Starting phenix.real_space_refine on Mon Feb 19 08:39:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/02_2024/8ihq_35452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/02_2024/8ihq_35452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/02_2024/8ihq_35452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/02_2024/8ihq_35452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/02_2024/8ihq_35452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihq_35452/02_2024/8ihq_35452_updated.pdb" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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 15112 2.51 5 N 4416 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 98": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 307": "OD1" <-> "OD2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 385": "OD1" <-> "OD2" Residue "C GLU 391": "OE1" <-> "OE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E ASP 307": "OD1" <-> "OD2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 386": "OD1" <-> "OD2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G ASP 277": "OD1" <-> "OD2" Residue "G ASP 307": "OD1" <-> "OD2" Residue "G ASP 386": "OD1" <-> "OD2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H ASP 307": "OD1" <-> "OD2" Residue "H ASP 386": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24128 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.15, per 1000 atoms: 0.55 Number of scatterers: 24128 At special positions: 0 Unit cell: (131.75, 131.75, 104.55, 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 4512 8.00 N 4416 7.00 C 15112 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: 9.11 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " 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 85 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " 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 85 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " 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=" NE2 HIS G 271 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " 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: 5664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 24 sheets defined 36.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.83 Creating SS restraints... Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 103 through 119 removed outlier: 4.161A 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 191 through 203 removed outlier: 3.538A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) 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 304 Processing helix chain 'A' and resid 312 through 323 Proline residue: A 316 - end of helix removed outlier: 4.796A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 353 through 363 removed outlier: 4.047A pdb=" N GLU A 362 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.614A pdb=" N GLN A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.078A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 115 " --> pdb=" O VAL B 111 " (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 191 through 204 Processing helix chain 'B' and resid 231 through 244 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 304 Processing helix chain 'B' and resid 312 through 324 Proline residue: B 316 - end of helix removed outlier: 4.784A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.828A pdb=" N MET B 360 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU B 362 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.620A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.543A pdb=" N VAL B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 103 through 120 removed outlier: 4.061A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 120 " --> pdb=" O LYS C 116 " (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 191 through 204 Processing helix chain 'C' and resid 231 through 244 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 304 Processing helix chain 'C' and resid 312 through 324 Proline residue: C 316 - end of helix removed outlier: 4.786A pdb=" N ALA C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.861A pdb=" N MET C 360 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 362 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 376 through 382 removed outlier: 3.620A 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 96 No H-bonds generated for 'chain 'D' and resid 94 through 96' Processing helix chain 'D' and resid 103 through 120 removed outlier: 4.062A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 120 " --> pdb=" O LYS D 116 " (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 191 through 204 Processing helix chain 'D' and resid 231 through 244 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 304 Processing helix chain 'D' and resid 312 through 324 Proline residue: D 316 - end of helix removed outlier: 4.786A pdb=" N ALA D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.828A pdb=" N MET D 360 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 362 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.620A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.512A pdb=" N VAL D 412 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 120 removed outlier: 4.146A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 231 through 243 removed outlier: 3.504A pdb=" N ASP E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) 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: 3.918A 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: 3.761A pdb=" N GLY E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER E 326 " --> pdb=" O GLY E 322 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 363 removed outlier: 3.665A pdb=" N MET E 360 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 361 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 362 " --> pdb=" O TYR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 374 removed outlier: 3.910A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 382 removed outlier: 3.650A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 removed outlier: 3.872A pdb=" N VAL E 412 