chirality : 0.047 0.194 3680 Planarity : 0.005 0.052 4464 Dihedral : 5.356 52.819 3561 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.26 % Allowed : 16.34 % Favored : 80.40 % 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: -0.76 (0.14), residues: 3136 helix: 0.02 (0.14), residues: 1344 sheet: -0.30 (0.24), residues: 400 loop : -0.99 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 289 HIS 0.007 0.001 HIS B 251 PHE 0.014 0.002 PHE B 294 TYR 0.012 0.002 TYR C 369 ARG 0.006 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 313 time to evaluate : 2.800 Fit side-chains REVERT: A 419 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8738 (ttm) REVERT: B 37 GLN cc_start: 0.7622 (mt0) cc_final: 0.7340 (mp10) REVERT: C 37 GLN cc_start: 0.7625 (mt0) cc_final: 0.7386 (mt0) REVERT: D 37 GLN cc_start: 0.7730 (mt0) cc_final: 0.7495 (mp10) REVERT: E 55 LEU cc_start: 0.8024 (mm) cc_final: 0.7745 (mp) REVERT: E 98 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: E 155 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7347 (mmtt) REVERT: F 55 LEU cc_start: 0.8026 (mm) cc_final: 0.7765 (mp) REVERT: F 155 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7336 (mmtt) REVERT: G 55 LEU cc_start: 0.8025 (mm) cc_final: 0.7766 (mp) REVERT: G 155 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7360 (mmtt) REVERT: H 98 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: H 155 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7372 (mmtt) outliers start: 79 outliers final: 44 residues processed: 354 average time/residue: 1.5775 time to fit residues: 632.3683 Evaluate side-chains 364 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 313 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 307 ASP Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 259 LYS Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 307 ASP Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 375 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 10.0000 chunk 288 optimal weight: 0.0970 chunk 262 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 253 optimal weight: 0.0000 chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 0.0270 overall best weight: 0.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 93 GLN C 93 GLN D 93 GLN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24704 Z= 0.106 Angle : 0.472 6.432 33496 Z= 0.246 Chirality : 0.043 0.144 3680 Planarity : 0.004 0.052 4464 Dihedral : 4.570 29.298 3561 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 18.11 % Favored : 80.32 % 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: -0.34 (0.15), residues: 3136 helix: 0.40 (0.14), residues: 1336 sheet: -0.11 (0.24), residues: 400 loop : -0.77 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 79 HIS 0.007 0.001 HIS B 251 PHE 0.009 0.001 PHE A 294 TYR 0.007 0.001 TYR H 95 ARG 0.007 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 318 time to evaluate : 2.737 Fit side-chains REVERT: B 97 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6738 (mm-30) REVERT: C 97 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: D 97 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6764 (mm-30) REVERT: E 55 LEU cc_start: 0.8129 (mm) cc_final: 0.7831 (mp) REVERT: E 98 ASP cc_start: 0.7590 (m-30) cc_final: 0.7097 (m-30) REVERT: E 155 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7316 (mmtt) REVERT: E 331 LYS cc_start: 0.8380 (tttp) cc_final: 0.7996 (tttm) REVERT: F 55 LEU cc_start: 0.8126 (mm) cc_final: 0.7827 (mp) REVERT: F 155 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7308 (mmtt) REVERT: G 55 LEU cc_start: 0.8146 (mm) cc_final: 0.7841 (mp) REVERT: G 69 ASP cc_start: 0.6517 (t70) cc_final: 0.6310 (t0) REVERT: G 155 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7328 (mmtt) REVERT: H 69 ASP cc_start: 0.6522 (t70) cc_final: 0.6315 (t0) REVERT: H 98 ASP cc_start: 0.7572 (m-30) cc_final: 0.7085 (m-30) REVERT: H 155 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7342 (mmtt) REVERT: H 331 LYS cc_start: 0.8336 (tttm) cc_final: 0.8074 (tptt) outliers start: 38 outliers final: 21 residues processed: 339 average time/residue: 1.6434 time to fit residues: 629.8833 Evaluate side-chains 343 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 315 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 353 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 286 optimal weight: 0.0570 chunk 247 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 335 ASN B 53 GLN B 93 GLN B 335 ASN C 37 GLN C 53 GLN C 93 GLN C 335 ASN D 53 GLN D 93 GLN D 335 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24704 Z= 0.179 Angle : 0.542 7.969 33496 Z= 0.286 Chirality : 0.045 0.178 3680 Planarity : 0.004 0.051 4464 Dihedral : 4.933 36.127 3561 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.32 % Allowed : 18.56 % Favored : 80.12 % 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: -0.38 (0.14), residues: 3136 helix: 0.36 (0.14), residues: 1344 sheet: -0.10 (0.24), residues: 400 loop : -0.82 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS A 251 PHE 0.011 0.002 PHE C 294 TYR 0.010 0.001 TYR A 95 ARG 0.006 0.000 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 2.721 Fit side-chains REVERT: A 37 GLN cc_start: 0.7650 (mp10) cc_final: 0.7409 (mp10) REVERT: B 37 GLN cc_start: 0.7594 (mt0) cc_final: 0.7369 (mt0) REVERT: B 97 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: C 97 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: D 37 GLN cc_start: 0.7684 (mp10) cc_final: 0.7392 (mp10) REVERT: D 97 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: E 55 LEU cc_start: 0.8127 (mm) cc_final: 0.7840 (mp) REVERT: E 69 ASP cc_start: 0.6496 (t70) cc_final: 0.6292 (t0) REVERT: E 98 ASP cc_start: 0.7627 (m-30) cc_final: 0.7149 (m-30) REVERT: E 155 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7320 (mmtt) REVERT: E 331 LYS cc_start: 0.8414 (tttp) cc_final: 0.8055 (tttm) REVERT: F 55 LEU cc_start: 0.8126 (mm) cc_final: 0.7833 (mp) REVERT: F 155 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7309 (mmtt) REVERT: G 155 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7337 (mmtt) REVERT: G 331 LYS cc_start: 0.8366 (tttm) cc_final: 0.8054 (tptt) REVERT: H 98 ASP cc_start: 0.7605 (m-30) cc_final: 0.7126 (m-30) REVERT: H 155 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7347 (mmtt) REVERT: H 331 LYS cc_start: 0.8352 (tttm) cc_final: 0.8041 (tptt) outliers start: 32 outliers final: 21 residues processed: 327 average time/residue: 1.6303 time to fit residues: 603.6820 Evaluate side-chains 336 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 308 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 155 LYS Chi-restraints excluded: chain H residue 353 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 254 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 0.0070 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN B 93 GLN B 335 ASN C 93 GLN C 335 ASN D 93 GLN D 335 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120908 restraints weight = 23900.899| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.20 r_work: 0.3317 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24704 Z= 0.128 Angle : 0.501 7.228 33496 Z= 0.261 Chirality : 0.044 0.164 3680 Planarity : 0.004 0.050 4464 Dihedral : 4.678 34.483 3560 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.44 % Allowed : 18.56 % Favored : 79.99 % 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: -0.17 (0.14), residues: 3136 helix: 0.71 (0.15), residues: 1288 sheet: -0.02 (0.24), residues: 400 loop : -0.83 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.007 0.001 HIS A 251 PHE 0.011 0.001 PHE C 294 TYR 0.007 0.001 TYR A 95 ARG 0.007 0.000 ARG F 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9507.40 seconds wall clock time: 170 minutes 41.62 seconds (10241.62 seconds total)