Starting phenix.real_space_refine on Mon Jul 6 00:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibc_35339/07_2026/8ibc_35339_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibc_35339/07_2026/8ibc_35339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibc_35339/07_2026/8ibc_35339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibc_35339/07_2026/8ibc_35339.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibc_35339/07_2026/8ibc_35339_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibc_35339/07_2026/8ibc_35339_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 8 5.49 5 S 152 5.16 5 C 20185 2.51 5 N 5337 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31431 Number of models: 1 Model: "" Number of chains: 27 Chain: "AA" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3117 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 15, 'TRANS': 383} Chain breaks: 2 Chain: "AB" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3107 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 10, 'TRANS': 403} Chain breaks: 1 Chain: "AC" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "AD" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1896 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "AE" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "AF" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "AG" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "AH" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "AI" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 347 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain breaks: 3 Chain: "AJ" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "AK" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 278 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "Aa" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3131 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "Ab" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3101 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 10, 'TRANS': 402} Chain breaks: 2 Chain: "Ac" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "Ad" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1895 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "Ae" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Chain: "Af" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "Ag" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "Ah" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "Aj" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "Ak" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "AC" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'3PE': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 55 Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "Ac" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 134 Planarities with less than four sites: {'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 55 Chain: "Ad" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Time building chain proxies: 6.72, per 1000 atoms: 0.21 Number of scatterers: 31431 At special positions: 0 Unit cell: (157.3, 144.1, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 152 16.00 P 8 15.00 O 5743 8.00 N 5337 7.00 C 20185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYSAA 338 " - pdb=" SG CYSAA 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 217 " - pdb=" SG CYSAE 236 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 222 " - pdb=" SG CYSAE 238 " distance=2.00 Simple disulfide: pdb=" SG CYSAH 51 " - pdb=" SG CYSAH 65 " distance=2.04 Simple disulfide: pdb=" SG CYSAa 338 " - pdb=" SG CYSAa 360 " distance=2.04 Simple disulfide: pdb=" SG CYSAe 222 " - pdb=" SG CYSAe 238 " distance=2.10 Simple disulfide: pdb=" SG CYSAh 35 " - pdb=" SG CYSAh 79 " distance=2.03 Simple disulfide: pdb=" SG CYSAh 51 " - pdb=" SG CYSAh 65 " distance=2.03 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7306 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 16 sheets defined 58.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'AA' and resid 78 through 82 Processing helix chain 'AA' and resid 88 through 97 Processing helix chain 'AA' and resid 107 through 116 Processing helix chain 'AA' and resid 139 through 152 removed outlier: 3.536A pdb=" N GLUAA 145 " --> pdb=" O PROAA 141 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEUAA 147 " --> pdb=" O VALAA 143 " (cutoff:3.500A) Processing helix chain 'AA' and resid 157 through 176 removed outlier: 3.715A pdb=" N ASPAA 176 " --> pdb=" O METAA 172 " (cutoff:3.500A) Processing helix chain 'AA' and resid 178 through 187 Processing helix chain 'AA' and resid 204 through 210 Processing helix chain 'AA' and resid 212 through 224 Processing helix chain 'AA' and resid 225 through 227 No H-bonds generated for 'chain 'AA' and resid 225 through 227' Processing helix chain 'AA' and resid 238 through 249 Processing helix chain 'AA' and resid 300 through 312 Processing helix chain 'AA' and resid 361 through 363 No H-bonds generated for 'chain 'AA' and resid 361 through 363' Processing helix chain 'AA' and resid 364 through 382 Processing helix chain 'AA' and resid 384 through 398 Processing helix chain 'AA' and resid 405 through 419 Processing helix chain 'AA' and resid 425 through 435 Processing helix chain 'AA' and resid 437 through 449 Processing helix chain 'AA' and resid 467 through 475 Processing helix chain 'AB' and resid 68 through 72 removed outlier: 3.545A pdb=" N GLUAB 72 " --> pdb=" O SERAB 69 " (cutoff:3.500A) Processing helix chain 'AB' and resid 78 through 86 Processing helix chain 'AB' and resid 95 through 106 removed outlier: 3.663A pdb=" N VALAB 106 " --> pdb=" O GLYAB 102 " (cutoff:3.500A) Processing helix chain 'AB' and resid 129 through 143 Processing helix chain 'AB' and resid 147 through 166 removed outlier: 4.713A pdb=" N SERAB 156 " --> pdb=" O ALAAB 152 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLNAB 157 " --> pdb=" O ALAAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 168 through 182 removed outlier: 3.869A pdb=" N ARGAB 172 " --> pdb=" O ASNAB 168 " (cutoff:3.500A) Processing helix chain 'AB' and resid 201 through 213 Processing helix chain 'AB' and resid 214 through 216 No H-bonds generated for 'chain 'AB' and resid 214 through 216' Processing helix chain 'AB' and resid 226 through 237 removed outlier: 3.596A pdb=" N LEUAB 230 " --> pdb=" O SERAB 226 " (cutoff:3.500A) Processing helix chain 'AB' and resid 280 through 294 removed outlier: 3.828A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 308 through 315 Processing helix chain 'AB' and resid 346 through 363 Processing helix chain 'AB' and resid 367 through 387 Processing helix chain 'AB' and resid 388 through 404 Processing helix chain 'AB' and resid 408 through 419 Processing helix chain 'AB' and resid 420 through 434 Processing helix chain 'AC' and resid 10 through 19 removed outlier: 3.608A pdb=" N ILEAC 14 " --> pdb=" O LEUAC 10 " (cutoff:3.500A) Processing helix chain 'AC' and resid 28 through 31 Processing helix chain 'AC' and resid 32 through 53 Processing helix chain 'AC' and resid 61 through 72 Processing helix chain 'AC' and resid 75 through 104 Processing helix chain 'AC' and resid 105 through 108 removed outlier: 3.580A pdb=" N THRAC 108 " --> pdb=" O GLYAC 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 105 through 108' Processing helix chain 'AC' and resid 109 through 133 Processing helix chain 'AC' and resid 136 through 152 removed outlier: 3.507A pdb=" N LEUAC 150 " --> pdb=" O ILEAC 146 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SERAC 151 " --> pdb=" O THRAC 147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALAAC 152 " --> pdb=" O ASNAC 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 156 through 166 Processing helix chain 'AC' and resid 171 through 202 removed outlier: 3.553A pdb=" N ARGAC 177 " --> pdb=" O ALAAC 173 " (cutoff:3.500A) Proline residue: AC 186 - end of helix Processing helix chain 'AC' and resid 212 through 215 removed outlier: 4.576A pdb=" N ALAAC 215 " --> pdb=" O ASNAC 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 212 through 215' Processing helix chain 'AC' and resid 224 through 244 removed outlier: 3.500A pdb=" N ASPAC 228 " --> pdb=" O TYRAC 224 " (cutoff:3.500A) Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 284 removed outlier: 4.375A pdb=" N PHEAC 276 " --> pdb=" O TRPAC 272 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALAAC 277 " --> pdb=" O TYRAC 273 " (cutoff:3.500A) Processing helix chain 'AC' and resid 286 through 304 removed outlier: 3.505A pdb=" N ILEAC 298 " --> pdb=" O LEUAC 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAC 301 " --> pdb=" O SERAC 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 305 through 308 removed outlier: 3.963A pdb=" N HISAC 308 " --> pdb=" O PROAC 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 305 through 308' Processing helix chain 'AC' and resid 318 through 341 removed outlier: 3.760A pdb=" N GLYAC 340 " --> pdb=" O THRAC 336 " (cutoff:3.500A) Processing helix chain 'AC' and resid 346 through 364 Processing helix chain 'AC' and resid 364 through 377 Processing helix chain 'AD' and resid 106 through 120 Processing helix chain 'AD' and resid 131 through 136 removed outlier: 3.879A pdb=" N LEUAD 135 " --> pdb=" O ALAAD 131 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VALAD 136 " --> pdb=" O TYRAD 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 131 through 136' Processing helix chain 'AD' and resid 141 through 150 Processing helix chain 'AD' and resid 181 through 189 Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 207 through 216 removed outlier: 