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 120 removed outlier: 4.146A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 141 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 removed outlier: 3.502A pdb=" N ASP F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) 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: 3.916A 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: 3.791A pdb=" N GLY F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE F 325 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N SER F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 363 removed outlier: 3.669A pdb=" N MET F 360 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 361 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU F 362 " --> pdb=" O TYR F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 374 removed outlier: 3.913A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 382 removed outlier: 3.650A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 removed outlier: 3.870A pdb=" N VAL F 412 " --> pdb=" O ILE F 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 120 removed outlier: 4.146A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 141 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: 3.920A 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: 3.804A pdb=" N GLY G 322 " --> pdb=" O ALA G 318 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE G 325 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 363 removed outlier: 3.668A pdb=" N MET G 360 " --> pdb=" O PHE G 357 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 361 " --> pdb=" O VAL G 358 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU G 362 " --> pdb=" O TYR G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 374 removed outlier: 3.914A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 382 removed outlier: 3.666A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 removed outlier: 3.874A pdb=" N VAL G 412 " --> pdb=" O ILE G 409 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 120 removed outlier: 4.148A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 141 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: 3.915A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 334 Proline residue: H 316 - end of helix removed outlier: 3.801A pdb=" N GLY H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE H 325 " --> pdb=" O ILE H 321 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER H 326 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN H 327 " --> pdb=" O ALA H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 363 removed outlier: 3.676A pdb=" N MET H 360 " --> pdb=" O PHE H 357 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 361 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 362 " --> pdb=" O TYR H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 374 removed outlier: 3.913A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 382 removed outlier: 3.649A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 413 removed outlier: 3.875A pdb=" N VAL H 412 " --> pdb=" O ILE H 409 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.606A pdb=" N GLN A 53 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 5.271A 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: 3.747A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS A 420 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 5.217A 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: 7.047A pdb=" N TRP A 79 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL A 125 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP A 81 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP A 127 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.606A pdb=" N GLN B 53 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.749A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS B 420 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ILE B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 149 through 152 removed outlier: 7.047A pdb=" N TRP B 79 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL B 125 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 81 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP B 127 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.605A pdb=" N GLN C 53 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.745A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS C 420 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 149 through 152 removed outlier: 7.048A pdb=" N TRP C 79 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL C 125 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP C 81 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP C 127 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.606A pdb=" N GLN D 53 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.759A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS D 420 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 149 through 152 removed outlier: 7.047A pdb=" N TRP D 79 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL D 125 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP D 81 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP D 127 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.650A pdb=" N GLN E 53 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA E 47 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.650A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 426 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 149 through 152 removed outlier: 7.065A pdb=" N TRP E 79 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL E 125 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP E 81 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASP E 127 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.720A pdb=" N GLN F 53 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA F 47 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.650A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 426 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 149 through 152 removed outlier: 7.021A pdb=" N TRP F 79 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL