Starting phenix.real_space_refine on Sat Sep 28 20:24:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptg_17870/09_2024/8ptg_17870.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptg_17870/09_2024/8ptg_17870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptg_17870/09_2024/8ptg_17870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptg_17870/09_2024/8ptg_17870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptg_17870/09_2024/8ptg_17870.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptg_17870/09_2024/8ptg_17870.cif" } resolution = 2.9 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= 0.006 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 27 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12645 2.51 5 N 3600 2.21 5 O 3888 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20292 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "B" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "C" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "D" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "E" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "F" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3297 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "R" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 6, 'rna3p': 8} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.76, per 1000 atoms: 0.68 Number of scatterers: 20292 At special positions: 0 Unit cell: (112.347, 149.139, 137.313, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 27 15.00 Mg 6 11.99 F 18 9.00 O 3888 8.00 N 3600 7.00 C 12645 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.7 seconds 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 23 sheets defined 50.2% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.609A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.977A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.576A pdb=" N HIS A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.511A pdb=" N HIS A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.748A pdb=" N ARG A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.818A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.101A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.751A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.661A pdb=" N ILE B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.608A pdb=" N ARG B 128 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.871A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.616A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.725A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.502A pdb=" N ALA B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.086A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 403 Processing helix chain 'B' and resid 408 through 419 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.575A pdb=" N ILE C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.577A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.834A pdb=" N ARG C 128 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.952A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 256 Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.811A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 4.336A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.701A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.587A pdb=" N ILE D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.579A pdb=" N ASN D 129 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 130 " --> pdb=" O ALA D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 130' Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 153 through 166 removed outlier: 3.543A pdb=" N LEU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR D 158 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.565A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 removed outlier: 3.689A pdb=" N LEU D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.848A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 346 through 352 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 404 Processing helix chain 'D' and resid 408 through 419 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.535A pdb=" N LEU E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 21 removed outlier: 3.543A pdb=" N MET E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.519A pdb=" N ILE E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.915A pdb=" N ASN E 129 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.791A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.661A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 removed outlier: 3.656A pdb=" N LEU E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.642A pdb=" N GLU E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 419 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 67 through 71 Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 123 through 129 removed outlier: 3.902A pdb=" N ASN F 129 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 153 through 166 removed outlier: 3.513A pdb=" N LEU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 223 Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 303 removed outlier: 3.569A pdb=" N LYS F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.728A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 Processing helix chain 'F' and resid 367 through 371 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 391 through 403 Processing helix chain 'F' and resid 408 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 56 removed outlier: 3.652A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR A 80 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS A 115 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS A 100 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL A 116 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SER A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A 118 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 96 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 49 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.791A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 209 