3.509A pdb=" N VALAD 211 " --> pdb=" O GLYAD 207 " (cutoff:3.500A) Processing helix chain 'AD' and resid 237 through 241 removed outlier: 4.099A pdb=" N ALAAD 241 " --> pdb=" O PROAD 238 " (cutoff:3.500A) Processing helix chain 'AD' and resid 262 through 279 Processing helix chain 'AD' and resid 281 through 317 Proline residue: AD 301 - end of helix removed outlier: 3.864A pdb=" N VALAD 313 " --> pdb=" O HISAD 309 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEUAD 314 " --> pdb=" O LYSAD 310 " (cutoff:3.500A) Processing helix chain 'AE' and resid 107 through 141 Processing helix chain 'AE' and resid 143 through 148 Processing helix chain 'AE' and resid 155 through 159 Processing helix chain 'AE' and resid 180 through 187 Processing helix chain 'AE' and resid 188 through 191 Processing helix chain 'AE' and resid 201 through 205 Processing helix chain 'AF' and resid 15 through 26 removed outlier: 3.720A pdb=" N GLYAF 26 " --> pdb=" O TYRAF 22 " (cutoff:3.500A) Processing helix chain 'AF' and resid 34 through 38 removed outlier: 3.684A pdb=" N LEUAF 38 " --> pdb=" O ASPAF 35 " (cutoff:3.500A) Processing helix chain 'AF' and resid 41 through 50 Processing helix chain 'AF' and resid 52 through 72 Processing helix chain 'AF' and resid 77 through 81 Processing helix chain 'AF' and resid 90 through 111 removed outlier: 4.176A pdb=" N TYRAF 94 " --> pdb=" O TYRAF 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUAF 97 " --> pdb=" O PROAF 93 " (cutoff:3.500A) Processing helix chain 'AG' and resid 21 through 24 Processing helix chain 'AG' and resid 29 through 72 removed outlier: 3.850A pdb=" N ILEAG 35 " --> pdb=" O PHEAG 31 " (cutoff:3.500A) Proline residue: AG 36 - end of helix removed outlier: 5.323A pdb=" N LEUAG 47 " --> pdb=" O ARGAG 43 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGAG 48 " --> pdb=" O GLUAG 44 " (cutoff:3.500A) Proline residue: AG 51 - end of helix Processing helix chain 'AH' and resid 26 through 38 Processing helix chain 'AH' and resid 38 through 58 Processing helix chain 'AH' and resid 65 through 88 removed outlier: 4.475A pdb=" N ASPAH 71 " --> pdb=" O GLUAH 67 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHEAH 85 " --> pdb=" O ALAAH 81 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYSAH 86 " --> pdb=" O HISAH 82 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASNAH 87 " --> pdb=" O LYSAH 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUAH 88 " --> pdb=" O LEUAH 84 " (cutoff:3.500A) Processing helix chain 'AI' and resid 11 through 16 Processing helix chain 'AJ' and resid 17 through 48 removed outlier: 4.351A pdb=" N ARGAJ 34 " --> pdb=" O LEUAJ 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 10 through 37 Proline residue: AK 19 - end of helix Processing helix chain 'Aa' and resid 78 through 82 Processing helix chain 'Aa' and resid 88 through 97 Processing helix chain 'Aa' and resid 106 through 116 removed outlier: 4.177A pdb=" N GLUAa 110 " --> pdb=" O GLYAa 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAa 116 " --> pdb=" O GLUAa 112 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 139 through 152 Processing helix chain 'Aa' and resid 157 through 176 Processing helix chain 'Aa' and resid 178 through 192 Processing helix chain 'Aa' and resid 204 through 210 Processing helix chain 'Aa' and resid 212 through 224 Processing helix chain 'Aa' and resid 225 through 227 No H-bonds generated for 'chain 'Aa' and resid 225 through 227' Processing helix chain 'Aa' and resid 238 through 249 Processing helix chain 'Aa' and resid 299 through 312 removed outlier: 4.195A pdb=" N THRAa 303 " --> pdb=" O PROAa 299 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 361 through 363 No H-bonds generated for 'chain 'Aa' and resid 361 through 363' Processing helix chain 'Aa' and resid 364 through 382 Processing helix chain 'Aa' and resid 384 through 400 removed outlier: 3.903A pdb=" N VALAa 388 " --> pdb=" O THRAa 384 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 405 through 419 Processing helix chain 'Aa' and resid 425 through 435 Processing helix chain 'Aa' and resid 437 through 449 Processing helix chain 'Aa' and resid 467 through 475 Processing helix chain 'Ab' and resid 68 through 72 removed outlier: 3.543A pdb=" N GLUAb 72 " --> pdb=" O SERAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 78 through 86 Processing helix chain 'Ab' and resid 95 through 106 removed outlier: 4.348A pdb=" N ILEAb 103 " --> pdb=" O ILEAb 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALAb 106 " --> pdb=" O GLYAb 102 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 129 through 143 Processing helix chain 'Ab' and resid 147 through 166 removed outlier: 4.714A pdb=" N SERAb 156 " --> pdb=" O ALAAb 152 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLNAb 157 " --> pdb=" O ALAAb 153 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 168 through 182 removed outlier: 3.870A pdb=" N ARGAb 172 " --> pdb=" O ASNAb 168 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 201 through 213 Processing helix chain 'Ab' and resid 214 through 216 No H-bonds generated for 'chain 'Ab' and resid 214 through 216' Processing helix chain 'Ab' and resid 226 through 237 removed outlier: 3.593A pdb=" N LEUAb 230 " --> pdb=" O SERAb 226 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLUAb 235 " --> pdb=" O LYSAb 231 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLNAb 236 " --> pdb=" O GLNAb 232 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHEAb 237 " --> pdb=" O VALAb 233 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 280 through 294 removed outlier: 4.196A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALAAb 285 " --> pdb=" O ALAAb 281 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 307 through 312 Processing helix chain 'Ab' and resid 346 through 363 Processing helix chain 'Ab' and resid 367 through 387 Processing helix chain 'Ab' and resid 388 through 404 Processing helix chain 'Ab' and resid 408 through 419 Processing helix chain 'Ab' and resid 420 through 434 Processing helix chain 'Ac' and resid 9 through 19 Processing helix chain 'Ac' and resid 28 through 31 Processing helix chain 'Ac' and resid 32 through 53 Processing helix chain 'Ac' and resid 61 through 72 Processing helix chain 'Ac' and resid 75 through 104 Processing helix chain 'Ac' and resid 105 through 108 removed outlier: 3.580A pdb=" N THRAc 108 " --> pdb=" O GLYAc 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 105 through 108' Processing helix chain 'Ac' and resid 109 through 133 Processing helix chain 'Ac' and resid 136 through 151 removed outlier: 3.525A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 166 Processing helix chain 'Ac' and resid 171 through 202 removed outlier: 3.553A pdb=" N ARGAc 177 " --> pdb=" O ALAAc 173 " (cutoff:3.500A) Proline residue: Ac 186 - end of helix Processing helix chain 'Ac' and resid 212 through 215 removed outlier: 4.576A pdb=" N ALAAc 215 " --> pdb=" O ASNAc 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 212 through 215' Processing helix chain 'Ac' and resid 224 through 241 Processing helix chain 'Ac' and resid 252 through 257 Processing helix chain 'Ac' and resid 271 through 273 No H-bonds generated for 'chain 'Ac' and resid 271 through 273' Processing helix chain 'Ac' and resid 274 through 284 Processing helix chain 'Ac' and resid 286 through 304 removed outlier: 3.505A pdb=" N ILEAc 298 " --> pdb=" O LEUAc 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 308 removed outlier: 3.962A pdb=" N HISAc 308 " --> pdb=" O PROAc 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 305 through 308' Processing helix chain 'Ac' and resid 318 through 341 removed outlier: 3.759A pdb=" N GLYAc 340 " --> pdb=" O THRAc 336 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 346 through 364 Processing helix chain 'Ac' and resid 364 through 377 Processing helix chain 'Ad' and resid 96 through 100 Processing helix chain 'Ad' and resid 108 through 120 removed outlier: 3.541A pdb=" N ARGAd 112 " --> pdb=" O THRAd 108 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 121 through 124 removed outlier: 3.510A pdb=" N CYSAd 124 " --> pdb=" O CYSAd 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 121 through 124' Processing helix chain 'Ad' and resid 131 through 136 removed outlier: 3.866A pdb=" N LEUAd 135 " --> pdb=" O ALAAd 131 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALAd 136 " --> pdb=" O TYRAd 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 131 through 136' Processing helix chain 'Ad' and resid 141 through 152 removed outlier: 3.757A pdb=" N VALAd 152 " --> pdb=" O LEUAd 148 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 181 through 189 Processing helix chain 'Ad' and resid 199 through 204 Processing helix chain 'Ad' and resid 206 through 216 Processing helix chain 'Ad' and resid 237 through 241 removed outlier: 4.099A pdb=" N ALAAd 241 " --> pdb=" O PROAd 238 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 262 through 279 Processing helix chain 'Ad' and resid 281 through 317 Proline residue: Ad 301 - end of helix removed outlier: 3.864A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEUAd 314 " --> pdb=" O LYSAd 310 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 79 through 83 removed outlier: 3.744A pdb=" N VALAe 83 " --> pdb=" O HISAe 80 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 104 through 141 removed outlier: 3.693A pdb=" N GLUAe 108 " --> pdb=" O LYSAe 104 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALAAe 109 " --> pdb=" O GLUAe 105 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 143 through 