F 125 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP F 81 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASP F 127 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.662A pdb=" N GLN G 53 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA G 47 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.652A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 426 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 149 through 152 removed outlier: 7.068A pdb=" N TRP G 79 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL G 125 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP G 81 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASP G 127 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 66 through 70 removed outlier: 3.652A pdb=" N GLN H 53 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA H 47 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.653A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 426 " --> pdb=" O VAL H 418 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 149 through 152 removed outlier: 7.066A pdb=" N TRP H 79 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL H 125 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP H 81 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASP H 127 " --> pdb=" O ASP H 81 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2241 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: 7.78 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5989 1.33 - 1.45: 4852 1.45 - 1.57: 13639 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24608 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.326 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" NZ KCX F 210 " pdb=" CX KCX F 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 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 1.78e+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 1.76e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 24603 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.83: 784 106.83 - 113.62: 13207 113.62 - 120.41: 9542 120.41 - 127.20: 9565 127.20 - 133.99: 278 Bond angle restraints: 33376 Sorted by residual: angle pdb=" CA GLY G 179 " pdb=" C GLY G 179 " pdb=" O GLY G 179 " ideal model delta sigma weight residual 122.29 118.22 4.07 8.10e-01 1.52e+00 2.53e+01 angle pdb=" CA GLY E 179 " pdb=" C GLY E 179 " pdb=" O GLY E 179 " ideal model delta sigma weight residual 122.39 118.05 4.34 9.30e-01 1.16e+00 2.18e+01 angle pdb=" N VAL G 178 " pdb=" CA VAL G 178 " pdb=" C VAL G 178 " ideal model delta sigma weight residual 112.96 108.52 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" CA THR H 230 " pdb=" C THR H 230 " pdb=" O THR H 230 " ideal model delta sigma weight residual 121.72 117.39 4.33 1.18e+00 7.18e-01 1.35e+01 angle pdb=" CA GLY D 215 " pdb=" C GLY D 215 " pdb=" O GLY D 215 " ideal model delta sigma weight residual 122.75 118.27 4.48 1.27e+00 6.20e-01 1.25e+01 ... (remaining 33371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 12701 17.64 - 35.28: 1360 35.28 - 52.91: 377 52.91 - 70.55: 113 70.55 - 88.19: 25 Dihedral angle restraints: 14576 sinusoidal: 5632 harmonic: 8944 Sorted by residual: dihedral pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " pdb=" SG CYS H 75 " pdb=" CB CYS H 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.29 37.29 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS G 27 " pdb=" SG CYS G 27 " pdb=" SG CYS G 75 " pdb=" CB CYS G 75 " ideal model delta sinusoidal sigma weight residual -86.00 -123.17 37.17 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA GLY E 346 " pdb=" C GLY E 346 " pdb=" N VAL E 347 " pdb=" CA VAL E 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 14573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2827 0.050 - 0.100: 645 0.100 - 0.151: 186 0.151 - 0.201: 12 0.201 - 0.251: 2 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CA VAL C 188 " pdb=" N VAL C 188 " pdb=" C VAL C 188 " pdb=" CB VAL C 188 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU D 70 " pdb=" N LEU D 70 " pdb=" C LEU D 70 " pdb=" CB LEU D 70 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL D 188 " pdb=" N VAL D 188 " pdb=" C VAL D 188 " pdb=" CB VAL D 188 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 3669 not shown) Planarity restraints: 4448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 55 " -0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO D 56 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 55 " 0.053 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO C 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 55 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO B 56 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.044 5.00e-02 4.00e+02 ... (remaining 4445 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 274 2.66 - 3.22: 20673 3.22 - 3.78: 35764 3.78 - 4.34: 54877 4.34 - 4.90: 89606 Nonbonded interactions: 201194 Sorted by model distance: nonbonded pdb=" OQ1 KCX C 210 " pdb="ZN ZN C 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX A 210 " pdb="ZN ZN A 501 " model vdw 2.095 2.230 nonbonded pdb=" OQ1 KCX B 210 " pdb="ZN ZN B 501 " model vdw 2.096 2.230 nonbonded pdb=" OQ1 KCX D 210 " pdb="ZN ZN D 501 " model vdw 2.097 2.230 nonbonded pdb=" NZ LYS D 155 " pdb=" O SER D 156 " model vdw 2.243 2.520 ... (remaining 201189 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: 2.710 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: 0.020 Extract box with map and model: 11.030 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 69.050 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.190 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 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 0.085 24608 Z= 0.260 Angle : 0.586 7.097 33376 Z= 0.356 Chirality : 0.046 0.251 3672 Planarity : 0.005 0.082 4448 Dihedral : 16.578 88.189 8888 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.62 % Allowed : 18.