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 removed outlier: 3.791A pdb=" N ASN A 306 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.525A pdb=" N ILE A 168 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.823A pdb=" N ILE B 79 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR B 80 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS B 115 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.951A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 203 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 263 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ASP B 265 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 207 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.951A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.348A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 57 removed outlier: 3.819A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N LYS C 115 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE C 49 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 209 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.674A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.533A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.771A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.894A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR D 80 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LYS D 115 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYS D 100 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL D 116 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU D 118 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 96 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.659A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.659A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ARG D 173 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU D 343 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 175 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 345 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D 177 " --> pdb=" O LEU D 345 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.817A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR E 80 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS E 115 " --> pdb=" O TYR E 80 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.757A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL E 203 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU E 263 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET E 205 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.757A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 49 through 57 removed outlier: 3.886A pdb=" N ILE F 79 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR F 80 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LYS F 115 " --> pdb=" O TYR F 80 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU F 113 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG F 102 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER F 98 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL F 119 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR F 96 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.864A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL F 203 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU F 263 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET F 205 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASP F 265 " --> pdb=" O MET F 205 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU F 207 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU F 204 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 138 through 139 removed outlier: 3.864A pdb=" N ASN F 306 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 178 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ARG F 173 " --> pdb=" O MET F 341 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU F 343 " --> pdb=" O ARG F 173 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU F 345 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL F 177 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N GLU F 342 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN F 361 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS F 344 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.513A pdb=" N ILE F 168 " --> pdb=" O LEU F 145 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.80 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6746 1.34 - 1.46: 3796 1.46 - 1.58: 9833 1.58 - 1.70: 47 1.70 - 1.83: 198 Bond restraints: 20620 Sorted by residual: bond pdb=" F2 BEF E1002 " pdb="BE BEF E1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" F2 BEF C1002 " pdb="BE BEF C1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F2 BEF F1002 " pdb="BE BEF F1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" F2 BEF B 503 " pdb="BE BEF B 503 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 20615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 27773 5.15 - 10.30: 75 10.30 - 15.45: 11 15.45 - 20.60: 0 20.60 - 25.75: 3 Bond angle restraints: 27862 Sorted by residual: angle pdb=" OP2 C R 92 " pdb=" P C R 92 " pdb=" O5' C R 92 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" OP1 C R 92 " pdb=" P C R 92 " pdb=" O5' C R 92 " ideal model delta sigma weight residual 108.00 83.28 24.72 3.00e+00 1.11e-01 6.79e+01 angle pdb=" OP1 C R 92 " pdb=" P C R 92 " pdb=" OP2 C R 92 " ideal model delta sigma weight residual 119.60 141.04 -21.44 3.00e+00 1.11e-01 5.11e+01 angle pdb=" CA PRO D 76 " pdb=" N PRO D 76 " pdb=" CD PRO D 76 " ideal model delta sigma weight residual 112.00 103.80 8.20 1.40e+00 5.10e-01 3.43e+01 angle pdb=" F2 BEF D1002 " pdb="BE BEF D1002 " pdb=" F3 BEF D1002 " ideal model delta sigma weight residual 119.96 106.69 13.27 3.00e+00 1.11e-01 1.96e+01 ... (remaining 27857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12316 35.90 - 71.80: 435 71.80 - 107.71: 27 107.71 - 143.61: 2 143.61 - 179.51: 6 Dihedral angle restraints: 12786 sinusoidal: 5556 harmonic: 7230 Sorted by residual: dihedral pdb=" O4' U R 14 " pdb=" C1' U R 14 " pdb=" N1 U R 14 " pdb=" C2 U R 14 " ideal model delta sinusoidal sigma weight residual 200.00 49.45 150.55 