Starting phenix.real_space_refine on Fri Apr 12 02:22:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/04_2024/8j85_36060_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/04_2024/8j85_36060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/04_2024/8j85_36060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/04_2024/8j85_36060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/04_2024/8j85_36060_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j85_36060/04_2024/8j85_36060_updated.pdb" } resolution = 2.7 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= 0.040 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: 6 Type Number sf(0) Gaussians Zn 16 6.06 5 S 72 5.16 5 Cl 8 4.86 5 C 15288 2.51 5 N 4432 2.21 5 O 4560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 88": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 407": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 407": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 131": "OE1" <-> "OE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G GLU 407": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 407": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24376 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3017 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 12.37, per 1000 atoms: 0.51 Number of scatterers: 24376 At special positions: 0 Unit cell: (145.35, 145.35, 104.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 16 29.99 Cl 8 17.00 S 72 16.00 O 4560 8.00 N 4432 7.00 C 15288 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=2.01 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.01 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.01 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.01 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.02 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.01 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=2.02 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: 9.48 Conformation dependent library (CDL) restraints added in 4.2 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 85 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " 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 85 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " 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 85 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 24 sheets defined 37.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.587A pdb=" N ASP A 98 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.587A pdb=" N ALA A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) 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 321 Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 367 through 374 removed outlier: 3.886A pdb=" N ALA A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.586A pdb=" N ASP B 98 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 99' Processing helix chain 'B' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.585A pdb=" N ALA B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 312 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 354 through 363 Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.891A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.587A pdb=" N ASP C 98 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 99 " --> pdb=" O SER C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 95 through 99' Processing helix chain 'C' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 191 through 204 Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.583A pdb=" N ALA C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 312 through 321 Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 354 through 363 Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.888A pdb=" N ALA C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.586A pdb=" N ASP D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE D 99 " --> pdb=" O SER D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 99' Processing helix chain 'D' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 141 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 231 through 243 removed outlier: 3.584A pdb=" N ALA D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 312 through 321 Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 354 through 363 Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.889A pdb=" N ALA D 374 " --> pdb=" O ALA D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 382 Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.588A pdb=" N ASP E 98 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE E 99 " --> pdb=" O SER E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 95 through 99' Processing helix chain 'E' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 231 through 243 removed outlier: 3.588A pdb=" N ALA E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.631A 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 304 Processing helix chain 'E' and resid 312 through 321 Proline residue: E 316 - end of helix Processing helix chain 'E' and resid 325 through 335 Processing helix chain 'E' and resid 354 through 363 Processing helix chain 'E' and resid 367 through 374 removed outlier: 3.886A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 382 Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'F' and resid 95 through 99 removed outlier: 3.587A pdb=" N ASP F 98 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE F 99 " --> pdb=" O SER F 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 95 through 99' Processing helix chain 'F' and resid 103 through 119 removed outlier: 4.163A 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 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 231 through 243 removed outlier: 3.585A pdb=" N ALA F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.632A 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 304 Processing helix chain 'F' and resid 312 through 321 Proline residue: F 316 - end of helix Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 367 through 374 removed outlier: 3.890A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 382 Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.587A pdb=" N ASP G 98 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE G 99 " --> pdb=" O SER G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 99' Processing helix chain 'G' and resid 103 through 119 removed outlier: 4.163A 