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3136 helix: 0.01 (0.14), residues: 1320 sheet: 0.35 (0.25), residues: 384 loop : -1.04 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 289 HIS 0.007 0.001 HIS E 251 PHE 0.011 0.001 PHE F 294 TYR 0.009 0.001 TYR C 333 ARG 0.014 0.000 ARG D 281 *********************** 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 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 333 time to evaluate : 2.712 Fit side-chains REVERT: B 281 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7310 (ttp-110) REVERT: C 331 LYS cc_start: 0.7476 (tttp) cc_final: 0.7252 (ttpp) REVERT: D 281 ARG cc_start: 0.7667 (mtm110) cc_final: 0.7245 (ttp-110) REVERT: E 98 ASP cc_start: 0.8069 (t0) cc_final: 0.7609 (m-30) REVERT: E 131 GLU cc_start: 0.7465 (mp0) cc_final: 0.7239 (mp0) REVERT: E 397 ASP cc_start: 0.8441 (m-30) cc_final: 0.8116 (m-30) REVERT: F 98 ASP cc_start: 0.8085 (t0) cc_final: 0.7615 (m-30) REVERT: F 385 ASP cc_start: 0.7668 (p0) cc_final: 0.7108 (t0) REVERT: F 397 ASP cc_start: 0.8419 (m-30) cc_final: 0.8112 (m-30) REVERT: G 26 GLN cc_start: 0.8018 (mt0) cc_final: 0.7731 (mt0) REVERT: G 98 ASP cc_start: 0.8075 (t0) cc_final: 0.7605 (m-30) REVERT: G 335 ASN cc_start: 0.7684 (m-40) cc_final: 0.7352 (m110) REVERT: G 385 ASP cc_start: 0.7720 (p0) cc_final: 0.7187 (t0) REVERT: G 397 ASP cc_start: 0.8462 (m-30) cc_final: 0.8114 (m-30) REVERT: H 26 GLN cc_start: 0.8005 (mt0) cc_final: 0.7736 (mt0) REVERT: H 98 ASP cc_start: 0.8071 (t0) cc_final: 0.7599 (m-30) REVERT: H 385 ASP cc_start: 0.7701 (p0) cc_final: 0.7167 (t0) REVERT: H 397 ASP cc_start: 0.8429 (m-30) cc_final: 0.8122 (m-30) outliers start: 15 outliers final: 9 residues processed: 346 average time/residue: 1.5741 time to fit residues: 614.8819 Evaluate side-chains 326 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 317 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 283 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN C 285 GLN D 285 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 24608 Z= 0.415 Angle : 0.597 7.329 33376 Z= 0.321 Chirality : 0.049 0.144 3672 Planarity : 0.006 0.065 4448 Dihedral : 5.976 54.335 3558 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.18 % Allowed : 16.64 % Favored : 79.18 % 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: -0.97 (0.14), residues: 3136 helix: -0.25 (0.14), residues: 1320 sheet: 0.98 (0.31), residues: 248 loop : -1.23 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 289 HIS 0.006 0.001 HIS D 251 PHE 0.018 0.002 PHE H 294 TYR 0.014 0.002 TYR C 333 ARG 0.004 0.000 ARG D 281 *********************** 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 399 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 298 time to evaluate : 2.841 Fit side-chains REVERT: A 50 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5750 (mtt90) REVERT: A 172 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: B 50 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.5771 (mtt90) REVERT: B 172 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: C 50 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.5754 (mtt90) REVERT: C 172 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: D 50 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5746 (mtt90) REVERT: D 172 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: E 98 ASP cc_start: 0.8149 (t0) cc_final: 0.7553 (m-30) REVERT: E 331 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7463 (ttmm) REVERT: E 356 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6291 (tt0) REVERT: F 98 ASP cc_start: 0.8165 (t0) cc_final: 0.7561 (m-30) REVERT: F 155 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7325 (mptm) REVERT: F 173 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7248 (tmm-80) REVERT: F 356 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6319 (tt0) REVERT: G 26 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: G 98 ASP cc_start: 0.8160 (t0) cc_final: 0.7507 (m-30) REVERT: G 356 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6287 (tt0) REVERT: H 26 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: H 98 ASP cc_start: 0.8151 (t0) cc_final: 0.7505 (m-30) REVERT: H 356 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6289 (tt0) outliers start: 101 outliers final: 39 residues processed: 359 average time/residue: 1.4898 time to fit residues: 607.3998 Evaluate side-chains 346 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 290 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 252 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN D 404 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24608 Z= 0.226 Angle : 0.490 7.600 33376 Z= 0.258 Chirality : 0.044 0.130 3672 Planarity : 0.005 0.054 4448 Dihedral : 5.534 54.068 3554 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.15 % Allowed : 17.80 % Favored : 79.06 % 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: -0.77 (0.14), residues: 3136 helix: 0.04 (0.14), residues: 1312 sheet: 0.55 (0.27), residues: 328 loop : -1.22 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 289 HIS 0.006 0.001 HIS E 271 PHE 0.013 0.001 PHE H 294 TYR 0.011 0.002 TYR C 333 ARG 0.005 0.000 ARG B 281 *********************** 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 368 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 292 time to evaluate : 2.713 Fit side-chains REVERT: A 50 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.5709 (mtt90) REVERT: A 66 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.6250 (ttm170) REVERT: A 222 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8031 (ttt180) REVERT: A 356 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: B 50 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5714 (mtt90) REVERT: B 66 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6444 (ttm170) REVERT: B 222 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8028 (ttt180) REVERT: C 50 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6599 (mtt90) REVERT: C 66 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6411 (ttm170) REVERT: C 222 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8038 (ttt180) REVERT: D 50 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5695 (mtt90) REVERT: D 66 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.6426 (ttm170) REVERT: E 98 ASP cc_start: 0.8112 (t0) cc_final: 0.7433 (m-30) REVERT: E 302 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6353 (mt-10) REVERT: E 356 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6236 (tt0) REVERT: F 53 GLN cc_start: 0.8229 (pt0) cc_final: 0.7797 (mt0) REVERT: F 98 ASP cc_start: 0.8127 (t0) cc_final: 0.7438 (m-30) REVERT: F 173 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7203 (tmm-80) REVERT: F 302 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6346 (mt-10) REVERT: F 356 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: G 98 ASP cc_start: 0.8112 (t0) cc_final: 0.7427 (m-30) REVERT: G 271 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7477 (m-70) REVERT: G 302 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: G 356 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6235 (tt0) REVERT: H 98 ASP cc_start: 0.8107 (t0) cc_final: 0.7425 (m-30) REVERT: H 302 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6356 (mt-10) REVERT: H 356 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6172 (tt0) outliers start: 76 outliers final: 27 residues processed: 337 average time/residue: 1.5591 time to fit residues: 596.0049 Evaluate side-chains 329 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 280 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 0.0040 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 42 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS G 176 HIS H 42 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24608 Z= 0.330 Angle : 0.547 7.344 33376 Z= 0.291 Chirality : 0.047 0.140 3672 Planarity : 0.005 0.052 4448 Dihedral : 5.546 54.723 3545 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.44 % Allowed : 17.63 % Favored : 78.93 % 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: -0.89 (0.14), residues: 3136 helix: -0.11 (0.14), residues: 1312 sheet: 0.94 (0.31), residues: 248 loop : -1.23 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.007 0.001 HIS E 271 PHE 0.015 0.002 PHE F 294 TYR 0.013 0.002 TYR C 333 ARG 0.006 0.000 ARG D 281 *********************** 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 371 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 288 time to evaluate : 2.777 Fit side-chains REVERT: A 50 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.5912 (mtt90) REVERT: A 66 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6240 (ttm170) REVERT: A 222 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8054 (ttt180) REVERT: A 356 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: B 50 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5925 (mtt90) REVERT: B 222 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8052 (ttt180) REVERT: C 50 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.5727 (mtt90) REVERT: C 116 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7768 (mtpt) REVERT: C 222 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8060 (ttt180) REVERT: D 50 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5888 (mtt90) REVERT: E 98 ASP cc_start: 0.8073 (t0) cc_final: 0.7412 (m-30) REVERT: E 331 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7458 (ttmm) REVERT: E 356 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6277 (tt0) REVERT: F 53 GLN cc_start: 0.8233 (pt0) cc_final: 0.7786 (mt0) REVERT: F 98 ASP cc_start: 0.8088 (t0) cc_final: 0.7417 (m-30) REVERT: F 155 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7422 (mptm) REVERT: F 173 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7311 (tmm-80) REVERT: F 356 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6280 (tt0) REVERT: G 98 ASP cc_start: 0.8073 (t0) cc_final: 0.7411 (m-30) REVERT: G 356 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6233 (tt0) REVERT: H 98 ASP cc_start: 0.8067 (t0) cc_final: 0.7405 (m-30) REVERT: H 173 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7419 (tmm-80) REVERT: H 356 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6271 (tt0) outliers start: 83 outliers final: 32 residues processed: 337 average time/residue: 1.5522 time to fit residues: 591.9380 Evaluate side-chains 330 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN B 404 ASN C 285 GLN D 285 GLN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 24608 Z= 0.422 Angle : 0.608 7.722 33376 Z= 0.325 Chirality : 0.050 0.149 3672 Planarity : 0.006 0.050 4448 Dihedral : 5.802 55.109 3545 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.43 % Allowed : 16.72 % Favored : 78.85 % 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: -1.11 (0.14), residues: 3136 helix: -0.31 (0.14), residues: 1312 sheet: 0.81 (0.31), residues: 248 loop : -1.33 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 289 HIS 0.009 0.001 HIS G 271 PHE 0.018 0.002 PHE H 294 TYR 0.014 0.003 TYR C 333 ARG 0.008 0.000 ARG A 281 *********************** 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 395 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 288 time to evaluate : 4.080 Fit side-chains REVERT: A 50 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.5844 (mtt90) REVERT: A 172 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: A 356 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: B 50 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5856 (mtt90) REVERT: B 66 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.6421 (ttm170) REVERT: B 172 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: C 50 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.5774 (mtt90) REVERT: C 66 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6426 (ttm170) REVERT: C 116 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7790 (mtpt) REVERT: C 172 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7402 (pt0) REVERT: D 50 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.5808 (mtt90) REVERT: D 66 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6410 (ttm170) REVERT: D 172 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7167 (pt0) REVERT: E 98 ASP cc_start: 0.8126 (t0) cc_final: 0.7494 (m-30) REVERT: E 131 GLU cc_start: 0.7908 (mp0) cc_final: 