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' C R 13 " pdb=" C1' C R 13 " pdb=" N1 C R 13 " pdb=" C2 C R 13 " ideal model delta sinusoidal sigma weight residual -128.00 51.51 -179.51 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C R 99 " pdb=" C1' C R 99 " pdb=" N1 C R 99 " pdb=" C2 C R 99 " ideal model delta sinusoidal sigma weight residual -128.00 51.28 -179.28 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2811 0.070 - 0.140: 364 0.140 - 0.210: 1 0.210 - 0.280: 0 0.280 - 0.350: 1 Chirality restraints: 3177 Sorted by residual: chirality pdb=" P C R 92 " pdb=" OP1 C R 92 " pdb=" OP2 C R 92 " pdb=" O5' C R 92 " both_signs ideal model delta sigma weight residual True 2.41 -2.06 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA GLU C 414 " pdb=" N GLU C 414 " pdb=" C GLU C 414 " pdb=" CB GLU C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CG LEU E 403 " pdb=" CB LEU E 403 " pdb=" CD1 LEU E 403 " pdb=" CD2 LEU E 403 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 3174 not shown) Planarity restraints: 3549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 381 " -0.035 2.00e-02 2.50e+03 3.57e-02 3.19e+01 pdb=" CG TRP F 381 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP F 381 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 381 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 381 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 381 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 381 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP F 381 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 353 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.44e+01 pdb=" NE ARG E 353 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 353 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 353 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 353 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 414 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" CD GLU C 414 " 0.059 2.00e-02 2.50e+03 pdb=" OE1 GLU C 414 " -0.021 2.00e-02 2.50e+03 pdb=" OE2 GLU C 414 " -0.021 2.00e-02 2.50e+03 ... (remaining 3546 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 12 2.12 - 2.82: 6089 2.82 - 3.51: 28582 3.51 - 4.21: 48220 4.21 - 4.90: 87892 Nonbonded interactions: 170795 Sorted by model distance: nonbonded pdb=" N LYS E 181 " pdb=" F1 BEF E1002 " model vdw 1.427 3.070 nonbonded pdb=" NH2 ARG C 366 " pdb=" F1 BEF B 503 " model vdw 1.767 3.070 nonbonded pdb=" O2B ADP E1000 " pdb="MG MG E1001 " model vdw 1.969 2.170 nonbonded pdb=" O1B ADP A1000 " pdb="MG MG A1001 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR C 185 " pdb="MG MG C1001 " model vdw 2.014 2.170 ... (remaining 170790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 17.140 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: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.040 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 20620 Z= 0.269 Angle : 0.755 25.750 27862 Z= 0.344 Chirality : 0.042 0.350 3177 Planarity : 0.005 0.150 3549 Dihedral : 17.756 179.510 8106 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.02 % Allowed : 23.82 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.98 (0.17), residues: 2502 helix: 1.41 (0.16), residues: 1092 sheet: 0.03 (0.26), residues: 441 loop : 0.23 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.005 TRP F 381 HIS 0.004 0.001 HIS F 256 PHE 0.017 0.001 PHE A 62 TYR 0.021 0.001 TYR D 80 ARG 0.015 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 239 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6747 (pmm) REVERT: A 29 MET cc_start: 0.5696 (tmm) cc_final: 0.4109 (pmm) REVERT: C 244 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (mp0) outliers start: 65 outliers final: 53 residues processed: 294 average time/residue: 1.5051 time to fit residues: 492.8161 Evaluate side-chains 286 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 231 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 292 ASN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 193 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 GLN C 193 GLN E 42 HIS E 59 GLN E 193 GLN E 241 GLN F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20620 Z= 0.200 Angle : 0.615 7.899 27862 Z= 0.300 Chirality : 0.042 0.135 3177 Planarity : 0.004 0.053 3549 Dihedral : 13.169 179.908 3128 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.67 % Allowed : 20.75 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2502 helix: 1.53 (0.16), residues: 1101 sheet: 0.19 (0.27), residues: 381 loop : 0.01 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 381 HIS 0.005 0.001 HIS F 256 PHE 0.011 0.001 PHE C 232 TYR 0.015 0.001 TYR D 110 ARG 0.008 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 256 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6762 (pmm) REVERT: A 56 GLU cc_start: 0.8419 (tt0) cc_final: 0.8192 (pt0) REVERT: A 244 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8237 (mm-30) REVERT: B 244 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8197 (mm-30) REVERT: B 334 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8344 (tm-30) REVERT: C 21 MET cc_start: 0.8986 (ppp) cc_final: 0.8779 (tmt) REVERT: C 244 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: C 414 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: D 41 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8400 (pp30) REVERT: D 374 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8011 (tm-30) REVERT: E 353 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7899 (ttp-110) REVERT: F 244 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8342 (mm-30) outliers start: 79 outliers final: 35 residues processed: 314 average time/residue: 1.5285 time to fit residues: 533.8836 Evaluate side-chains 276 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 200 optimal weight: 0.0970 chunk 222 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN C 193 GLN E 59 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20620 Z= 0.186 Angle : 0.601 8.475 27862 Z= 0.288 Chirality : 0.042 0.136 3177 Planarity : 0.004 0.052 3549 Dihedral : 12.851 179.755 3087 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.81 % Allowed : 21.12 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2502 helix: 1.61 (0.16), residues: 1101 sheet: 0.07 (0.27), residues: 399 loop : 0.05 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 381 HIS 0.005 0.001 HIS F 256 PHE 0.010 0.001 PHE D 232 TYR 0.019 0.001 TYR B 110 ARG 0.008 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 257 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8417 (tt0) cc_final: 0.8149 (pt0) REVERT: A 244 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8235 (mm-30) REVERT: B 5 GLU cc_start: 0.9464 (mp0) cc_final: 0.9227 (mp0) REVERT: B 244 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8163 (mm-30) REVERT: C 21 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8664 (tmt) REVERT: C 244 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: C 374 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7921 (tp-100) REVERT: C 414 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: D 41 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8445 (pp30) REVERT: D 374 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7915 (tm-30) REVERT: E 342 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: E 353 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7941 (ttp-110) REVERT: F 29 MET cc_start: 0.5546 (pmm) cc_final: 0.4857 (mpp) REVERT: F 244 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8328 (mm-30) REVERT: F 374 GLN cc_start: 0.8669 (tp40) cc_final: 0.8463 (mm-40) REVERT: F 401 ASN cc_start: 0.8928 (t0) cc_final: 0.8592 (t0) outliers start: 82 outliers final: 42 residues processed: 316 average time/residue: 1.5320 time to fit residues: 538.1616 Evaluate side-chains 285 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 238 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN E 59 GLN E 193 GLN E 241 GLN F 41 GLN F 241 GLN F 374 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20620 Z= 0.239 Angle : 0.607 9.222 27862 Z= 0.291 Chirality : 0.042 0.137 3177 Planarity : 0.004 0.049 3549 Dihedral : 12.627 179.848 3079 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.04 % Allowed : 21.82 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2502 helix: 1.64 (0.16), residues: 1107 sheet: -0.00 (0.26), residues: 399 loop : 0.02 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 381 HIS 0.005 0.001 HIS E 239 PHE 0.013 0.001 PHE D 232 TYR 0.020 0.001 TYR D 110 ARG 0.009 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 252 time to evaluate : 2.274 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.4323 (OUTLIER) cc_final: 0.4007 (pmt-80) REVERT: A 56 GLU cc_start: 0.8396 (tt0) cc_final: 0.8149 (pt0) REVERT: B 5 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.9228 (mp0) REVERT: B 42 HIS cc_start: 0.8097 (t-90) cc_final: 0.7873 (t-90) REVERT: B 244 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 21 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8617 (tmt) REVERT: C 244 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: C 374 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7894 (tp-100) REVERT: C 414 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: D 41 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8429 (pp30) REVERT: D 374 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7937 (tm-30) REVERT: E 342 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: E 353 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7966 (ttp-110) REVERT: F 41 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8752 (mp10) REVERT: F 211 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: F 244 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8297 (mm-30) outliers start: 87 outliers final: 43 residues processed: 317 average time/residue: 1.5520 time to fit residues: 547.0775 Evaluate side-chains 289 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 237 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN B 241 GLN E 59 GLN E 193 GLN E 241 GLN E 275 ASN F 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20620 Z= 0.278 Angle : 0.632 9.471 27862 Z= 0.303 Chirality : 0.043 0.141 3177 Planarity : 0.004 0.049 3549 Dihedral : 12.492 179.931 3074 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.90 % Allowed : 22.47 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2502 helix: 1.62 (0.16), residues: 1110 sheet: -0.05 (0.26), residues: 399 loop : 0.01 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 381 HIS 0.005 0.001 HIS A 239 PHE 0.013 0.001 PHE C 232 TYR 0.018 0.001 TYR B 332 ARG 0.010 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 243 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8385 (tt0) cc_final: 0.8128 (pt0) REVERT: B 5 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.9232 (mp0) REVERT: B 42 HIS cc_start: 0.8106 (t-90) cc_final: 0.7901 (t-90) REVERT: C 21 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8593 (tmt) REVERT: C 244 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7944 (mp0) REVERT: C 374 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7981 (tp-100) REVERT: C 414 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: D 41 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8439 (pp30) REVERT: D 374 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7961 (tm-30) REVERT: E 42 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: E 342 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: E 353 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8087 (ttp-110) REVERT: F 29 MET cc_start: 0.5483 (pmm) cc_final: 0.4877 (mpp) REVERT: F 211 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8239 (tp30) REVERT: F 244 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8288 (mm-30) outliers start: 84 outliers final: 51 residues processed: 303 average time/residue: 1.5564 time to fit residues: 523.8453 Evaluate side-chains 293 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 234 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 40.