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 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 191 through 204 Processing helix chain 'G' and resid 231 through 243 removed outlier: 3.583A pdb=" N ALA G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) 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 304 Processing helix chain 'G' and resid 312 through 321 Proline residue: G 316 - end of helix Processing helix chain 'G' and resid 325 through 335 Processing helix chain 'G' and resid 354 through 363 Processing helix chain 'G' and resid 367 through 374 removed outlier: 3.888A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 382 Processing helix chain 'G' and resid 409 through 413 Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.586A pdb=" N ASP H 98 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 95 through 99' Processing helix chain 'H' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 141 Processing helix chain 'H' and resid 172 through 178 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 191 through 204 Processing helix chain 'H' and resid 231 through 243 removed outlier: 3.583A pdb=" N ALA H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) 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 304 Processing helix chain 'H' and resid 312 through 321 Proline residue: H 316 - end of helix Processing helix chain 'H' and resid 325 through 335 Processing helix chain 'H' and resid 354 through 363 Processing helix chain 'H' and resid 367 through 374 removed outlier: 3.889A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 382 Processing helix chain 'H' and resid 409 through 413 Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 3.794A pdb=" N GLN A 53 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 5.040A 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: 3.560A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 420 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 5.376A 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: 7.028A pdb=" N TRP A 79 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 125 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 81 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.795A pdb=" N GLN B 53 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.038A 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: 3.557A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS B 420 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 5.377A 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: 7.030A pdb=" N TRP B 79 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL B 125 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 81 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.791A pdb=" N GLN C 53 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.042A 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: 3.554A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS C 420 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.376A 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: 7.028A pdb=" N TRP C 79 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL C 125 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP C 81 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.793A pdb=" N GLN D 53 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.041A 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: 3.556A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS D 420 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 5.375A 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: 7.030A pdb=" N TRP D 79 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL D 125 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP D 81 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.794A pdb=" N GLN E 53 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA E 47 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.039A 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: 3.559A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.377A 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: 7.028A pdb=" N TRP E 79 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL E 125 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP E 81 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.795A pdb=" N GLN F 53 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA F 47 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 5.039A 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: 3.558A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.378A 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: 7.030A pdb=" N TRP F 79 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL F 125 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP F 81 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 5.546A 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: 3.792A pdb=" N GLN G 53 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA G 47 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.041A 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: 3.555A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.376A 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: 7.028A pdb=" N TRP G 79 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL G 125 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP G 81 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 5.547A 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: 3.794A pdb=" N GLN H 53 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA H 47 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.041A 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: 3.556A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.375A 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: 7.029A pdb=" N TRP H 79 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL H 125 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP H 81 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ASP H 127 " --> pdb=" O ASP H 81 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.00 Time building geometry restraints manager: 10.