0.7688 (mt-10) REVERT: E 331 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7449 (ttmm) REVERT: E 356 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: F 53 GLN cc_start: 0.8238 (pt0) cc_final: 0.7772 (mt0) REVERT: F 98 ASP cc_start: 0.8142 (t0) cc_final: 0.7500 (m-30) REVERT: F 155 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7334 (mptm) REVERT: F 173 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7335 (tmm-80) REVERT: F 356 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: G 98 ASP cc_start: 0.8128 (t0) cc_final: 0.7491 (m-30) REVERT: G 155 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7338 (mptm) REVERT: G 356 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6821 (tt0) REVERT: H 26 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7814 (mt0) REVERT: H 98 ASP cc_start: 0.8123 (t0) cc_final: 0.7487 (m-30) REVERT: H 173 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7410 (tmm-80) REVERT: H 356 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6829 (tt0) outliers start: 107 outliers final: 46 residues processed: 354 average time/residue: 1.5288 time to fit residues: 613.5081 Evaluate side-chains 350 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 281 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 301 optimal weight: 0.3980 chunk 250 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 99 optimal weight: 0.3980 chunk 158 optimal weight: 9.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 285 GLN C 285 GLN C 404 ASN D 285 GLN D 404 ASN E 176 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24608 Z= 0.150 Angle : 0.454 7.339 33376 Z= 0.235 Chirality : 0.043 0.140 3672 Planarity : 0.005 0.046 4448 Dihedral : 5.111 54.155 3545 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.61 % Allowed : 18.75 % Favored : 78.64 % 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: -0.58 (0.14), residues: 3136 helix: 0.25 (0.14), residues: 1296 sheet: 0.57 (0.28), residues: 304 loop : -1.10 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.006 0.001 HIS H 251 PHE 0.010 0.001 PHE G 294 TYR 0.009 0.001 TYR B 333 ARG 0.008 0.000 ARG C 281 *********************** 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 355 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 292 time to evaluate : 2.653 Fit side-chains REVERT: A 50 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6621 (mtt90) REVERT: A 66 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6235 (ttm170) REVERT: A 356 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: B 50 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6625 (mtt90) REVERT: B 66 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6400 (ttm170) REVERT: C 50 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6582 (mtt90) REVERT: C 66 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6404 (ttm170) REVERT: D 50 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6594 (mtt90) REVERT: D 66 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6396 (ttm170) REVERT: E 98 ASP cc_start: 0.8041 (t0) cc_final: 0.7382 (m-30) REVERT: E 131 GLU cc_start: 0.7717 (mp0) cc_final: 0.7499 (mt-10) REVERT: E 235 LYS cc_start: 0.8238 (mttp) cc_final: 0.7882 (mttm) REVERT: E 302 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: E 356 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6120 (tt0) REVERT: F 98 ASP cc_start: 0.8058 (t0) cc_final: 0.7390 (m-30) REVERT: F 173 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7282 (tmm-80) REVERT: F 235 LYS cc_start: 0.8240 (mttp) cc_final: 0.7892 (mttm) REVERT: F 302 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: F 356 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6155 (tt0) REVERT: F 397 ASP cc_start: 0.8445 (m-30) cc_final: 0.8115 (m-30) REVERT: G 98 ASP cc_start: 0.8046 (t0) cc_final: 0.7381 (m-30) REVERT: G 302 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6458 (mp0) REVERT: G 356 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6120 (tt0) REVERT: H 98 ASP cc_start: 0.8036 (t0) cc_final: 0.7377 (m-30) REVERT: H 131 GLU cc_start: 0.7886 (mp0) cc_final: 0.7601 (mt-10) REVERT: H 302 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: H 356 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6165 (tt0) outliers start: 63 outliers final: 35 residues processed: 331 average time/residue: 1.6079 time to fit residues: 599.8179 Evaluate side-chains 340 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 287 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 302 GLU Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 300 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN B 404 ASN C 285 GLN C 404 ASN D 285 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24608 Z= 0.344 Angle : 0.560 8.024 33376 Z= 0.297 Chirality : 0.048 0.142 3672 Planarity : 0.005 0.051 4448 Dihedral : 5.585 54.900 3545 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.52 % Allowed : 17.84 % Favored : 78.64 % 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: -0.86 (0.14), residues: 3136 helix: -0.04 (0.14), residues: 1312 sheet: 0.84 (0.30), residues: 248 loop : -1.25 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 289 HIS 0.006 0.001 HIS G 271 PHE 0.016 0.002 PHE H 294 TYR 0.013 0.002 TYR C 333 ARG 0.009 0.000 ARG D 281 *********************** 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 373 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 288 time to evaluate : 3.010 Fit side-chains REVERT: A 50 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6686 (mtt90) REVERT: A 172 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: A 356 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: B 50 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6699 (mtt90) REVERT: B 172 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: C 50 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.5780 (mtt90) REVERT: C 66 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6448 (ttm170) REVERT: C 116 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7745 (mtpt) REVERT: C 172 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: D 50 