148 Processing helix chain 'Ae' and resid 168 through 172 Processing helix chain 'Ae' and resid 180 through 190 Processing helix chain 'Ae' and resid 200 through 205 Processing helix chain 'Af' and resid 15 through 26 Processing helix chain 'Af' and resid 33 through 38 Processing helix chain 'Af' and resid 41 through 51 Processing helix chain 'Af' and resid 52 through 72 Processing helix chain 'Af' and resid 77 through 81 Processing helix chain 'Af' and resid 91 through 111 removed outlier: 3.859A pdb=" N GLUAf 97 " --> pdb=" O PROAf 93 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 21 through 24 Processing helix chain 'Ag' and resid 29 through 72 removed outlier: 3.850A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 4.580A pdb=" N LEUAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGAg 48 " --> pdb=" O GLUAg 44 " (cutoff:3.500A) Proline residue: Ag 51 - end of helix Processing helix chain 'Ah' and resid 26 through 38 Processing helix chain 'Ah' and resid 38 through 58 Processing helix chain 'Ah' and resid 65 through 88 removed outlier: 4.533A pdb=" N PHEAh 85 " --> pdb=" O ALAAh 81 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYSAh 86 " --> pdb=" O HISAh 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASNAh 87 " --> pdb=" O LYSAh 83 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 8 through 14 Processing helix chain 'Aj' and resid 17 through 48 removed outlier: 3.530A pdb=" N GLUAj 33 " --> pdb=" O ALAAj 29 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARGAj 34 " --> pdb=" O LEUAj 30 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 8 through 37 Proline residue: Ak 19 - end of helix Processing helix chain 'Ak' and resid 40 through 45 removed outlier: 3.789A pdb=" N TRPAk 44 " --> pdb=" O LEUAk 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VALAk 45 " --> pdb=" O ILEAk 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 40 through 45' Processing sheet with id=AA1, first strand: chain 'AA' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'AA' and resid 342 through 348 Processing sheet with id=AA3, first strand: chain 'AB' and resid 41 through 42 removed outlier: 6.157A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEUAB 110 " --> pdb=" O GLYAI 21 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLYAI 21 " --> pdb=" O LEUAB 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.670A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLYAB 442 " --> pdb=" O ILEAB 258 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLUAB 260 " --> pdb=" O GLYAB 442 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLYAB 334 " --> pdb=" O SERAB 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AC' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'AD' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'AE' and resid 164 through 166 Processing sheet with id=AA8, first strand: chain 'AE' and resid 234 through 235 removed outlier: 6.660A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AI' and resid 66 through 69 removed outlier: 6.530A pdb=" N VALAb 48 " --> pdb=" O LEUAb 220 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLYAb 222 " --> pdb=" O VALAb 48 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALAAb 50 " --> pdb=" O GLYAb 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Aa' and resid 49 through 52 Processing sheet with id=AB2, first strand: chain 'Aa' and resid 340 through 348 removed outlier: 3.855A pdb=" N SERAa 340 " --> pdb=" O VALAa 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ab' and resid 256 through 260 removed outlier: 3.538A pdb=" N GLYAb 256 " --> pdb=" O LYSAb 436 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ac' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'Ad' and resid 153 through 156 Processing sheet with id=AB6, first strand: chain 'Ae' and resid 174 through 178 removed outlier: 3.834A pdb=" N VALAe 211 " --> pdb=" O ARGAe 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ae' and resid 225 through 226 1796 hydrogen bonds defined for protein. 5166 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: 6.12 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 10125 1.35 - 1.54: 21430 1.54 - 1.73: 370 1.73 - 1.92: 258 1.92 - 2.11: 20 Bond restraints: 32203 Sorted by residual: bond pdb=" N PROAI 63 " pdb=" CD PROAI 63 " ideal model delta sigma weight residual 1.473 1.284 0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" N PROAd 182 " pdb=" CD PROAd 182 " ideal model delta sigma weight residual 1.473 1.310 0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" C METAB 240 " pdb=" N ARGAB 241 " ideal model delta sigma weight residual 1.331 1.448 -0.117 1.37e-02 5.33e+03 7.35e+01 bond pdb=" C3 U10AC 404 " pdb=" C4 U10AC 404 " ideal model delta sigma weight residual 1.341 1.487 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C1 U10AC 404 " pdb=" C6 U10AC 404 " ideal model delta sigma weight residual 1.345 1.482 -0.137 2.00e-02 2.50e+03 4.68e+01 ... (remaining 32198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 42411 3.25 - 6.50: 1083 6.50 - 9.75: 194 9.75 - 13.00: 24 13.00 - 16.25: 5 Bond angle restraints: 43717 Sorted by residual: angle pdb=" N HISAe 242 " pdb=" CA HISAe 242 " pdb=" C HISAe 242 " ideal model delta sigma weight residual 109.11 125.36 -16.25 1.42e+00 4.96e-01 1.31e+02 angle pdb=" N PROAI 63 " pdb=" CA PROAI 63 " pdb=" CB PROAI 63 " ideal model delta sigma weight residual 103.25 93.84 9.41 8.80e-01 1.29e+00 1.14e+02 angle pdb=" N LEUAA 187 " pdb=" CA LEUAA 187 " pdb=" C LEUAA 187 " ideal model delta sigma weight residual 112.38 100.39 11.99 1.22e+00 6.72e-01 9.66e+01 angle pdb=" N GLUAa 385 " pdb=" CA GLUAa 385 " pdb=" C GLUAa 385 " ideal model delta sigma weight residual 111.36 121.95 -10.59 1.09e+00 8.42e-01 9.44e+01 angle pdb=" CA PROAI 63 " pdb=" N PROAI 63 " pdb=" CD PROAI 63 " ideal model delta sigma weight residual 112.00 124.81 -12.81 1.40e+00 5.10e-01 8.37e+01 ... (remaining 43712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 17777 17.90 - 35.79: 1114 35.79 - 53.69: 175 53.69 - 71.58: 62 71.58 - 89.48: 26 Dihedral angle restraints: 19154 sinusoidal: 7807 harmonic: 11347 Sorted by residual: dihedral pdb=" C2B HEMAC 402 " pdb=" C3B HEMAC 402 " pdb=" CAB HEMAC 402 " pdb=" CBB HEMAC 402 " ideal model delta sinusoidal sigma weight residual -0.00 -78.32 78.32 2 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" C2C HEMAC 401 " pdb=" C3C HEMAC 401 " pdb=" CAC HEMAC 401 " pdb=" CBC HEMAC 401 " ideal model delta sinusoidal sigma weight residual 0.00 70.22 -70.22 2 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" C2C HEMAC 402 " pdb=" C3C HEMAC 402 " pdb=" CAC HEMAC 402 " pdb=" CBC HEMAC 402 " ideal model delta sinusoidal sigma weight residual 0.00 66.70 -66.70 2 1.00e+01 1.00e-02 4.05e+01 ... (remaining 19151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4135 0.079 - 0.159: 545 0.159 - 0.238: 53 0.238 - 0.318: 10 0.318 - 0.397: 3 Chirality restraints: 4746 Sorted by residual: chirality pdb=" CA SERAe 241 " pdb=" N SERAe 241 " pdb=" C SERAe 241 " pdb=" CB SERAe 241 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYRAe 243 " pdb=" N TYRAe 243 " pdb=" C TYRAe 243 " pdb=" CB TYRAe 243 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA ILEAA 471 " pdb=" N ILEAA 471 " pdb=" C ILEAA 471 " pdb=" CB ILEAA 471 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4743 not shown) Planarity restraints: 5552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10Ac 404 " -0.018 2.00e-02 2.50e+03 2.42e-01 1.75e+03 pdb=" C1M U10Ac 404 " 0.236 2.00e-02 2.50e+03 pdb=" C2 U10Ac 404 " -0.048 2.00e-02 2.50e+03 pdb=" C3 U10Ac 404 " 0.050 2.00e-02 2.50e+03 pdb=" C4 U10Ac 404 " 0.062 2.00e-02 2.50e+03 pdb=" C5 U10Ac 404 " -0.088 2.00e-02 2.50e+03 pdb=" C6 U10Ac 404 " 0.087 2.00e-02 2.50e+03 pdb=" C7 U10Ac 404 " 0.216 2.00e-02 2.50e+03 pdb=" O2 U10Ac 404 " -0.429 2.00e-02 2.50e+03 pdb=" O3 U10Ac 404 " 0.164 2.00e-02 2.50e+03 pdb=" O4 U10Ac 404 " 0.294 2.00e-02 2.50e+03 pdb=" O5 U10Ac 404 " -0.527 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 U10Ac 404 " -0.320 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C13 U10Ac 404 " 0.472 2.00e-02 2.50e+03 pdb=" C14 U10Ac 404 " 0.098 2.00e-02 2.50e+03 pdb=" C15 U10Ac 404 " -0.073 2.00e-02 2.50e+03 pdb=" C16 U10Ac 404 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ6Ac 405 " -0.315 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C13 UQ6Ac 405 " 0.459 2.00e-02 2.50e+03 pdb=" C14 UQ6Ac 405 " 0.098 2.00e-02 2.50e+03 pdb=" C15 UQ6Ac 405 " -0.186 2.00e-02 2.50e+03 pdb=" C16 UQ6Ac 405 " -0.056 2.00e-02 2.50e+03 ... (remaining 5549 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 694 2.63 - 3.20: 32327 3.20 - 3.77: 53992 3.77 - 4.33: 75541 4.33 - 4.90: 116667 Nonbonded interactions: 279221 Sorted by model distance: nonbonded pdb=" O TYRAC 223 " pdb=" NE1 TRPAD 311 " model vdw 2.063 3.120 nonbonded pdb=" NE2 HISAC 83 " pdb="FE HEMAC 401 " model vdw 2.076 3.080 nonbonded pdb=" NE2 HISAc 83 " pdb="FE HEMAc 401 " model vdw 2.096 3.080 nonbonded pdb=" NH2 ARGAa 58 " pdb=" O LEUAa 417 " model vdw 2.102 3.120 nonbonded pdb=" O GLYAD 100 " pdb=" NZ LYSAD 286 " model vdw 2.125 3.120 ... (remaining 279216 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 'AA' and resid 44 through 477) selection = (chain 'Aa' and (resid 44 through 255 or resid 267 through 312 or resid 338 thro \ ugh 477)) } ncs_group { reference = (chain 'AB' and (resid 36 through 300 or resid 307 through 312 or resid 316 thro \ ugh 453)) selection = (chain 'Ab' and (resid 36 through 300 or resid 307 through 453)) } ncs_group { reference = chain 'AC' selection = (chain 'Ac' and (resid 8 through 402 or (resid 403 and (name N or name C1 or nam \ e C11 or name C12 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or resid 404 through 405)) } ncs_group { reference = (chain 'AD' and (resid 88 through 324 or resid 401)) selection = (chain 'Ad' and resid 88 through 401) } ncs_group { reference = chain 'AE' selection = (chain 'Ae' and (resid 79 through 103 or resid 107 through 274)) } ncs_group { reference = chain 'AF' selection = chain 'Af' } ncs_group { reference = chain 'AG' selection = (chain 'Ag' and resid 4 through 79) } ncs_group { reference = chain 'AH' selection = (chain 'Ah' and resid 25 through 88) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.470 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 : 0.010 0.341 32218 Z= 0.579 Angle : 1.257 29.332 43733 Z= 0.796 Chirality : 0.055 0.397 4746 Planarity : 0.010 0.273 5552 Dihedral : 12.652 89.478 11824 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 32.