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4176 1.31 - 1.44: 6600 1.44 - 1.56: 13960 1.56 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 24872 Sorted by residual: bond pdb=" CB 97U A 503 " pdb=" CG 97U A 503 " ideal model delta sigma weight residual 1.505 1.386 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" CB 97U F 503 " pdb=" CG 97U F 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" CB 97U B 503 " pdb=" CG 97U B 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB 97U E 503 " pdb=" CG 97U E 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CB 97U G 503 " pdb=" CG 97U G 503 " ideal model delta sigma weight residual 1.505 1.387 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 24867 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 832 107.13 - 113.85: 13596 113.85 - 120.57: 10111 120.57 - 127.29: 8956 127.29 - 134.01: 257 Bond angle restraints: 33752 Sorted by residual: angle pdb=" N VAL E 132 " pdb=" CA VAL E 132 " pdb=" C VAL E 132 " ideal model delta sigma weight residual 113.53 105.76 7.77 9.80e-01 1.04e+00 6.29e+01 angle pdb=" N VAL A 132 " pdb=" CA VAL A 132 " pdb=" C VAL A 132 " ideal model delta sigma weight residual 113.53 105.81 7.72 9.80e-01 1.04e+00 6.20e+01 angle pdb=" N VAL B 132 " pdb=" CA VAL B 132 " pdb=" C VAL B 132 " ideal model delta sigma weight residual 113.53 106.15 7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" N VAL F 132 " pdb=" CA VAL F 132 " pdb=" C VAL F 132 " ideal model delta sigma weight residual 113.53 106.15 7.38 9.80e-01 1.04e+00 5.67e+01 angle pdb=" N VAL H 132 " pdb=" CA VAL H 132 " pdb=" C VAL H 132 " ideal model delta sigma weight residual 113.53 106.16 7.37 9.80e-01 1.04e+00 5.65e+01 ... (remaining 33747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12714 17.95 - 35.90: 1513 35.90 - 53.84: 418 53.84 - 71.79: 117 71.79 - 89.74: 54 Dihedral angle restraints: 14816 sinusoidal: 5856 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY H 346 " pdb=" C GLY H 346 " pdb=" N VAL H 347 " pdb=" CA VAL H 347 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLY C 346 " pdb=" C GLY C 346 " pdb=" N VAL C 347 " pdb=" CA VAL C 347 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 14813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3058 0.066 - 0.132: 535 0.132 - 0.198: 77 0.198 - 0.264: 10 0.264 - 0.330: 8 Chirality restraints: 3688 Sorted by residual: chirality pdb=" CA 97U F 503 " pdb=" N 97U F 503 " pdb=" C 97U F 503 " pdb=" CB 97U F 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA 97U A 503 " pdb=" N 97U A 503 " pdb=" C 97U A 503 " pdb=" CB 97U A 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA 97U B 503 " pdb=" N 97U B 503 " pdb=" C 97U B 503 " pdb=" CB 97U B 503 " both_signs ideal model delta sigma weight residual False 2.30 2.63 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 3685 not shown) Planarity restraints: 4496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 73 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C LYS E 73 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS E 73 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL E 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 73 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LYS G 73 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS G 73 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL G 74 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 73 " -0.012 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C LYS H 73 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS H 73 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL H 74 " -0.013 2.00e-02 2.50e+03 ... (remaining 4493 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 24 2.35 - 2.99: 12050 2.99 - 3.62: 33927 3.62 - 4.26: 58067 4.26 - 4.90: 99358 Nonbonded interactions: 203426 Sorted by model distance: nonbonded pdb="ZN ZN B 502 " pdb=" OAX 97U B 503 " model vdw 1.711 2.230 nonbonded pdb="ZN ZN F 502 " pdb=" OAX 97U F 503 " model vdw 1.712 2.230 nonbonded pdb="ZN ZN D 502 " pdb=" OAX 97U D 503 " model vdw 1.739 2.230 nonbonded pdb="ZN ZN H 502 " pdb=" OAX 97U H 503 " model vdw 1.739 2.230 nonbonded pdb="ZN ZN C 502 " pdb=" OAX 97U C 503 " model vdw 1.743 2.230 ... (remaining 203421 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: 6.140 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: 11.500 Check model and map are aligned: 0.320 Set scattering table: 0.230 Process input model: 67.940 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.220 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:18.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.006 0.119 24872 Z= 0.437 Angle : 0.749 10.908 33752 Z= 0.447 Chirality : 0.054 0.330 3688 Planarity : 0.005 0.040 4496 Dihedral : 17.827 89.739 9112 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.32 % Allowed : 18.87 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3136 helix: 0.69 (0.15), residues: 1208 sheet: 0.51 (0.26), residues: 400 loop : -1.51 (0.14), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.007 0.001 HIS H 251 PHE 0.011 0.001 PHE F 299 TYR 0.009 0.001 TYR E 333 ARG 0.002 0.000 ARG G 199 *********************** 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 499 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 467 time to evaluate : 2.659 Fit side-chains REVERT: A 23 VAL cc_start: 0.7512 (t) cc_final: 0.7286 (p) REVERT: A 76 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7667 (tt) REVERT: A 315 ARG cc_start: 0.7221 (ttt90) cc_final: 0.6972 (mtp-110) REVERT: B 76 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7027 (tt) REVERT: B 315 ARG cc_start: 0.7248 (ttt90) cc_final: 0.6992 (mtp-110) REVERT: C 315 ARG cc_start: 0.7212 (ttt90) cc_final: 0.6988 (mtp-110) REVERT: D 23 VAL cc_start: 0.7542 (t) cc_final: 0.7298 (p) REVERT: D 76 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7474 (tt) REVERT: D 315 ARG cc_start: 0.7278 (ttt90) cc_final: 0.7017 (mtp-110) REVERT: E 23 VAL cc_start: 0.7401 (t) cc_final: 0.6840 (p) REVERT: E 93 GLN cc_start: 0.7613 (mp10) cc_final: 0.7241 (mm-40) REVERT: E 281 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7213 (ttm110) REVERT: E 385 ASP cc_start: 0.7465 (p0) cc_final: 0.7129 (p0) REVERT: E 397 ASP cc_start: 0.7632 (m-30) cc_final: 0.7389 (m-30) REVERT: F 23 VAL cc_start: 0.7642 (t) cc_final: 0.7063 (p) REVERT: F 93 GLN cc_start: 0.7566 (mp10) cc_final: 0.7214 (mm-40) REVERT: F 385 ASP cc_start: 0.7481 (p0) cc_final: 0.7180 (p0) REVERT: F 397 ASP cc_start: 0.7617 (m-30) cc_final: 0.7370 (m-30) REVERT: G 23 VAL cc_start: 0.7427 (t) cc_final: 0.6918 (p) REVERT: G 93 GLN cc_start: 0.7546 (mp10) cc_final: 0.7198 (mm-40) REVERT: G 275 MET cc_start: 0.9094 (ttm) cc_final: 0.8882 (ttp) REVERT: G 385 ASP cc_start: 0.7437 (p0) cc_final: 0.7127 (p0) REVERT: G 397 ASP cc_start: 0.7609 (m-30) cc_final: 0.7381 (m-30) REVERT: H 23 VAL cc_start: 0.7421 (t) cc_final: 0.6866 (p) REVERT: H 93 GLN cc_start: 0.7587 (mp10) cc_final: 0.7233 (mm-40) REVERT: H 385 ASP cc_start: 0.7475 (p0) cc_final: 0.7126 (p0) REVERT: H 397 ASP cc_start: 0.7616 (m-30) cc_final: 0.7381 (m-30) outliers start: 32 outliers final: 5 residues processed: 493 average time/residue: 1.8850 time to fit residues: 1031.4835 Evaluate side-chains 249 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 353 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 283 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 HIS ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 HIS ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 24872 Z= 0.261 Angle : 0.548 7.663 33752 Z= 0.288 Chirality : 0.047 0.210 3688 Planarity : 0.005 0.048 4496 Dihedral : 8.316 76.072 3767 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.35 % Allowed : 20.16 % Favored : 76.49 % 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: -0.36 (0.14), residues: 3136 helix: 0.83 (0.15), residues: 1216 sheet: 0.29 (0.24), residues: 400 loop : -1.28 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 79 HIS 0.007 0.001 HIS B 176 PHE 0.011 0.002 PHE D 122 TYR 0.013 0.002 TYR C 95 ARG 0.004 0.000 ARG B 355 *********************** 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 345 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 264 time to evaluate : 2.726 Fit side-chains REVERT: A 220 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8235 (t80) REVERT: A 315 ARG cc_start: 0.7223 (ttt90) cc_final: 0.6890 (mtp-110) REVERT: B 172 GLU cc_start: 0.7512 (tp30) cc_final: 0.6839 (tm-30) REVERT: B 220 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8283 (t80) REVERT: B 312 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7157 (tp30) REVERT: B 315 ARG cc_start: 0.7298 (ttt90) cc_final: 0.7032 (mtp-110) REVERT: C 31 PHE cc_start: 0.8336 (t80) cc_final: 0.7981 (t80) REVERT: C 172 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: C 220 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8264 (t80) REVERT: C 315 ARG cc_start: 0.7298 (ttt90) cc_final: 0.6992 (mtp-110) REVERT: D 172 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: D 220 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8275 (t80) REVERT: D 315 ARG cc_start: 0.7341 (ttt90) cc_final: 0.7035 (mtp-110) REVERT: E 93 GLN cc_start: 0.7564 (mp10) cc_final: 0.7170 (mm-40) REVERT: E 173 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6007 (ttm170) REVERT: E 338 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7000 (mtt180) REVERT: E 385 ASP cc_start: 0.7954 (p0) cc_final: 0.7692 (p0) REVERT: F 88 GLU cc_start: 0.7467 (pt0) cc_final: 0.7255 (pt0) REVERT: F 93 GLN cc_start: 0.7559 (mp10) cc_final: 0.7162 (mm-40) REVERT: F 173 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6071 (ttm170) REVERT: F 338 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6963 (mtt180) REVERT: F 385 ASP cc_start: 0.7920 (p0) cc_final: 0.7687 (p0) REVERT: G 31 PHE cc_start: 0.7787 (t80) cc_final: 0.7563 (t80) REVERT: G 93 GLN cc_start: 0.7608 (mp10) cc_final: 0.7205 (mm-40) REVERT: G 173 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6046 (ttm170) REVERT: G 338 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6985 (mtt180) REVERT: G 385 ASP cc_start: 0.7912 (p0) cc_final: 0.7653 (p0) REVERT: H 31 PHE cc_start: 0.7785 (t80) cc_final: 0.7556 (t80) REVERT: H 88 GLU cc_start: 0.7489 (pt0) cc_final: 0.7288 (pt0) REVERT: H 93 GLN cc_start: 0.7610 (mp10) cc_final: 0.7206 (mm-40) REVERT: H 173 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6116 (ttm170) REVERT: H 338 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6979 (mtt180) REVERT: H 385 ASP cc_start: 0.7903 (p0) cc_final: 0.7670 (p0) outliers start: 81 outliers final: 25 residues processed: 330 average time/residue: 1.6076 time to fit residues: 603.2326 Evaluate side-chains 269 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 230 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 220 TYR Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 220 TYR Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 220 TYR Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 306 optimal weight: 4.9990 chunk 252 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS E 271 HIS E 345 GLN ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 GLN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN G 345 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 345 GLN ** H 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24872 Z= 0.364 Angle : 0.606 8.811 33752 Z= 0.319 Chirality : 0.049 0.216 3688 Planarity : 0.005 0.053 4496 Dihedral : 8.654 71.226 3766 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.26 % Allowed : 18.00 % Favored : 76.74 % 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: -0.55 (0.14), residues: 3136 helix: 0.56 (0.14), residues: 1216 sheet: 0.07 (0.23), residues: 400 loop : -1.23 (0.14), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 79 HIS 0.018 0.002 HIS G 251 PHE 0.013 0.002 PHE C 122 TYR 0.015 0.002 TYR D 95 ARG 0.003 0.001 ARG F 355 *********************** 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 357 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 230 time to evaluate : 2.412 Fit side-chains REVERT: A 131 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: A 172 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: A 259 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7816 (ttmp) REVERT: A 315 ARG cc_start: 0.7285 (ttt90) cc_final: 0.6963 (mtp-110) REVERT: B 131 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6602 (pp20) REVERT: B 172 GLU cc_start: 0.7533 (tp30) cc_final: 0.6829 (tm-30) REVERT: B 259 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7796 (ttmp) REVERT: B 312 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7286 (tp30) REVERT: B 315 ARG cc_start: 0.7360 (ttt90) cc_final: 0.7041 (mtp-110) REVERT: C 66 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.4720 (ttm170) REVERT: C 131 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6595 (pp20) REVERT: C 172 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: C 259 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7839 (ttmp) REVERT: C 315 ARG cc_start: 0.7349 (ttt90) cc_final: 0.7042 (mtp-110) REVERT: C 385 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6714 (p0) REVERT: D 131 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6602 (pp20) REVERT: D 259 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7813 (ttmp) REVERT: D 315 ARG cc_start: 0.7370 (ttt90) cc_final: 0.7053 (mtp-110) REVERT: D 385 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6710 (p0) REVERT: E 93 GLN cc_start: 0.7769 (mp10) cc_final: 0.7232 (mm-40) REVERT: E 173 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5986 (ttm170) REVERT: E 338 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7065 (mtt180) REVERT: F 88 GLU cc_start: 0.7559 (pt0) cc_final: 0.7352 (pt0) REVERT: F 93 GLN cc_start: 0.7763 (mp10) cc_final: 0.7225 (mm-40) REVERT: F 173 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.5947 (ttm170) REVERT: F 338 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7019 (mtt180) REVERT: F 385 ASP cc_start: 0.8166 (p0) cc_final: 0.7949 (p0) REVERT: G 93 GLN cc_start: 0.7754 (mp10) cc_final: 0.7221 (mm-40) REVERT: G 173 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5992 (ttm170) REVERT: G 338 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7042 (mtt180) REVERT: G 385 ASP cc_start: 0.8175 (p0) cc_final: 0.7931 (p0) REVERT: H 88 GLU cc_start: 0.7569 (pt0) cc_final: 0.7338 (pt0) REVERT: H 93 GLN cc_start: 0.7753 (mp10) cc_final: 0.7219 (mm-40) REVERT: H 173 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.5969 (ttm170) REVERT: H 338 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7012 (mtt180) REVERT: H 385 ASP cc_start: 0.8141 (p0) cc_final: 0.7932 (p0) outliers start: 127 outliers final: 57 residues processed: 330 average time/residue: 1.6469 time to fit residues: 613.0677 Evaluate side-chains 299 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 221 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 385 ASP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 251 HIS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 301 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 81 optimal weight: 0.0770 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 GLN ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 24872 Z= 0.192 Angle : 0.494 7.207 33752 Z= 0.257 Chirality : 0.045 0.221 3688 Planarity : 0.005 0.046 4496 Dihedral : 7.479 60.017 3766 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.01 % Allowed : 17.72 % Favored : 77.28 % 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: -0.31 (0.14), residues: 3136 helix: 0.81 (0.15), residues: 1208 sheet: 0.02 (0.23), residues: 400 loop : -1.08 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 79 HIS 0.026 0.001 HIS E 251 PHE 0.010 0.001 PHE E 294 TYR 0.010 0.001 TYR A 95 ARG 0.002 0.000 ARG G 109 *********************** 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 356 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 235 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: A 259 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7705 (ttmp) REVERT: A 315 ARG cc_start: 0.7317 (ttt90) cc_final: 0.6882 (mtp-110) REVERT: B 172 GLU cc_start: 0.7486 (tp30) cc_final: 0.6863 (tm-30) REVERT: B 259 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7697 (ttmp) REVERT: B 312 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7276 (tp30) REVERT: B 315 ARG cc_start: 0.7280 (ttt90) cc_final: 0.6958 (mtp-110) REVERT: C 66 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.4645 (ttm170) REVERT: C 172 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: C 259 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7737 (ttmp) REVERT: C 315 ARG cc_start: 0.7334 (ttt90) cc_final: 0.7043 (mtp-110) REVERT: D 259 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7710 (ttmp) REVERT: D 315 ARG cc_start: 0.7322 (ttt90) cc_final: 0.7025 (mtp-110) REVERT: E 119 MET cc_start: 0.8863 (mmt) cc_final: 0.8369 (mmt) REVERT: E 173 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.5934 (ttm170) REVERT: E 338 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7086 (mtt180) REVERT: E 353 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8306 (m110) REVERT: F 88 GLU cc_start: 0.7440 (pt0) cc_final: 0.7199 (pt0) REVERT: F 173 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.5911 (ttm170) REVERT: F 338 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7058 (mtt180) REVERT: F 385 ASP cc_start: 0.8133 (p0) cc_final: 0.7907 (p0) REVERT: G 173 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.5927 (ttm170) REVERT: G 338 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7054 (mtt180) REVERT: G 385 ASP cc_start: 0.8136 (p0) cc_final: 0.7908 (p0) REVERT: H 119 MET cc_start: 0.8860 (mmt) cc_final: 0.8363 (mmt) REVERT: H 173 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5993 (ttm170) REVERT: H 338 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7049 (mtt180) REVERT: H 385 ASP cc_start: 0.8124 (p0) cc_final: 0.7904 (p0) outliers start: 121 outliers final: 56 residues processed: 338 average time/residue: 1.7456 time to fit residues: 668.2866 Evaluate side-chains 292 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 220 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 5.9990 chunk 171 optimal weight: 0.0370 chunk 4 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 270 optimal weight: 0.0670 chunk 76 optimal weight: 3.9990 overall best weight: 2.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24872 Z= 0.280 Angle : 0.547 7.930 33752 Z= 0.285 Chirality : 0.047 0.218 3688 Planarity : 0.005 0.050 4496 Dihedral : 8.158 61.897 3764 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.46 % Allowed : 17.22 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3136 helix: 0.67 (0.15), residues: 1216 sheet: -0.35 (0.23), residues: 408 loop : -0.99 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 79 HIS 0.015 0.002 HIS E 251 PHE 0.011 0.002 PHE D 31 TYR 0.012 0.002 TYR A 95 ARG 0.002 0.000 ARG G 109 *********************** 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 355 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 223 time to evaluate : 2.982 Fit side-chains REVERT: A 131 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6639 (pp20) REVERT: A 172 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: A 259 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7744 (ttmp) REVERT: A 315 ARG cc_start: 0.7340 (ttt90) cc_final: 0.6968 (mtp-110) REVERT: B 172 GLU cc_start: 0.7486 (tp30) cc_final: 0.6855 (tm-30) REVERT: B 259 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7722 (ttmp) REVERT: B 312 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7303 (tp30) REVERT: B 315 ARG cc_start: 0.7379 (ttt90) cc_final: 0.6615 (ttt-90) REVERT: C 66 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.4635 (ttm170) REVERT: C 172 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6796 (OUTLIER) REVERT: C 259 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7761 (ttmp) REVERT: C 315 ARG cc_start: 0.7370 (ttt90) cc_final: 0.7042 (mtp-110) REVERT: D 259 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7737 (ttmp) REVERT: D 315 ARG cc_start: 0.7344 (ttt90) cc_final: 0.7020 (mtp-110) REVERT: E 173 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.5950 (ttm170) REVERT: E 281 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.7169 (ttm110) REVERT: E 338 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7053 (mtt180) REVERT: F 88 GLU cc_start: 0.7547 (pt0) cc_final: 0.7318 (pt0) REVERT: F 173 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.5936 (ttm170) REVERT: F 283 MET cc_start: 0.8678 (ttm) cc_final: 0.8444 (mtp) REVERT: F 338 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7020 (mtt180) REVERT: G 173 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.5951 (ttm170) REVERT: G 338 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7048 (mtt180) REVERT: H 173 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6010 (ttm170) REVERT: H 338 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7032 (mtt180) outliers start: 132 outliers final: 72 residues processed: 332 average time/residue: 1.6072 time to fit residues: 604.1697 Evaluate side-chains 297 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 210 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 301 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN ** C 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 ASN ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 404 ASN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24872 Z= 0.141 Angle : 0.472 6.790 33752 Z= 0.242 Chirality : 0.044 0.219 3688 Planarity : 0.004 0.041 4496 Dihedral : 6.900 59.826 3764 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.51 % Allowed : 18.17 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3136 helix: 0.95 (0.15), residues: 1208 sheet: -0.24 (0.23), residues: 408 loop : -0.90 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 79 HIS 0.011 0.001 HIS G 251 PHE 0.009 0.001 PHE A 31 TYR 0.009 0.001 TYR A 333 ARG 0.002 0.000 ARG G 109 *********************** 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 350 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 241 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: A 172 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: A 259 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7674 (ttmp) REVERT: B 172 GLU cc_start: 0.7492 (tp30) cc_final: 0.6853 (tm-30) REVERT: B 259 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7656 (ttmp) REVERT: B 312 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7220 (tp30) REVERT: B 315 ARG cc_start: 0.7304 (ttt90) cc_final: 0.6962 (mtp-110) REVERT: C 66 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.4612 (ttm170) REVERT: C 172 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: C 259 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7688 (ttmp) REVERT: D 39 LYS cc_start: 0.6848 (mttm) cc_final: 0.6578 (mmtp) REVERT: D 259 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7652 (ttmp) REVERT: E 173 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.5988 (ttm170) REVERT: E 281 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.7206 (ttm110) REVERT: E 303 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7421 (mmtt) REVERT: E 338 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7001 (mtt180) REVERT: F 303 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7378 (mmtt) REVERT: F 338 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6921 (mtt180) REVERT: G 173 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5996 (ttm170) REVERT: G 303 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7405 (mmtt) REVERT: G 338 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6951 (mtt180) REVERT: H 88 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: H 173 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6009 (ttm170) outliers start: 109 outliers final: 57 residues processed: 326 average time/residue: 1.5011 time to fit residues: 562.6664 Evaluate side-chains 300 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 10.0000 chunk 34 optimal weight: 0.0980 chunk 171 optimal weight: 0.2980 chunk 220 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 ASN ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS G 271 HIS G 335 ASN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24872 Z= 0.150 Angle : 0.474 6.772 33752 Z= 0.242 Chirality : 0.044 0.219 3688 Planarity : 0.004 0.044 4496 Dihedral : 6.797 59.860 3758 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.68 % Allowed : 18.09 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3136 helix: 1.00 (0.15), residues: 1216 sheet: -0.24 (0.23), residues: 408 loop : -0.77 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 79 HIS 0.011 0.001 HIS H 251 PHE 0.010 0.001 PHE A 31 TYR 0.009 0.001 TYR E 333 ARG 0.001 0.000 ARG H 355 *********************** 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 348 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 235 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: A 172 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: A 259 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7666 (ttmp) REVERT: B 172 GLU cc_start: 0.7529 (tp30) cc_final: 0.6892 (tm-30) REVERT: B 259 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7647 (ttmp) REVERT: B 312 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7206 (tp30) REVERT: B 315 ARG cc_start: 0.7297 (ttt90) cc_final: 0.6955 (mtp-110) REVERT: C 172 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: C 259 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7684 (ttmp) REVERT: D 39 LYS cc_start: 0.6784 (mttm) cc_final: 0.6576 (mmtp) REVERT: D 259 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7649 (ttmp) REVERT: E 173 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5979 (ttm170) REVERT: E 281 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.7166 (ttm110) REVERT: E 303 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7414 (mmtt) REVERT: E 338 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7101 (mtt180) REVERT: F 