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN B 241 GLN E 59 GLN E 193 GLN E 241 GLN F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20620 Z= 0.234 Angle : 0.623 9.919 27862 Z= 0.297 Chirality : 0.042 0.142 3177 Planarity : 0.004 0.048 3549 Dihedral : 12.404 179.990 3074 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.90 % Allowed : 22.84 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2502 helix: 1.67 (0.16), residues: 1110 sheet: 0.01 (0.26), residues: 393 loop : -0.03 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.011 0.001 PHE B 232 TYR 0.023 0.001 TYR D 110 ARG 0.010 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 248 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8355 (tt0) cc_final: 0.8094 (pt0) REVERT: B 5 GLU cc_start: 0.9462 (OUTLIER) cc_final: 0.9236 (mp0) REVERT: B 42 HIS cc_start: 0.8119 (t-90) cc_final: 0.7898 (t-90) REVERT: B 244 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 298 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8580 (mmmm) REVERT: B 334 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 21 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8578 (tmt) REVERT: C 244 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: C 374 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7991 (tp-100) REVERT: C 414 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: D 41 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8392 (pp30) REVERT: D 374 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 42 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7932 (t-90) REVERT: E 342 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: E 353 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8079 (ttp-110) REVERT: F 29 MET cc_start: 0.5576 (pmm) cc_final: 0.4927 (mpp) REVERT: F 211 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: F 244 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8280 (mm-30) outliers start: 84 outliers final: 46 residues processed: 312 average time/residue: 1.5536 time to fit residues: 537.8141 Evaluate side-chains 287 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 232 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 145 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN E 59 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20620 Z= 0.192 Angle : 0.638 10.614 27862 Z= 0.303 Chirality : 0.042 0.140 3177 Planarity : 0.004 0.054 3549 Dihedral : 12.242 179.807 3068 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.99 % Allowed : 23.07 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2502 helix: 1.72 (0.16), residues: 1107 sheet: -0.01 (0.26), residues: 393 loop : -0.01 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.009 0.001 PHE B 232 TYR 0.022 0.001 TYR B 332 ARG 0.012 0.000 ARG C 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 242 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.5478 (tmm) cc_final: 0.3926 (mmp) REVERT: A 56 GLU cc_start: 0.8340 (tt0) cc_final: 0.8118 (pt0) REVERT: B 5 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9241 (mp0) REVERT: B 42 HIS cc_start: 0.8106 (t-90) cc_final: 0.7886 (t-90) REVERT: B 244 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 298 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8551 (mmmm) REVERT: B 334 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8463 (tm-30) REVERT: B 342 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7941 (mt-10) REVERT: C 21 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8521 (tmt) REVERT: C 244 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: C 374 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7973 (tp-100) REVERT: C 414 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: D 41 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8371 (pp30) REVERT: D 374 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7940 (tm-30) REVERT: E 42 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7913 (t-90) REVERT: E 342 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: E 353 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8122 (ttp-110) REVERT: F 29 MET cc_start: 0.5682 (pmm) cc_final: 0.4980 (mpp) REVERT: F 211 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (tp30) REVERT: F 244 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8311 (mm-30) REVERT: F 334 GLU cc_start: 0.8529 (tp30) cc_final: 0.8243 (tp30) outliers start: 86 outliers final: 45 residues processed: 307 average time/residue: 1.5149 time to fit residues: 517.9291 Evaluate side-chains 288 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 234 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 0.7980 chunk 95 optimal weight: 0.0470 chunk 142 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN E 59 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20620 Z= 0.178 Angle : 0.638 11.192 27862 Z= 0.301 Chirality : 0.042 0.137 3177 Planarity : 0.004 0.055 3549 Dihedral : 12.136 179.658 3068 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.53 % Allowed : 23.54 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2502 helix: 1.75 (0.16), residues: 1107 sheet: -0.01 (0.26), residues: 393 loop : 0.00 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.009 0.001 PHE B 232 TYR 0.027 0.001 TYR B 332 ARG 0.013 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 245 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.5641 (tmm) cc_final: 0.3927 (mmp) REVERT: A 56 GLU cc_start: 0.8308 (tt0) cc_final: 0.8083 (pt0) REVERT: B 5 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9244 (mp0) REVERT: B 42 HIS cc_start: 0.8106 (t-90) cc_final: 0.7879 (t-90) REVERT: B 244 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 334 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 342 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8027 (mt-10) REVERT: C 21 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8496 (tmt) REVERT: C 244 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: C 374 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7952 (tp-100) REVERT: C 414 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: D 41 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8365 (pp30) REVERT: D 374 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7907 (tm-30) REVERT: E 42 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7907 (t-90) REVERT: E 226 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: E 342 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: E 353 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8033 (ttp-110) REVERT: F 244 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8296 (mm-30) REVERT: F 334 GLU cc_start: 0.8503 (tp30) cc_final: 0.8232 (tp30) outliers start: 76 outliers final: 43 residues processed: 303 average time/residue: 1.5081 time to fit residues: 507.8218 Evaluate side-chains 290 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 234 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20620 Z= 0.232 Angle : 0.660 12.200 27862 Z= 0.313 Chirality : 0.043 0.146 3177 Planarity : 0.004 0.057 3549 Dihedral : 12.141 179.969 3066 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.30 % Allowed : 23.86 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.17), residues: 2502 helix: 1.72 (0.16), residues: 1107 sheet: -0.13 (0.27), residues: 387 loop : 0.00 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 381 HIS 0.004 0.001 HIS A 239 PHE 0.014 0.001 PHE A 62 TYR 0.024 0.001 TYR B 332 ARG 0.014 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 239 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.5627 (tmm) cc_final: 0.3977 (mmp) REVERT: B 5 GLU cc_start: 0.9455 (OUTLIER) cc_final: 0.9249 (mp0) REVERT: B 42 HIS cc_start: 0.8117 (t-90) cc_final: 0.7860 (t-90) REVERT: B 244 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8089 (mm-30) REVERT: C 21 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8495 (tmt) REVERT: C 244 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: C 374 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7990 (tp-100) REVERT: C 414 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: D 41 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8357 (pp30) REVERT: D 374 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7896 (tm-30) REVERT: E 20 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8388 (p0) REVERT: E 42 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7945 (t-90) REVERT: E 226 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: E 342 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: E 353 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8080 (ttp-110) REVERT: F 244 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8284 (mm-30) REVERT: F 334 GLU cc_start: 0.8509 (tp30) cc_final: 0.8266 (tp30) outliers start: 71 outliers final: 44 residues processed: 290 average time/residue: 1.5712 time to fit residues: 506.8938 Evaluate side-chains 291 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 238 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 226 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20620 Z= 0.282 Angle : 0.689 12.527 27862 Z= 0.328 Chirality : 0.043 0.157 3177 Planarity : 0.004 0.059 3549 Dihedral : 12.197 179.671 3066 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.97 % Allowed : 24.42 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2502 helix: 1.66 (0.16), residues: 1107 sheet: -0.14 (0.27), residues: 387 loop : -0.02 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 381 HIS 0.005 0.001 HIS A 239 PHE 0.014 0.001 PHE A 62 TYR 0.025 0.002 TYR D 110 ARG 0.015 0.000 ARG F 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5004 Ramachandran restraints generated. 2502 Oldfield, 0 Emsley, 2502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 243 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.5653 (tmm) cc_final: 0.4011 (mmp) REVERT: A 129 ASN cc_start: 0.7936 (p0) cc_final: 0.7374 (t0) REVERT: B 5 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.9250 (mp0) REVERT: B 21 MET cc_start: 0.8441 (tmm) cc_final: 0.7625 (ppp) REVERT: B 244 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8076 (mm-30) REVERT: C 21 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8484 (tmt) REVERT: C 244 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: C 374 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8044 (tp-100) REVERT: C 414 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: D 41 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8361 (pp30) REVERT: D 374 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7950 (tm-30) REVERT: E 20 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8360 (p0) REVERT: E 42 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7930 (t-90) REVERT: E 226 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7906 (tt0) REVERT: E 342 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: E 353 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8202 (ttp-110) REVERT: F 244 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8271 (mm-30) REVERT: F 334 GLU cc_start: 0.8535 (tp30) cc_final: 0.8298 (tp30) outliers start: 64 outliers final: 42 residues processed: 291 average time/residue: 1.5478 time to fit residues: 500.3319 Evaluate side-chains 287 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 236 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain B residue 5 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 42 HIS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain F residue 52 ASP Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 155 GLU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 341 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 201 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 220 GLN B 241 GLN B 378 GLN E 193 GLN E 241 GLN ** E 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.071354 restraints weight = 41829.640| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.57 r_work: 0.2928 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20620 Z= 0.270 Angle : 0.696 12.932 27862 Z= 0.333 Chirality : 0.043 0.179 3177 Planarity : 0.004 0.063 3549 Dihedral : 12.198 179.732 3066 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.83 % Allowed : 24.74 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2502 helix: 1.64 (0.16), residues: 1107 sheet: -0.15 (0.26), residues: 399 loop : 0.02 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.005 0.001 HIS A 239 PHE 0.016 0.001 PHE A 62 TYR 0.024 0.001 TYR B 332 ARG 0.014 0.000 ARG C 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8800.09 seconds wall clock time: 154 minutes 20.46 seconds (9260.46 seconds total)