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 3849 helix: -0.76 (0.10), residues: 2032 sheet: -0.50 (0.27), residues: 389 loop : -1.59 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAE 250 TYR 0.031 0.002 TYRAF 56 PHE 0.049 0.002 PHEAc 183 TRP 0.025 0.002 TRPAc 141 HIS 0.009 0.001 HISAE 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00934 / 0.58 (32203) covalent geometry : angle 1.24637 / 0.79 (43717) SS BOND : bond 0.02954 / 1.12 ( 8) SS BOND : angle 8.79038 / 5.80 ( 16) hydrogen bonds : bond 0.18840 / 12.45 ( 1796) hydrogen bonds : angle 7.50291 / 5.26 ( 5166) Misc. bond : bond 0.17404 / 7.21 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1523 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 444 ILE cc_start: 0.7871 (mt) cc_final: 0.7583 (mt) REVERT: AB 166 PHE cc_start: 0.7600 (m-10) cc_final: 0.7218 (m-10) REVERT: AB 390 GLU cc_start: 0.8207 (pp20) cc_final: 0.7960 (pm20) REVERT: AC 25 SER cc_start: 0.6790 (p) cc_final: 0.5555 (p) REVERT: AC 53 MET cc_start: 0.7488 (mtt) cc_final: 0.6744 (mtm) REVERT: AC 113 TRP cc_start: 0.7773 (t-100) cc_final: 0.7457 (t-100) REVERT: AC 118 LEU cc_start: 0.8603 (tp) cc_final: 0.8284 (tp) REVERT: AC 309 THR cc_start: 0.6967 (p) cc_final: 0.6639 (t) REVERT: AC 343 VAL cc_start: 0.8695 (t) cc_final: 0.8430 (p) REVERT: AE 91 TYR cc_start: 0.6382 (m-80) cc_final: 0.6060 (m-80) REVERT: AE 135 GLN cc_start: 0.7319 (mt0) cc_final: 0.6989 (mt0) REVERT: AE 167 PHE cc_start: 0.7986 (m-80) cc_final: 0.6980 (m-10) REVERT: AF 57 ASN cc_start: 0.7370 (m-40) cc_final: 0.7050 (m-40) REVERT: AG 17 TYR cc_start: 0.7526 (m-80) cc_final: 0.7205 (m-80) REVERT: AG 54 VAL cc_start: 0.8643 (t) cc_final: 0.8440 (t) REVERT: AI 20 ARG cc_start: 0.6800 (mtm180) cc_final: 0.6393 (mpt180) REVERT: AI 73 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8260 (Cg_endo) REVERT: Aa 149 ASP cc_start: 0.8281 (m-30) cc_final: 0.8009 (m-30) REVERT: Aa 440 MET cc_start: 0.7607 (ptp) cc_final: 0.7396 (ptm) REVERT: Ab 292 LEU cc_start: 0.8259 (tp) cc_final: 0.8034 (tp) REVERT: Ab 382 TYR cc_start: 0.8530 (t80) cc_final: 0.8165 (t80) REVERT: Ac 89 MET cc_start: 0.8377 (tpp) cc_final: 0.7840 (tmm) REVERT: Ac 118 LEU cc_start: 0.8384 (tp) cc_final: 0.8032 (tp) REVERT: Ac 230 LEU cc_start: 0.8792 (tp) cc_final: 0.8386 (tt) REVERT: Ac 343 VAL cc_start: 0.8874 (t) cc_final: 0.8570 (p) REVERT: Ad 104 SER cc_start: 0.8938 (p) cc_final: 0.8686 (t) REVERT: Ad 128 ASP cc_start: 0.8254 (m-30) cc_final: 0.8022 (m-30) REVERT: Ad 154 VAL cc_start: 0.7892 (t) cc_final: 0.7651 (t) REVERT: Ae 243 TYR cc_start: 0.5258 (p90) cc_final: 0.5043 (p90) REVERT: Ae 249 ILE cc_start: 0.7322 (tp) cc_final: 0.6943 (tp) REVERT: Af 68 ASP cc_start: 0.8273 (t70) cc_final: 0.7967 (t0) REVERT: Ag 57 TYR cc_start: 0.8423 (t80) cc_final: 0.7908 (t80) REVERT: Ah 43 LYS cc_start: 0.8363 (mttm) cc_final: 0.8162 (pttm) REVERT: Aj 23 LEU cc_start: 0.8905 (tp) cc_final: 0.8276 (tp) REVERT: Ak 23 MET cc_start: 0.7382 (mmt) cc_final: 0.7132 (tpp) REVERT: Ak 42 LEU cc_start: 0.8215 (mt) cc_final: 0.7947 (mp) outliers start: 6 outliers final: 2 residues processed: 1527 average time/residue: 0.2168 time to fit residues: 517.6351 Evaluate side-chains 879 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 877 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 223 VAL Chi-restraints excluded: chain Aa residue 249 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 43 GLN AA 103 ASN AA 173 GLN ** AA 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AB 139 ASN AB 167 GLN AC 312 GLN AC 345 HIS AD 115 GLN AD 189 ASN AD 190 ASN ** AE 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 74 GLN AH 37 GLN AH 78 HIS AH 82 HIS ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 119 HIS Aa 181 ASN Aa 207 ASN Aa 434 GLN Ab 118 ASN ** Ab 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 284 ASN Ab 298 HIS ** Ac 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 148 ASN Ac 331 ASN Ac 341 GLN Ad 90 HIS ** Ad 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 155 GLN Ad 190 ASN ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Ah 82 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.126440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097907 restraints weight = 75105.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101216 restraints weight = 36707.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103482 restraints weight = 23728.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.104934 restraints weight = 17899.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105773 restraints weight = 14923.487| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.481 32218 Z= 0.185 Angle : 0.804 16.839 43733 Z= 0.393 Chirality : 0.047 0.441 4746 Planarity : 0.006 0.085 5552 Dihedral : 9.707 89.917 4584 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.09 % Allowed : 15.25 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 3849 helix: 0.79 (0.11), residues: 2033 sheet: 0.02 (0.27), residues: 355 loop : -0.65 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAA 278 TYR 0.026 0.002 TYRAc 75 PHE 0.030 0.002 PHEAc 276 TRP 0.029 0.002 TRPAC 77 HIS 0.010 0.002 HISAc 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (32203) covalent geometry : angle 0.80304 / 0.39 (43717) SS BOND : bond 0.00446 / 0.16 ( 8) SS BOND : angle 2.20217 / 1.55 ( 16) hydrogen bonds : bond 0.05319 / 3.61 ( 1796) hydrogen bonds : angle 5.34019 / 3.74 ( 5166) Misc. bond : bond 0.33306 / 15.26 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 956 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 104 ARG cc_start: 0.8278 (mpt90) cc_final: 0.8070 (mpt90) REVERT: AA 114 GLU cc_start: 0.8425 (tp30) cc_final: 0.7935 (mt-10) REVERT: AA 240 GLN cc_start: 0.8611 (tp-100) cc_final: 0.8369 (tp-100) REVERT: AA 444 ILE cc_start: 0.8897 (mt) cc_final: 0.8636 (mm) REVERT: AB 197 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7115 (mtp) REVERT: AB 235 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: AB 395 GLU cc_start: 0.8602 (tp30) cc_final: 0.8374 (tm-30) REVERT: AC 36 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7988 (tp) REVERT: AC 133 LEU cc_start: 0.8761 (mt) cc_final: 0.8559 (mt) REVERT: AC 159 THR cc_start: 0.8459 (m) cc_final: 0.8077 (p) REVERT: AC 189 ILE cc_start: 0.8438 (mt) cc_final: 0.8230 (tt) REVERT: AC 216 ASP cc_start: 0.8460 (t0) cc_final: 0.8030 (t70) REVERT: AC 232 ILE cc_start: 0.9118 (mm) cc_final: 0.8840 (mt) REVERT: AC 242 LEU cc_start: 0.8991 (tp) cc_final: 0.8701 (tp) REVERT: AC 244 LEU cc_start: 0.8920 (mt) cc_final: 0.8581 (mt) REVERT: AD 96 TRP cc_start: 0.7405 (m100) cc_final: 0.6880 (m100) REVERT: AD 155 GLN cc_start: 0.8798 (pt0) cc_final: 0.8426 (pm20) REVERT: AD 164 MET cc_start: 0.6712 (tmm) cc_final: 0.6349 (tmm) REVERT: AD 190 ASN cc_start: 0.8562 (m-40) cc_final: 0.8116 (p0) REVERT: AE 165 MET cc_start: 0.4672 (tpp) cc_final: 0.4401 (tpp) REVERT: AE 167 PHE cc_start: 0.8002 (m-80) cc_final: 0.7146 (m-10) REVERT: AE 231 PHE cc_start: 0.7060 (t80) cc_final: 0.6075 (t80) REVERT: AF 33 MET cc_start: 0.7153 (mmt) cc_final: 0.6461 (mmt) REVERT: AF 48 ILE cc_start: 0.8766 (pt) cc_final: 0.8549 (pt) REVERT: AF 53 GLU cc_start: 0.7678 (tp30) cc_final: 0.7163 (tp30) REVERT: AF 57 ASN cc_start: 0.8123 (m-40) cc_final: 0.7690 (m-40) REVERT: AF 82 THR cc_start: 0.8276 (p) cc_final: 0.8014 (p) REVERT: AF 99 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8122 (pt) REVERT: AF 101 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8123 (mt-10) REVERT: AG 17 TYR cc_start: 0.7972 (m-80) cc_final: 0.7486 (m-80) REVERT: AG 24 GLN cc_start: 0.7680 (pt0) cc_final: 0.7115 (pt0) REVERT: AG 71 LYS cc_start: 0.8033 (tptp) cc_final: 0.7577 (ptmm) REVERT: AG 78 TYR cc_start: 0.7229 (m-80) cc_final: 0.6873 (m-80) REVERT: AH 87 ASN cc_start: 0.8250 (t0) cc_final: 0.8042 (t0) REVERT: AI 73 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: AK 24 TRP cc_start: 0.6346 (m100) cc_final: 0.6002 (m100) REVERT: Aa 162 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7123 (tm-30) REVERT: Aa 199 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: Aa 274 GLU cc_start: 0.8503 (pt0) cc_final: 0.7966 (pt0) REVERT: Aa 353 LEU cc_start: 0.8533 (mt) cc_final: 0.8298 (mt) REVERT: Aa 368 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8166 (tpt) REVERT: Aa 377 MET cc_start: 0.9433 (tpp) cc_final: 0.8434 (tpp) REVERT: Aa 381 THR cc_start: 0.8919 (m) cc_final: 0.8387 (p) REVERT: Aa 475 MET cc_start: 0.8210 (tpp) cc_final: 0.7883 (tpp) REVERT: Aa 477 TRP cc_start: 0.7575 (m-10) cc_final: 0.6821 (m-10) REVERT: Ab 63 LEU cc_start: 0.7385 (pt) cc_final: 0.7182 (pp) REVERT: Ab 139 ASN cc_start: 0.6899 (m-40) cc_final: 0.6688 (t0) REVERT: Ab 173 