173 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5806 (ttm170) REVERT: F 338 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7021 (mtt180) REVERT: G 173 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.5982 (ttm170) REVERT: G 303 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7389 (mmtt) REVERT: G 338 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7059 (mtt180) REVERT: H 119 MET cc_start: 0.8787 (mmt) cc_final: 0.8334 (mmt) REVERT: H 303 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7327 (mmtt) REVERT: H 338 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7068 (mtt180) outliers start: 113 outliers final: 71 residues processed: 326 average time/residue: 1.5093 time to fit residues: 561.8454 Evaluate side-chains 311 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 223 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 303 LYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 ASN ** G 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24872 Z= 0.178 Angle : 0.490 6.978 33752 Z= 0.252 Chirality : 0.045 0.218 3688 Planarity : 0.004 0.045 4496 Dihedral : 7.095 59.987 3758 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.59 % Allowed : 18.38 % Favored : 77.03 % 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: -0.06 (0.14), residues: 3136 helix: 0.99 (0.15), residues: 1216 sheet: -0.30 (0.22), residues: 408 loop : -0.77 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.026 0.001 HIS G 251 PHE 0.011 0.001 PHE A 31 TYR 0.009 0.001 TYR E 333 ARG 0.003 0.000 ARG D 416 *********************** 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 339 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 228 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.6731 (mttm) cc_final: 0.6250 (mttp) REVERT: A 131 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: A 172 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: A 259 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7680 (ttmp) REVERT: B 131 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6657 (pp20) REVERT: B 172 GLU cc_start: 0.7516 (tp30) cc_final: 0.6881 (tm-30) REVERT: B 259 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7647 (ttmp) REVERT: B 312 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7195 (tp30) REVERT: B 315 ARG cc_start: 0.7313 (ttt90) cc_final: 0.6971 (mtp-110) REVERT: C 131 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6632 (pp20) REVERT: C 172 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: C 259 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7705 (ttmp) REVERT: D 131 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6649 (pp20) REVERT: D 259 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7665 (ttmp) REVERT: E 119 MET cc_start: 0.8836 (mmt) cc_final: 0.8361 (mmt) REVERT: E 173 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.5932 (ttm170) REVERT: E 281 ARG cc_start: 0.7521 (ttp-110) cc_final: 0.7179 (ttm110) REVERT: E 303 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7404 (mmtt) REVERT: E 338 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7126 (mtt180) REVERT: F 88 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: F 173 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.5811 (ttm170) REVERT: F 303 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7396 (mmtt) REVERT: F 338 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7083 (mtt180) REVERT: G 119 MET cc_start: 0.8851 (mmt) cc_final: 0.8343 (mmt) REVERT: G 173 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5938 (ttm170) REVERT: G 303 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7416 (mmtt) REVERT: G 338 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7107 (mtt180) REVERT: H 119 MET cc_start: 0.8837 (mmt) cc_final: 0.8361 (mmt) REVERT: H 173 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.5925 (ttm170) REVERT: H 303 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7330 (mmtt) REVERT: H 338 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7081 (mtt180) outliers start: 111 outliers final: 73 residues processed: 315 average time/residue: 1.5586 time to fit residues: 556.9190 Evaluate side-chains 320 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 224 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 303 LYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 20.0000 chunk 288 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 253 optimal weight: 0.0970 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.0970 overall best weight: 1.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 ASN G 335 ASN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24872 Z= 0.199 Angle : 0.506 7.459 33752 Z= 0.259 Chirality : 0.045 0.219 3688 Planarity : 0.004 0.046 4496 Dihedral : 7.427 59.914 3758 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.35 % Allowed : 18.67 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3136 helix: 0.95 (0.15), residues: 1216 sheet: -0.33 (0.22), residues: 408 loop : -0.77 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.012 0.001 HIS G 251 PHE 0.011 0.001 PHE A 31 TYR 0.009 0.001 TYR A 95 ARG 0.003 0.000 ARG D 416 *********************** 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 331 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 226 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.6767 (mttm) cc_final: 0.6266 (mttp) REVERT: A 131 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: A 172 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: A 259 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7700 (ttmp) REVERT: B 39 LYS cc_start: 0.7444 (mmtp) cc_final: 0.6953 (mttm) REVERT: B 131 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6728 (pp20) REVERT: B 172 GLU cc_start: 0.7521 (tp30) cc_final: 0.6881 (tm-30) REVERT: B 259 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7667 (ttmp) REVERT: B 312 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7269 (tp30) REVERT: B 315 ARG cc_start: 0.7309 (ttt90) cc_final: 0.6980 (mtp-110) REVERT: C 131 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6699 (pp20) REVERT: C 172 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: C 259 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7702 (ttmp) REVERT: D 39 LYS cc_start: 0.7375 (mmtp) cc_final: 0.6898 (mttm) REVERT: D 131 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6634 (pp20) REVERT: D 259 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7682 (ttmp) REVERT: E 