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5820 (mtt90) REVERT: D 66 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6443 (ttm170) REVERT: E 98 ASP cc_start: 0.8092 (t0) cc_final: 0.7477 (m-30) REVERT: E 131 GLU cc_start: 0.7840 (mp0) cc_final: 0.7629 (mt-10) REVERT: E 356 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6275 (tt0) REVERT: F 98 ASP cc_start: 0.8109 (t0) cc_final: 0.7484 (m-30) REVERT: F 173 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7314 (tmm-80) REVERT: F 356 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6306 (tt0) REVERT: G 98 ASP cc_start: 0.8094 (t0) cc_final: 0.7475 (m-30) REVERT: G 356 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6269 (tt0) REVERT: H 98 ASP cc_start: 0.8088 (t0) cc_final: 0.7471 (m-30) REVERT: H 131 GLU cc_start: 0.7907 (mp0) cc_final: 0.7686 (mt-10) REVERT: H 173 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7412 (tmm-80) REVERT: H 271 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7672 (m-70) REVERT: H 356 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6258 (tt0) outliers start: 85 outliers final: 42 residues processed: 347 average time/residue: 1.5020 time to fit residues: 592.3548 Evaluate side-chains 341 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 281 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 271 HIS Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 191 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN B 285 GLN C 285 GLN D 285 GLN F 42 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24608 Z= 0.168 Angle : 0.464 7.809 33376 Z= 0.239 Chirality : 0.043 0.138 3672 Planarity : 0.005 0.054 4448 Dihedral : 5.099 53.797 3545 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.32 % Allowed : 19.37 % Favored : 78.31 % 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: -0.54 (0.14), residues: 3136 helix: 0.26 (0.14), residues: 1312 sheet: 0.38 (0.24), residues: 384 loop : -1.11 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 79 HIS 0.006 0.001 HIS H 251 PHE 0.012 0.001 PHE H 294 TYR 0.009 0.001 TYR B 333 ARG 0.011 0.000 ARG B 281 *********************** 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 354 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 298 time to evaluate : 2.973 Fit side-chains REVERT: A 50 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6589 (mtt90) REVERT: A 66 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6220 (ttm170) REVERT: A 356 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: B 50 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6581 (mtt90) REVERT: B 66 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6476 (ttm170) REVERT: C 50 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.6560 (mtt90) REVERT: C 66 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6443 (ttm170) REVERT: D 50 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6554 (mtt90) REVERT: D 66 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6436 (ttm170) REVERT: E 98 ASP cc_start: 0.8056 (t0) cc_final: 0.7392 (m-30) REVERT: E 131 GLU cc_start: 0.7696 (mp0) cc_final: 0.7458 (mt-10) REVERT: E 235 LYS cc_start: 0.8234 (mttp) cc_final: 0.7874 (mttm) REVERT: E 356 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6144 (tt0) REVERT: E 397 ASP cc_start: 0.8447 (m-30) cc_final: 0.8120 (m-30) REVERT: F 98 ASP cc_start: 0.8072 (t0) cc_final: 0.7398 (m-30) REVERT: F 131 GLU cc_start: 0.7623 (mp0) cc_final: 0.7420 (mt-10) REVERT: F 235 LYS cc_start: 0.8208 (mttp) cc_final: 0.7874 (mttm) REVERT: F 356 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6176 (tt0) REVERT: F 397 ASP cc_start: 0.8418 (m-30) cc_final: 0.8114 (m-30) REVERT: G 98 ASP cc_start: 0.8062 (t0) cc_final: 0.7388 (m-30) REVERT: G 356 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: H 98 ASP cc_start: 0.8055 (t0) cc_final: 0.7381 (m-30) REVERT: H 131 GLU cc_start: 0.7678 (mp0) cc_final: 0.7439 (mt-10) REVERT: H 173 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7325 (tmm-80) REVERT: H 356 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6220 (tt0) outliers start: 56 outliers final: 37 residues processed: 335 average time/residue: 1.6007 time to fit residues: 605.8325 Evaluate side-chains 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU 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: 3.9990 chunk 262 optimal weight: 0.0770 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.0070 overall best weight: 1.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN A 404 ASN B 285 GLN C 285 GLN D 285 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24608 Z= 0.209 Angle : 0.486 7.875 33376 Z= 0.252 Chirality : 0.044 0.137 3672 Planarity : 0.005 0.059 4448 Dihedral : 5.178 53.639 3544 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.65 % Allowed : 18.96 % Favored : 78.39 % 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: -0.51 (0.14), residues: 3136 helix: 0.28 (0.14), residues: 1312 sheet: 0.65 (0.28), residues: 304 loop : -1.06 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 289 HIS 0.006 0.001 HIS E 271 PHE 0.012 0.001 PHE E 294 TYR 0.010 0.001 TYR C 333 ARG 0.012 0.000 ARG B 281 *********************** 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 358 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 294 time to evaluate : 2.663 Fit side-chains REVERT: A 50 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6585 (mtt90) REVERT: A 66 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6243 (ttm170) REVERT: A 356 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: B 50 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6597 (mtt90) REVERT: B 66 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.6474 (ttm170) REVERT: C 50 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6584 (mtt90) REVERT: C 66 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6499 (ttm170) REVERT: D 50 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6562 (mtt90) REVERT: D 66 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6493 (ttm170) REVERT: E 98 ASP cc_start: 0.8065 (t0) cc_final: 0.7393 (m-30) REVERT: E 131 GLU cc_start: 0.7713 (mp0) cc_final: 0.7478 (mt-10) REVERT: E 302 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6303 (mt-10) REVERT: E 356 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: F 98 ASP cc_start: 0.8078 (t0) cc_final: 0.7400 (m-30) REVERT: F 131 GLU cc_start: 0.7600 (mp0) cc_final: 0.7399 (mt-10) REVERT: F 302 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6296 (mt-10) REVERT: F 356 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6164 (tt0) REVERT: G 52 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6947 (mmt180) REVERT: G 98 ASP cc_start: 0.8067 (t0) cc_final: 0.7391 (m-30) REVERT: G 356 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6132 (tt0) REVERT: H 98 ASP cc_start: 0.8062 (t0) cc_final: 0.7385 (m-30) REVERT: H 131 GLU cc_start: 0.7699 (mp0) cc_final: 0.7479 (mt-10) REVERT: H 173 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7348 (tmm-80) REVERT: H 302 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6309 (mt-10) REVERT: H 356 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6139 (tt0) outliers start: 64 outliers final: 44 residues processed: 338 average time/residue: 1.5614 time to fit residues: 600.5564 Evaluate side-chains 355 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 294 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 302 GLU Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.0000 chunk 296 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 286 optimal weight: 0.6980 chunk 247 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN B 404 ASN C 285 GLN D 285 GLN D 404 ASN E 106 HIS F 106 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 HIS G 176 HIS H 106 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24608 Z= 0.124 Angle : 0.437 7.557 33376 Z= 0.221 Chirality : 0.042 0.129 3672 Planarity : 0.005 0.058 4448 Dihedral : 4.696 53.074 3544 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.40 % Allowed : 19.12 % Favored : 78.48 % 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: -0.19 (0.15), residues: 3136 helix: 0.58 (0.14), residues: 1304 sheet: 0.64 (0.24), residues: 384 loop : -0.97 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 79 HIS 0.006 0.001 HIS F 251 PHE 0.010 0.001 PHE E 294 TYR 0.008 0.001 TYR B 333 ARG 0.014 0.000 ARG B 281 ********************** 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 362 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 304 time to evaluate : 2.715 Fit side-chains REVERT: A 50 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6098 (mtt90) REVERT: A 66 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6293 (ttm170) REVERT: A 356 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7092 (tt0) REVERT: B 50 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6534 (mtt90) REVERT: B 66 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6466 (ttm170) REVERT: C 50 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6029 (mtt90) REVERT: C 66 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6486 (ttm170) REVERT: D 50 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6088 (mtt90) REVERT: D 66 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6493 (ttm170) REVERT: D 281 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7368 (ttp-110) REVERT: E 131 GLU cc_start: 0.7668 (mp0) cc_final: 0.7434 (mt-10) REVERT: E 235 LYS cc_start: 0.8272 (mttp) cc_final: 0.7926 (mttm) REVERT: E 356 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6230 (tt0) REVERT: E 397 ASP cc_start: 0.8353 (m-30) cc_final: 0.8027 (m-30) REVERT: F 98 ASP cc_start: 0.8044 (t0) cc_final: 0.7827 (t0) REVERT: F 131 GLU cc_start: 0.7500 (mp0) cc_final: 0.7270 (mt-10) REVERT: F 235 LYS cc_start: 0.8174 (mttp) cc_final: 0.7848 (mttm) REVERT: F 356 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: F 385 ASP cc_start: 0.7694 (p0) cc_final: 0.7012 (t0) REVERT: F 397 ASP cc_start: 0.8330 (m-30) cc_final: 0.8025 (m-30) REVERT: G 52 ARG cc_start: 0.7187 (mmt180) cc_final: 0.6965 (mmt180) REVERT: G 356 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6225 (tt0) REVERT: G 385 ASP cc_start: 0.7737 (p0) cc_final: 0.7075 (t0) REVERT: G 397 ASP cc_start: 0.8419 (m-30) cc_final: 0.8060 (m-30) REVERT: H 131 GLU cc_start: 0.7677 (mp0) cc_final: 0.7441 (mt-10) REVERT: H 173 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7592 (tmm-80) REVERT: H 356 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6228 (tt0) REVERT: H 385 ASP cc_start: 0.7693 (p0) cc_final: 0.7038 (t0) outliers start: 58 outliers final: 36 residues processed: 341 average time/residue: 1.6050 time to fit residues: 616.8944 Evaluate side-chains 345 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 295 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 66 ARG Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 326 SER Chi-restraints excluded: chain E residue 356 GLU Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 326 SER Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 326 SER Chi-restraints excluded: chain G residue 356 GLU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 326 SER Chi-restraints excluded: chain H residue 356 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 GLN B 285 GLN B 404 ASN C 285 GLN D 285 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 HIS ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112734 restraints weight = 25310.454| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.36 r_work: 0.3186 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24608 Z= 0.351 Angle : 0.574 8.508 33376 Z= 0.303 Chirality : 0.048 0.142 3672 Planarity : 0.005 0.062 4448 Dihedral : 5.496 54.522 3544 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.61 % Allowed : 19.21 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3136 helix: 0.08 (0.14), residues: 1320 sheet: 1.06 (0.30), residues: 248 loop : -1.14 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 289 HIS 0.009 0.001 HIS E 271 PHE 0.015 0.002 PHE F 294 TYR 0.012 0.002 TYR C 333 ARG 0.013 0.000 ARG C 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9110.17 seconds wall clock time: 161 minutes 36.46 seconds (9696.46 seconds total)