ILE cc_start: 0.8237 (tp) cc_final: 0.7855 (tp) REVERT: Ab 199 LYS cc_start: 0.8324 (tttm) cc_final: 0.8003 (tttm) REVERT: Ab 218 MET cc_start: 0.7796 (mtm) cc_final: 0.7576 (mtp) REVERT: Ab 293 LEU cc_start: 0.8703 (mt) cc_final: 0.8495 (mm) REVERT: Ab 395 GLU cc_start: 0.8382 (tp30) cc_final: 0.7688 (tp30) REVERT: Ac 15 ASN cc_start: 0.8256 (t0) cc_final: 0.7958 (t0) REVERT: Ac 100 ARG cc_start: 0.8783 (tmm-80) cc_final: 0.8487 (tmm-80) REVERT: Ac 118 LEU cc_start: 0.8432 (tp) cc_final: 0.8034 (tp) REVERT: Ac 165 TRP cc_start: 0.7119 (m-10) cc_final: 0.6641 (m-10) REVERT: Ac 216 ASP cc_start: 0.8522 (t0) cc_final: 0.8016 (t0) REVERT: Ac 257 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7379 (ptp) REVERT: Ac 271 GLU cc_start: 0.7767 (tt0) cc_final: 0.7214 (tt0) REVERT: Ac 272 TRP cc_start: 0.8331 (p-90) cc_final: 0.8091 (p-90) REVERT: Ac 292 LEU cc_start: 0.8735 (mm) cc_final: 0.8414 (mm) REVERT: Ac 352 GLN cc_start: 0.8497 (mt0) cc_final: 0.8285 (mt0) REVERT: Ad 119 GLN cc_start: 0.8824 (mt0) cc_final: 0.8527 (tm-30) REVERT: Ad 134 HIS cc_start: 0.8042 (m90) cc_final: 0.7534 (m90) REVERT: Ad 208 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: Ae 108 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8075 (mp0) REVERT: Ae 165 MET cc_start: 0.6977 (tpp) cc_final: 0.6711 (mpp) REVERT: Ae 187 GLU cc_start: 0.7790 (mm-30) cc_final: 0.6874 (mm-30) REVERT: Af 33 MET cc_start: 0.8528 (mtm) cc_final: 0.8180 (mtm) REVERT: Af 97 GLU cc_start: 0.8173 (tp30) cc_final: 0.7730 (tp30) REVERT: Af 101 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8350 (mt-10) REVERT: Af 106 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8173 (mt-10) REVERT: Ag 11 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8523 (mt) REVERT: Ag 29 SER cc_start: 0.8720 (m) cc_final: 0.8095 (t) REVERT: Ag 33 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8386 (mtmt) REVERT: Ag 39 LEU cc_start: 0.8942 (mt) cc_final: 0.8606 (mt) REVERT: Ag 47 LEU cc_start: 0.9013 (mt) cc_final: 0.8570 (tp) REVERT: Ag 57 TYR cc_start: 0.8790 (t80) cc_final: 0.8478 (t80) REVERT: Ag 66 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8118 (tm-30) REVERT: Ag 70 SER cc_start: 0.9319 (t) cc_final: 0.8986 (p) REVERT: Ah 50 LEU cc_start: 0.9251 (mt) cc_final: 0.8897 (mt) REVERT: Aj 23 LEU cc_start: 0.9213 (tp) cc_final: 0.8566 (tp) REVERT: Aj 32 PHE cc_start: 0.9089 (t80) cc_final: 0.8855 (t80) REVERT: Aj 43 ILE cc_start: 0.8926 (mm) cc_final: 0.8691 (tt) REVERT: Ak 18 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8535 (tt) REVERT: Ak 23 MET cc_start: 0.7080 (mmt) cc_final: 0.6577 (tpp) REVERT: Ak 39 ARG cc_start: 0.7269 (tmt-80) cc_final: 0.6622 (ptt-90) outliers start: 135 outliers final: 74 residues processed: 1027 average time/residue: 0.1894 time to fit residues: 316.2308 Evaluate side-chains 875 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 791 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 183 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 220 LEU Chi-restraints excluded: chain AA residue 252 SER Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 388 VAL Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 79 THR Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 197 MET Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 413 LEU Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 36 LEU Chi-restraints excluded: chain AC residue 82 MET Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 124 MET Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 236 PHE Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AE residue 176 VAL Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 73 LEU Chi-restraints excluded: chain AH residue 77 ASP Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 16 SER Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 368 MET Chi-restraints excluded: chain Aa residue 379 LEU Chi-restraints excluded: chain Aa residue 433 ILE Chi-restraints excluded: chain Ab residue 65 VAL Chi-restraints excluded: chain Ab residue 69 SER Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 177 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 451 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ad residue 208 GLU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 43 ASP Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 56 VAL Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 54 LYS Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 93 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 80 optimal weight: 0.0010 chunk 62 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 332 optimal weight: 4.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 207 ASN AA 247 GLN AA 402 HIS AB 284 ASN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 80 GLN ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 118 ASN ** Ab 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 68 HIS Ac 331 ASN ** Ad 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 37 GLN ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093758 restraints weight = 75618.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096901 restraints weight = 37205.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099014 restraints weight = 24239.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.100194 restraints weight = 18520.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101220 restraints weight = 15808.402| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.569 32218 Z= 0.186 Angle : 0.746 20.984 43733 Z= 0.362 Chirality : 0.045 0.373 4746 Planarity : 0.005 0.065 5552 Dihedral : 9.454 89.508 4583 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.64 % Allowed : 17.82 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3849 helix: 1.08 (0.11), residues: 2026 sheet: 0.26 (0.28), residues: 351 loop : -0.40 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAE 170 TYR 0.028 0.002 TYRAb 382 PHE 0.025 0.002 PHEAg 67 TRP 0.025 0.002 TRPAc 77 HIS 0.032 0.002 HISAH 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (32203) covalent geometry : angle 0.74300 / 0.36 (43717) SS BOND : bond 0.01102 / 0.58 ( 8) SS BOND : angle 3.55146 / 2.19 ( 16) hydrogen bonds : bond 0.04705 / 3.19 ( 1796) hydrogen bonds : angle 5.09776 / 3.57 ( 5166) Misc. bond : bond 0.33997 / 14.95 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 822 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 104 ARG cc_start: 0.8039 (mpt90) cc_final: 0.7813 (mpt90) REVERT: AA 114 GLU cc_start: 0.8404 (tp30) cc_final: 0.7846 (mm-30) REVERT: AA 240 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8378 (tp-100) REVERT: AA 255 ARG cc_start: 0.7007 (mpp-170) cc_final: 0.6668 (mpp-170) REVERT: AA 444 ILE cc_start: 0.8881 (mt) cc_final: 0.8676 (mm) REVERT: AB 48 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8620 (m) REVERT: AB 104 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8169 (tt0) REVERT: AB 147 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6932 (mtm-85) REVERT: AB 235 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: AC 26 ASN cc_start: 0.8892 (p0) cc_final: 0.8608 (p0) REVERT: AC 89 MET cc_start: 0.8981 (mmm) cc_final: 0.8755 (mmm) REVERT: AC 118 LEU cc_start: 0.9278 (tp) cc_final: 0.9023 (tp) REVERT: AC 160 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8493 (tt) REVERT: AC 163 TRP cc_start: 0.8431 (t60) cc_final: 0.7751 (t60) REVERT: AC 216 ASP cc_start: 0.8583 (t0) cc_final: 0.8249 (t0) REVERT: AC 244 LEU cc_start: 0.9008 (mt) cc_final: 0.8566 (mt) REVERT: AC 272 TRP cc_start: 0.7974 (p-90) cc_final: 0.7634 (p-90) REVERT: AC 316 MET cc_start: 0.8394 (ttm) cc_final: 0.7937 (ttm) REVERT: AC 337 TRP cc_start: 0.9061 (t60) cc_final: 0.8571 (t60) REVERT: AD 96 TRP cc_start: 0.7374 (m100) cc_final: 0.6457 (m100) REVERT: AD 155 GLN cc_start: 0.8777 (pt0) cc_final: 0.8432 (pm20) REVERT: AD 164 MET cc_start: 0.6638 (tmm) cc_final: 0.5699 (tmm) REVERT: AD 190 ASN cc_start: 0.8585 (m-40) cc_final: 0.8263 (p0) REVERT: AD 212 PHE cc_start: 0.8342 (t80) cc_final: 0.8138 (t80) REVERT: AD 244 MET cc_start: 0.8065 (ttp) cc_final: 0.7730 (ttm) REVERT: AD 268 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7815 (ttmm) REVERT: AE 165 MET cc_start: 0.5485 (tpp) cc_final: 0.5148 (tpp) REVERT: AE 167 PHE cc_start: 0.8086 (m-80) cc_final: 0.7406 (m-10) REVERT: AE 197 ASP cc_start: 0.4217 (m-30) cc_final: 0.3942 (m-30) REVERT: AF 33 MET cc_start: 0.7348 (mmt) cc_final: 0.6681 (mmt) REVERT: AF 38 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8768 (mm) REVERT: AF 57 ASN cc_start: 0.8108 (m-40) cc_final: 0.7806 (m-40) REVERT: AF 101 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8463 (mt-10) REVERT: AG 17 TYR cc_start: 0.8048 (m-80) cc_final: 0.7541 (m-80) REVERT: AG 71 LYS cc_start: 0.8106 (tptp) cc_final: 0.7708 (ptmm) REVERT: AG 78 TYR cc_start: 0.7183 (m-80) cc_final: 0.6809 (m-80) REVERT: AH 39 GLU cc_start: 0.8935 (pm20) cc_final: 0.8529 (pp20) REVERT: AH 85 PHE cc_start: 0.7593 (m-10) cc_final: 0.6331 (m-10) REVERT: AI 73 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.7974 (Cg_endo) REVERT: Aa 92 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7925 (t80) REVERT: Aa 96 LEU cc_start: 0.9086 (mt) cc_final: 0.8829 (mt) REVERT: Aa 162 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7071 (tm-30) REVERT: Aa 229 MET cc_start: 0.7495 (mmt) cc_final: 0.7071 (mmt) REVERT: Aa 292 GLU cc_start: 0.7661 (pp20) cc_final: 0.7321 (tm-30) REVERT: Aa 381 THR cc_start: 0.8950 (m) cc_final: 0.8691 (p) REVERT: Aa 410 CYS cc_start: 0.8445 (p) cc_final: 0.7790 (p) REVERT: Aa 435 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8035 (tm-30) REVERT: Aa 440 MET