173 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.5916 (ttm170) REVERT: E 281 ARG cc_start: 0.7533 (ttp-110) cc_final: 0.7191 (ttm110) REVERT: E 303 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7409 (mmtt) REVERT: E 338 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7104 (mtt180) REVERT: F 88 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: F 173 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.5811 (ttm170) REVERT: F 303 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7379 (mmtt) REVERT: F 338 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7077 (mtt180) REVERT: G 88 GLU cc_start: 0.7646 (pt0) cc_final: 0.7415 (pt0) REVERT: G 119 MET cc_start: 0.8882 (mmt) cc_final: 0.8311 (mmt) REVERT: G 173 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5921 (ttm170) REVERT: G 303 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7421 (mmtt) REVERT: G 338 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7068 (mtt180) REVERT: H 88 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: H 173 ARG cc_start: 0.7136 (OUTLIER) cc_final: 0.5795 (ttm170) REVERT: H 303 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7363 (mmtt) REVERT: H 338 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7090 (mtt180) outliers start: 105 outliers final: 75 residues processed: 313 average time/residue: 1.5490 time to fit residues: 550.7817 Evaluate side-chains 322 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 223 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 338 ARG Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 172 GLU Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 303 LYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 338 ARG Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 404 ASN E 410 ASN ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 335 ASN G 410 ASN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24872 Z= 0.120 Angle : 0.460 6.413 33752 Z= 0.234 Chirality : 0.043 0.221 3688 Planarity : 0.004 0.040 4496 Dihedral : 6.282 58.967 3758 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.23 % Allowed : 19.83 % Favored : 76.95 % 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: 0.09 (0.15), residues: 3136 helix: 1.16 (0.15), residues: 1208 sheet: -0.11 (0.23), residues: 400 loop : -0.76 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP H 79 HIS 0.009 0.001 HIS F 251 PHE 0.011 0.001 PHE B 31 TYR 0.008 0.001 TYR D 333 ARG 0.003 0.000 ARG C 416 ********************** 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 324 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 246 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.6726 (mttm) cc_final: 0.6402 (mttm) REVERT: A 172 GLU cc_start: 0.7182 (tt0) cc_final: 0.6875 (tm-30) REVERT: A 259 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7773 (ttmp) REVERT: B 39 LYS cc_start: 0.7465 (mmtp) cc_final: 0.6987 (mttp) REVERT: B 172 GLU cc_start: 0.7510 (tp30) cc_final: 0.6911 (tm-30) REVERT: B 312 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7219 (tp30) REVERT: C 172 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: C 259 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7748 (ttmp) REVERT: E 173 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.5952 (ttm170) REVERT: E 281 ARG cc_start: 0.7535 (ttp-110) cc_final: 0.7187 (ttm110) REVERT: E 303 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7393 (mmtt) REVERT: E 338 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7029 (mtt180) REVERT: F 173 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.5779 (ttm170) REVERT: F 303 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7356 (mmtt) REVERT: F 338 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6982 (mtt180) REVERT: G 173 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5959 (ttm170) REVERT: G 303 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7413 (mmtt) REVERT: H 303 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7352 (mmtt) outliers start: 78 outliers final: 57 residues processed: 315 average time/residue: 1.4494 time to fit residues: 523.0546 Evaluate side-chains 297 residues out of total 2416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 228 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 HIS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 251 HIS Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 251 HIS Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 356 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 HIS Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 HIS Chi-restraints excluded: chain F residue 303 LYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 303 LYS Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 358 VAL Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain H residue 208 LEU Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 HIS Chi-restraints excluded: chain H residue 303 LYS Chi-restraints excluded: chain H residue 313 VAL Chi-restraints excluded: chain H residue 358 VAL Chi-restraints excluded: chain H residue 389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 75 optimal weight: 0.0670 chunk 228 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 0.0970 chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 335 ASN E 410 ASN ** F 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN ** F 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 410 ASN G 335 ASN G 410 ASN ** H 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 335 ASN H 410 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.146549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122435 restraints weight = 23860.628| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.72 r_work: 0.3398 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24872 Z= 0.285 Angle : 0.561 7.735 33752 Z= 0.289 Chirality : 0.048 0.222 3688 Planarity : 0.005 0.050 4496 Dihedral : 8.213 62.727 3758 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.73 % Allowed : 19.37 % Favored : 76.90 % 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 (0.14), residues: 3136 helix: 0.84 (0.15), residues: 1216 sheet: -0.43 (0.22), residues: 408 loop : -0.79 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 289 HIS 0.013 0.001 HIS F 251 PHE 0.014 0.002 PHE B 31 TYR 0.011 0.002 TYR D 95 ARG 0.002 0.000 ARG A 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9376.06 seconds wall clock time: 167 minutes 51.07 seconds (10071.07 seconds total)