cc_start: 0.8410 (ptp) cc_final: 0.8123 (ptp) REVERT: Aa 475 MET cc_start: 0.8549 (tpp) cc_final: 0.7926 (tpp) REVERT: Ab 82 LEU cc_start: 0.8948 (tp) cc_final: 0.8734 (tp) REVERT: Ab 173 ILE cc_start: 0.8623 (tp) cc_final: 0.8052 (tp) REVERT: Ab 199 LYS cc_start: 0.8154 (tttm) cc_final: 0.7805 (tttm) REVERT: Ab 395 GLU cc_start: 0.8432 (tp30) cc_final: 0.7874 (tp30) REVERT: Ac 12 LYS cc_start: 0.7729 (tmtt) cc_final: 0.7024 (mptt) REVERT: Ac 20 ASP cc_start: 0.8043 (m-30) cc_final: 0.7770 (m-30) REVERT: Ac 26 ASN cc_start: 0.8745 (p0) cc_final: 0.8506 (p0) REVERT: Ac 44 GLN cc_start: 0.8005 (mm110) cc_final: 0.7711 (mm-40) REVERT: Ac 100 ARG cc_start: 0.8843 (tmm-80) cc_final: 0.8461 (tmm-80) REVERT: Ac 165 TRP cc_start: 0.7529 (m-10) cc_final: 0.6963 (m-10) REVERT: Ac 216 ASP cc_start: 0.8665 (t0) cc_final: 0.8316 (t0) REVERT: Ac 240 MET cc_start: 0.8303 (mmm) cc_final: 0.8025 (mmp) REVERT: Ac 292 LEU cc_start: 0.8820 (mm) cc_final: 0.8516 (mm) REVERT: Ac 373 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: Ad 119 GLN cc_start: 0.8899 (mt0) cc_final: 0.8525 (tm-30) REVERT: Ad 129 TYR cc_start: 0.8540 (m-10) cc_final: 0.8273 (m-10) REVERT: Ad 134 HIS cc_start: 0.8209 (m90) cc_final: 0.7660 (m90) REVERT: Ad 164 MET cc_start: 0.8139 (ptp) cc_final: 0.7845 (ppp) REVERT: Ad 189 ASN cc_start: 0.7422 (m-40) cc_final: 0.7160 (m-40) REVERT: Ae 140 MET cc_start: 0.8148 (mtp) cc_final: 0.7294 (ttm) REVERT: Ae 165 MET cc_start: 0.7112 (tpp) cc_final: 0.6612 (mpp) REVERT: Af 33 MET cc_start: 0.8515 (mtm) cc_final: 0.7906 (mtm) REVERT: Af 60 MET cc_start: 0.9014 (tpp) cc_final: 0.8073 (mpp) REVERT: Af 97 GLU cc_start: 0.8097 (tp30) cc_final: 0.7679 (tt0) REVERT: Af 103 LYS cc_start: 0.9374 (tppt) cc_final: 0.9163 (mmmm) REVERT: Ag 29 SER cc_start: 0.8888 (m) cc_final: 0.8390 (t) REVERT: Ag 47 LEU cc_start: 0.9097 (mt) cc_final: 0.8712 (tp) REVERT: Ag 57 TYR cc_start: 0.8759 (t80) cc_final: 0.8535 (t80) REVERT: Ag 66 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8004 (tm-30) REVERT: Ag 77 MET cc_start: 0.8045 (mtp) cc_final: 0.7706 (mtp) REVERT: Ah 62 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7262 (mp0) REVERT: Ah 67 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: Aj 20 THR cc_start: 0.7885 (m) cc_final: 0.7638 (p) REVERT: Aj 23 LEU cc_start: 0.9228 (tp) cc_final: 0.8524 (tp) REVERT: Aj 53 TRP cc_start: 0.8228 (t-100) cc_final: 0.7398 (t-100) REVERT: Ak 23 MET cc_start: 0.7282 (mmt) cc_final: 0.6134 (tpp) outliers start: 153 outliers final: 79 residues processed: 908 average time/residue: 0.1913 time to fit residues: 284.3951 Evaluate side-chains 810 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 723 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 183 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 366 ASP Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 48 VAL Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 79 THR Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 139 ASN Chi-restraints excluded: chain AB residue 147 ARG Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 160 LEU Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 237 LEU Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 138 VAL Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 38 LEU Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 16 SER Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 71 VAL Chi-restraints excluded: chain Aa residue 92 PHE Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 401 SER Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 343 GLN Chi-restraints excluded: chain Ab residue 371 VAL Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 238 ILE Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 364 ILE Chi-restraints excluded: chain Ac residue 373 GLU Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 239 HIS Chi-restraints excluded: chain Af residue 43 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ah residue 52 ASP Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 10 LEU Chi-restraints excluded: chain Aj residue 18 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 278 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 272 optimal weight: 0.7980 chunk 336 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 240 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 357 GLN AC 263 ASN AF 74 GLN AH 34 HIS AH 78 HIS Ab 139 ASN ** Ab 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN Ac 352 GLN Ad 309 HIS ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 78 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.088868 restraints weight = 77735.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091972 restraints weight = 38254.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094034 restraints weight = 25127.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095430 restraints weight = 19402.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096174 restraints weight = 16394.888| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.707 32218 Z= 0.265 Angle : 0.797 21.061 43733 Z= 0.388 Chirality : 0.047 0.363 4746 Planarity : 0.005 0.091 5552 Dihedral : 9.213 88.652 4583 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 5.73 % Allowed : 19.25 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3849 helix: 0.93 (0.11), residues: 2048 sheet: 0.05 (0.28), residues: 369 loop : -0.42 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGAH 54 TYR 0.018 0.002 TYRAf 21 PHE 0.034 0.002 PHEAJ 32 TRP 0.031 0.002 TRPAC 113 HIS 0.014 0.002 HISAH 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 (32203) covalent geometry : angle 0.79688 / 0.39 (43717) SS BOND : bond 0.00430 / 0.23 ( 8) SS BOND : angle 1.76678 / 0.91 ( 16) hydrogen bonds : bond 0.04839 / 3.26 ( 1796) hydrogen bonds : angle 5.13781 / 3.61 ( 5166) Misc. bond : bond 0.41092 / 18.89 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 751 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 114 GLU cc_start: 0.8391 (tp30) cc_final: 0.8022 (mm-30) REVERT: AA 131 TYR cc_start: 0.8792 (m-80) cc_final: 0.8375 (m-80) REVERT: AA 179 MET cc_start: 0.6696 (mtm) cc_final: 0.6380 (mtm) REVERT: AA 240 GLN cc_start: 0.8643 (tp40) cc_final: 0.8189 (tp-100) REVERT: AA 248 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8867 (tptp) REVERT: AA 255 ARG cc_start: 0.7346 (mpp-170) cc_final: 0.7099 (mpp-170) REVERT: AA 304 LEU cc_start: 0.9046 (mt) cc_final: 0.8517 (mt) REVERT: AB 197 MET cc_start: 0.7852 (mtp) cc_final: 0.7449 (ttm) REVERT: AB 235 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: AB 260 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7024 (tm-30) REVERT: AC 26 ASN cc_start: 0.9002 (p0) cc_final: 0.8801 (p0) REVERT: AC 42 MET cc_start: 0.7113 (tpt) cc_final: 0.6627 (tpp) REVERT: AC 163 TRP cc_start: 0.8664 (t60) cc_final: 0.7955 (t60) REVERT: AC 216 ASP cc_start: 0.8593 (t0) cc_final: 0.7941 (t0) REVERT: AC 316 MET cc_start: 0.8885 (ttm) cc_final: 0.8543 (ttm) REVERT: AC 337 TRP cc_start: 0.9041 (t60) cc_final: 0.8820 (t60) REVERT: AC 344 GLU cc_start: 0.8365 (tp30) cc_final: 0.8160 (tp30) REVERT: AD 96 TRP cc_start: 0.7477 (m100) cc_final: 0.6987 (m100) REVERT: AD 155 GLN cc_start: 0.8960 (pt0) cc_final: 0.8694 (pm20) REVERT: AD 244 MET cc_start: 0.8076 (ttp) cc_final: 0.7577 (ttp) REVERT: AE 88 PHE cc_start: 0.7906 (m-80) cc_final: 0.7164 (m-80) REVERT: AE 127 TYR cc_start: 0.7369 (t80) cc_final: 0.7082 (t80) REVERT: AE 165 MET cc_start: 0.5276 (tpp) cc_final: 0.4947 (tpp) REVERT: AE 167 PHE cc_start: 0.8031 (m-80) cc_final: 0.7425 (m-10) REVERT: AE 197 ASP cc_start: 0.3999 (m-30) cc_final: 0.3689 (m-30) REVERT: AF 33 MET cc_start: 0.7607 (mmt) cc_final: 0.6830 (mmt) REVERT: AF 53 GLU cc_start: 0.7427 (tp30) cc_final: 0.7148 (tp30) REVERT: AF 57 ASN cc_start: 0.8072 (m-40) cc_final: 0.7869 (m-40) REVERT: AG 17 TYR cc_start: 0.8156 (m-80) cc_final: 0.7619 (m-80) REVERT: AG 24 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7495 (pp30) REVERT: AG 71 LYS cc_start: 0.8125 (tptp) cc_final: 0.7719 (ptmm) REVERT: AG 78 TYR cc_start: 0.7172 (m-80) cc_final: 0.6791 (m-80) REVERT: AH 33 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8883 (mm-30) REVERT: AI 73 PRO cc_start: 0.8196 (Cg_exo) cc_final: 0.7993 (Cg_endo) REVERT: Aa 76 ASP cc_start: 0.8315 (t0) cc_final: 0.7824 (t0) REVERT: Aa 84 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: Aa 92 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8326 (t80) REVERT: Aa 149 ASP cc_start: 0.8952 (t0) cc_final: 0.8425 (t0) REVERT: Aa 172 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8325 (ttt) REVERT: Aa 229 MET cc_start: 0.7522 (mmt) cc_final: 0.7098 (mmt) REVERT: Aa 368 MET cc_start: 0.8831 (mmm) cc_final: 0.8469 (tpt) REVERT: Aa 377 MET cc_start: 0.9514 (tpp) cc_final: 0.9162 (mmm) REVERT: Aa 381 THR cc_start: 0.9061 (m) cc_final: 0.8852 (p) REVERT: Aa 435 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8271 (tm-30) REVERT: Aa 440 MET cc_start: 0.8487 (ptp) cc_final: 0.8228 (ptp) REVERT: Aa 445 CYS cc_start: 0.8470 (m) cc_final: 0.7371 (t) REVERT: Aa 473 SER cc_start: 0.8645 (m) cc_final: 0.8428 (p) REVERT: Ab 82 LEU cc_start: 0.9117 (tp) cc_final: 0.8879 (tp) REVERT: Ab 172 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7639 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8921 (tp) cc_final: 0.8393 (tp) REVERT: Ab 199 LYS cc_start: 0.8404 (tttm) cc_final: 0.8052 (tttm) REVERT: Ab 377 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8591 (ttmm) REVERT: Ab 387 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8051 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8894 (pp20) cc_final: 0.8049 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8722 (tp30) cc_final: 0.8213 (tp30) REVERT: Ac 12 LYS cc_start: 0.7721 (tmtt) cc_final: 0.7106 (mptt) REVERT: Ac 20 ASP cc_start: 0.8087 (m-30) cc_final: 0.7788 (m-30) REVERT: Ac 44 GLN cc_start: 0.7931 (mm110) cc_final: 0.7535 (mm-40) REVERT: Ac 58 ASP cc_start: 0.8808 (t0) cc_final: 0.8581 (t0) REVERT: Ac 165 TRP cc_start: 0.7417 (OUTLIER) cc_final: 0.7110 (m-10) REVERT: Ac 214 ASP cc_start: 0.8911 (m-30) cc_final: 0.8708 (m-30) REVERT: Ac 216 ASP cc_start: 0.8687 (t0) cc_final: 0.8363 (t0) REVERT: Ac 237 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9070 (tp) REVERT: Ac 271 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7756 (mt-10) REVERT: Ac 292 LEU cc_start: 0.8874 (mm) cc_final: 0.8551 (mm) REVERT: Ac 331 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8289 (p0) REVERT: Ac 358 TYR cc_start: 0.8660 (t80) cc_final: 0.7943 (t80) REVERT: Ac 378 LYS cc_start: 0.8601 (mtmt) cc_final: 0.8383 (mtmm) REVERT: Ad 119 GLN cc_start: 0.8729 (mt0) cc_final: 0.8445 (mt0) REVERT: Ad 164 MET cc_start: 0.8367 (ptp) cc_final: 0.7947 (ppp) REVERT: Ad 189 ASN cc_start: 0.7665 (m-40) cc_final: 0.7289 (m-40) REVERT: Ae 140 MET cc_start: 0.8284 (mtp) cc_final: 0.7323 (ttm) REVERT: Ae 167 PHE cc_start: 0.6507 (m-10) cc_final: 0.6302 (m-10) REVERT: Af 33 MET cc_start: 0.8574 (mtm) cc_final: 0.7899 (mtt) REVERT: Af 60 MET cc_start: 0.9027 (tpp) cc_final: 0.8039 (mpp) REVERT: Af 97 GLU cc_start: 0.8117 (tp30) cc_final: 0.7817 (tp30) REVERT: Af 100 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8659 (mtm110) REVERT: Ag 23 GLU cc_start: 0.7353 (tp30) cc_final: 0.6789 (tp30) REVERT: Ag 29 SER cc_start: 0.8812 (m) cc_final: 0.8386 (t) REVERT: Ag 66 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8381 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8891 (mt0) cc_final: 0.8651 (mt0) REVERT: Ah 89 LYS cc_start: 0.7462 (mmtt) cc_final: 0.7046 (mtpt) REVERT: Aj 20 THR cc_start: 0.7964 (m) cc_final: 0.7736 (p) REVERT: Aj 23 LEU cc_start: 0.9238 (tp) cc_final: 0.8537 (tp) REVERT: Aj 43 ILE cc_start: 0.9046 (tt) cc_final: 0.8842 (tt) REVERT: Aj 53 TRP cc_start: 0.8333 (t-100) cc_final: 0.7727 (t-100) REVERT: Ak 23 MET cc_start: 0.7315 (mmt) cc_final: 0.6177 (tpp) REVERT: Ak 39 ARG cc_start: 0.7481 (tpt90) cc_final: 0.6680 (ptt-90) outliers start: 189 outliers final: 111 residues processed: 857 average time/residue: 0.1847 time to fit residues: 259.0610 Evaluate side-chains 799 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 677 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 220 LEU Chi-restraints excluded: chain AA residue 248 LYS Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 366 ASP Chi-restraints excluded: chain AA residue 369 VAL Chi-restraints excluded: chain AA residue 388 VAL Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 55 TYR Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 79 THR Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 139 ASN Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 258 ILE Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 27 ILE Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 164 ILE Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 175 LEU Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 138 VAL Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AE residue 87 ASP Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 230 ASP Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 24 GLN Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AH residue 88 LEU Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 16 SER Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AI residue 67 THR Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 71 VAL Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 92 PHE Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 172 MET Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 139 ASN Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 194 ASP Chi-restraints excluded: chain Ab residue 371 VAL Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 233 LEU Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 364 ILE Chi-restraints excluded: chain Ac residue 376 MET Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 239 HIS Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 26 ASP Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 10 LEU Chi-restraints excluded: chain Aj residue 54 LYS Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 327 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 378 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 100 optimal weight: 0.0770 chunk 237 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 402 HIS AB 227 HIS ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 107 HIS AD 309 HIS AG 37 ASN AH 37 GLN ** AH 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 55 ASN Aa 393 ASN Ab 139 ASN Ab 236 GLN Ac 331 ASN Ac 352 GLN Ad 309 HIS Ae 242 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.121733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093101 restraints weight = 75333.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096268 restraints weight = 35904.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098396 restraints weight = 23024.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099791 restraints weight = 17444.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100516 restraints weight = 14605.582| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.434 32218 Z= 0.141 Angle : 0.690 15.560 43733 Z= 0.335 Chirality : 0.044 0.265 4746 Planarity : 0.004 0.060 5552 Dihedral : 8.884 88.964 4583 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.82 % Allowed : 21.70 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.14), residues: 3849 helix: 1.22 (0.11), residues: 2039 sheet: 0.01 (0.27), residues: 379 loop : -0.30 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAh 45 TYR 0.020 0.001 TYRAD 140 PHE 0.026 0.001 PHEAg 67 TRP 0.043 0.002 TRPAC 113 HIS 0.011 0.001 HISAH 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (32203) covalent geometry : angle 0.68855 / 0.33 (43717) SS BOND : bond 0.00409 / 0.21 ( 8) SS BOND : angle 2.40098 / 1.25 ( 16) hydrogen bonds : bond 0.04234 / 2.87 ( 1796) hydrogen bonds : angle 4.82247 / 3.38 ( 5166) Misc. bond : bond 0.27319 / 12.12 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 765 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 114 GLU cc_start: 0.8371 (tp30) cc_final: 0.7931 (mm-30) REVERT: AA 131 TYR cc_start: 0.8662 (m-80) cc_final: 0.8175 (m-10) REVERT: AA 240 GLN cc_start: 0.8671 (tp40) cc_final: 0.8401 (tp-100) REVERT: AA 292 GLU cc_start: 0.8424 (pp20) cc_final: 0.8060 (pp20) REVERT: AA 385 GLU cc_start: 0.8982 (pm20) cc_final: 0.8210 (pm20) REVERT: AB 180 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8067 (p) REVERT: AB 197 MET cc_start: 0.7778 (mtp) cc_final: 0.7312 (ttm) REVERT: AB 235 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: AB 260 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6949 (tm-30) REVERT: AC 163 TRP cc_start: 0.8657 (t60) cc_final: 0.8132 (t60) REVERT: AC 240 MET cc_start: 0.9187 (mmp) cc_final: 0.8797 (mmm) REVERT: AC 316 MET cc_start: 0.8810 (ttm) cc_final: 0.8464 (ttm) REVERT: AC 337 TRP cc_start: 0.9038 (t60) cc_final: 0.8782 (t60) REVERT: AD 96 TRP cc_start: 0.7434 (m100) cc_final: 0.7125 (m100) REVERT: AD 129 TYR cc_start: 0.8790 (m-80) cc_final: 0.8140 (m-80) REVERT: AD 155 GLN cc_start: 0.8913 (pt0) cc_final: 0.8630 (pm20) REVERT: AD 164 MET cc_start: 0.6936 (tmm) cc_final: 0.5644 (tmm) REVERT: AD 212 PHE cc_start: 0.8304 (t80) cc_final: 0.7560 (t80) REVERT: AD 244 MET cc_start: 0.8026 (ttp) cc_final: 0.7589 (ttp) REVERT: AE 165 MET cc_start: 0.5487 (tpp) cc_final: 0.5181 (tpp) REVERT: AE 167 PHE cc_start: 0.8083 (m-80) cc_final: 0.7586 (m-10) REVERT: AE 197 ASP cc_start: 0.4301 (m-30) cc_final: 0.4091 (m-30) REVERT: AE 248 ARG cc_start: 0.7140 (mtp85) cc_final: 0.6574 (mtp85) REVERT: AF 33 MET cc_start: 0.7627 (mmt) cc_final: 0.6833 (mmt) REVERT: AG 17 TYR cc_start: 0.8052 (m-80) cc_final: 0.7798 (m-80) REVERT: AG 71 LYS cc_start: 0.8122 (tptp) cc_final: 0.7813 (ptmm) REVERT: AG 78 TYR cc_start: 0.7089 (m-80) cc_final: 0.6731 (m-80) REVERT: AH 39 GLU cc_start: 0.8998 (pm20) cc_final: 0.8657 (pp20) REVERT: AH 66 THR cc_start: 0.7218 (m) cc_final: 0.6901 (t) REVERT: AI 77 ARG cc_start: 0.7121 (tmt-80) cc_final: 0.6908 (tmt-80) REVERT: AJ 34 ARG cc_start: 0.6508 (tpp80) cc_final: 0.6074 (tpp-160) REVERT: Aa 76 ASP cc_start: 0.8256 (t0) cc_final: 0.7685 (t0) REVERT: Aa 91 TYR cc_start: 0.8962 (t80) cc_final: 0.8290 (t80) REVERT: Aa 92 PHE cc_start: 0.8774 (t80) cc_final: 0.8458 (t80) REVERT: Aa 149 ASP cc_start: 0.8850 (t0) cc_final: 0.8323 (t0) REVERT: Aa 162 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7958 (tm-30) REVERT: Aa 171 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8822 (pt0) REVERT: Aa 172 MET cc_start: 0.8712 (ttt) cc_final: 0.8507 (ttt) REVERT: Aa 368 MET cc_start: 0.8820 (mmm) cc_final: 0.8493 (tpt) REVERT: Aa 377 MET cc_start: 0.9417 (tpp) cc_final: 0.9190 (mmm) REVERT: Aa 435 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8087 (tm-30) REVERT: Aa 440 MET cc_start: 0.8441 (ptp) cc_final: 0.7809 (ptp) REVERT: Aa 445 CYS cc_start: 0.8384 (m) cc_final: 0.7384 (t) REVERT: Aa 473 SER cc_start: 0.8529 (m) cc_final: 0.8300 (p) REVERT: Ab 82 LEU cc_start: 0.8991 (tp) cc_final: 0.8711 (tp) REVERT: Ab 173 ILE cc_start: 0.8649 (tp) cc_final: 0.8233 (tp) REVERT: Ab 199 LYS cc_start: 0.8321 (tttm) cc_final: 0.7942 (tttm) REVERT: Ab 377 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: Ab 387 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7729 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8868 (pp20) cc_final: 0.8243 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8661 (tp30) cc_final: 0.8216 (tp30) REVERT: Ac 12 LYS cc_start: 0.8003 (tmtt) cc_final: 0.7404 (mptt) REVERT: Ac 20 ASP cc_start: 0.8067 (m-30) cc_final: 0.7739 (m-30) REVERT: Ac 146 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6741 (mt) REVERT: Ac 165 TRP cc_start: 0.7385 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: Ac 202 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8237 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8633 (t0) cc_final: 0.8403 (t0) REVERT: Ac 271 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7588 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8828 (mt) cc_final: 0.8510 (mt) REVERT: Ac 358 TYR cc_start: 0.8554 (t80) cc_final: 0.7723 (t80) REVERT: Ad 119 GLN cc_start: 0.8692 (mt0) cc_final: 0.8421 (mt0) REVERT: Ad 164 MET cc_start: 0.8236 (ptp) cc_final: 0.7826 (ppp) REVERT: Ad 177 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9071 (mttm) REVERT: Ad 189 ASN cc_start: 0.7458 (m-40) cc_final: 0.7094 (m-40) REVERT: Ad 295 MET cc_start: 0.8381 (mmp) cc_final: 0.8041 (mmp) REVERT: Ae 140 MET cc_start: 0.8261 (mtp) cc_final: 0.7464 (ttm) REVERT: Ae 187 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7399 (mm-30) REVERT: Af 33 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7932 (mtt) REVERT: Af 60 MET cc_start: 0.8923 (tpp) cc_final: 0.7886 (mpp) REVERT: Af 70 THR cc_start: 0.9264 (m) cc_final: 0.9059 (p) REVERT: Af 107 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8484 (tm-30) REVERT: Ag 29 SER cc_start: 0.8843 (m) cc_final: 0.8397 (t) REVERT: Ag 66 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8317 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8771 (mt0) cc_final: 0.8488 (mt0) REVERT: Ah 53 ASN cc_start: 0.9055 (t0) cc_final: 0.8800 (m110) REVERT: Aj 23 LEU cc_start: 0.9238 (tp) cc_final: 0.8526 (tp) REVERT: Aj 53 TRP cc_start: 0.8348 (t-100) cc_final: 0.7633 (t-100) REVERT: Ak 23 MET cc_start: 0.7415 (mmt) cc_final: 0.6283 (tpp) REVERT: Ak 24 TRP cc_start: 0.7474 (m100) cc_final: 0.7122 (m100) REVERT: Ak 39 ARG cc_start: 0.7530 (tpt90) cc_final: 0.6790 (ptp90) outliers start: 126 outliers final: 76 residues processed: 832 average time/residue: 0.1785 time to fit residues: 244.8578 Evaluate side-chains 772 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 688 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 164 ILE Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 77 ASP Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 34 TRP Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 216 LEU Chi-restraints excluded: chain Aa residue 243 LEU Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 169 SER Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 146 ILE Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 239 HIS Chi-restraints excluded: chain Af residue 33 MET Chi-restraints excluded: chain Af residue 43 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 255 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 374 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 353 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 119 GLN ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 78 HIS ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 393 ASN Aa 434 GLN Ab 376 ASN ** Ac 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN Ac 352 GLN Ad 309 HIS ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 78 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.119785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.090990 restraints weight = 75639.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094061 restraints weight = 36657.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096163 restraints weight = 23719.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.097432 restraints weight = 18031.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098325 restraints weight = 15228.083| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.585 32218 Z= 0.197 Angle : 0.724 16.754 43733 Z= 0.351 Chirality : 0.045 0.256 4746 Planarity : 0.005 0.068 5552 Dihedral : 8.893 87.526 4583 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.15 % Allowed : 22.34 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.14), residues: 3849 helix: 1.20 (0.11), residues: 2045 sheet: -0.05 (0.27), residues: 377 loop : -0.28 (0.18), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAH 54 TYR 0.024 0.002 TYRAD 140 PHE 0.027 0.002 PHEAg 67 TRP 0.045 0.002 TRPAC 113 HIS 0.011 0.001 HISAd 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (32203) covalent geometry : angle 0.72222 / 0.35 (43717) SS BOND : bond 0.00908 / 0.47 ( 8) SS BOND : angle 2.49718 / 1.10 ( 16) hydrogen bonds : bond 0.04334 / 2.94 ( 1796) hydrogen bonds : angle 4.84540 / 3.40 ( 5166) Misc. bond : bond 0.32016 / 13.99 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 714 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 79 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.7208 (t) REVERT: AA 114 GLU cc_start: 0.8342 (tp30) cc_final: 0.8025 (mm-30) REVERT: AA 131 TYR cc_start: 0.8740 (m-80) cc_final: 0.8300 (m-80) REVERT: AA 240 GLN cc_start: 0.8697 (tp40) cc_final: 0.8416 (tp-100) REVERT: AA 292 GLU cc_start: 0.8441 (pp20) cc_final: 0.8113 (pp20) REVERT: AA 385 GLU cc_start: 0.8973 (pm20) cc_final: 0.8209 (pm20) REVERT: AB 197 MET cc_start: 0.7849 (mtp) cc_final: 0.7388 (ttm) REVERT: AB 235 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: AB 260 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7120 (tm-30) REVERT: AC 216 ASP cc_start: 0.8628 (t0) cc_final: 0.8072 (t70) REVERT: AD 96 TRP cc_start: 0.7595 (m100) cc_final: 0.7162 (m100) REVERT: AD 115 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8267 (tm-30) REVERT: AD 119 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8218 (mp10) REVERT: AD 155 GLN cc_start: 0.8931 (pt0) cc_final: 0.8722 (pm20) REVERT: AD 164 MET cc_start: 0.6972 (tmm) cc_final: 0.5610 (tmm) REVERT: AD 244 MET cc_start: 0.7839 (ttp) cc_final: 0.7391 (ttp) REVERT: AE 165 MET cc_start: 0.5524 (tpp) cc_final: 0.5189 (tpp) REVERT: AE 167 PHE cc_start: 0.8148 (m-80) cc_final: 0.7634 (m-10) REVERT: AE 248 ARG cc_start: 0.7217 (mtp85) cc_final: 0.6408 (mtp85) REVERT: AF 33 MET cc_start: 0.7642 (mmt) cc_final: 0.6835 (mmt) REVERT: AG 17 TYR cc_start: 0.8151 (m-80) cc_final: 0.7794 (m-80) REVERT: AG 71 LYS cc_start: 0.8015 (tptp) cc_final: 0.7745 (ptmm) REVERT: AG 78 TYR cc_start: 0.7144 (m-80) cc_final: 0.6699 (m-80) REVERT: AH 39 GLU cc_start: 0.9034 (pm20) cc_final: 0.8678 (pp20) REVERT: AH 48 LEU cc_start: 0.8880 (tt) cc_final: 0.8331 (mp) REVERT: AH 66 THR cc_start: 0.7002 (m) cc_final: 0.6799 (t) REVERT: AJ 34 ARG cc_start: 0.6663 (tpp80) cc_final: 0.5935 (tpp-160) REVERT: Aa 76 ASP cc_start: 0.8236 (t0) cc_final: 0.7736 (t0) REVERT: Aa 84 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: Aa 92 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8572 (t80) REVERT: Aa 149 ASP cc_start: 0.8904 (t0) cc_final: 0.8402 (t0) REVERT: Aa 172 MET cc_start: 0.8754 (ttt) cc_final: 0.8540 (ttt) REVERT: Aa 368 MET cc_start: 0.8810 (mmm) cc_final: 0.8402 (tpt) REVERT: Aa 377 MET cc_start: 0.9457 (tpp) cc_final: 0.9257 (mmm) REVERT: Aa 379 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8373 (tp) REVERT: Aa 435 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8134 (tm-30) REVERT: Aa 440 MET cc_start: 0.8480 (ptp) cc_final: 0.7967 (ptp) REVERT: Aa 445 CYS cc_start: 0.8449 (m) cc_final: 0.7288 (t) REVERT: Aa 473 SER cc_start: 0.8551 (m) cc_final: 0.8321 (p) REVERT: Ab 82 LEU cc_start: 0.8996 (tp) cc_final: 0.8777 (tp) REVERT: Ab 172 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7679 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8881 (tp) cc_final: 0.8489 (tp) REVERT: Ab 199 LYS cc_start: 0.8382 (tttm) cc_final: 0.7995 (tttm) REVERT: Ab 377 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8619 (ttmm) REVERT: Ab 387 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7837 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8896 (pp20) cc_final: 0.8297 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8657 (tp30) cc_final: 0.8143 (tp30) REVERT: Ac 12 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7547 (mptt) REVERT: Ac 20 ASP cc_start: 0.8100 (m-30) cc_final: 0.7758 (m-30) REVERT: Ac 118 LEU cc_start: 0.8838 (tp) cc_final: 0.8327 (tt) REVERT: Ac 146 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6602 (mt) REVERT: Ac 165 TRP cc_start: 0.7612 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: Ac 202 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8272 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8728 (t0) cc_final: 0.8426 (t0) REVERT: Ac 271 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7732 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8854 (mt) cc_final: 0.8538 (mt) REVERT: Ac 292 LEU cc_start: 0.9039 (pp) cc_final: 0.8837 (mm) REVERT: Ac 344 GLU cc_start: 0.8558 (tp30) cc_final: 0.8223 (tp30) REVERT: Ac 358 TYR cc_start: 0.8584 (t80) cc_final: 0.7754 (t80) REVERT: Ad 119 GLN cc_start: 0.8706 (mt0) cc_final: 0.8393 (mt0) REVERT: Ad 164 MET cc_start: 0.8316 (ptp) cc_final: 0.7926 (ppp) REVERT: Ad 189 ASN cc_start: 0.7536 (m-40) cc_final: 0.7088 (m-40) REVERT: Ae 140 MET cc_start: 0.8399 (mtp) cc_final: 0.7414 (ttm) REVERT: Ae 187 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7396 (mm-30) REVERT: Af 33 MET cc_start: 0.8544 (mtm) cc_final: 0.8001 (mtt) REVERT: Af 60 MET cc_start: 0.8942 (tpp) cc_final: 0.7921 (mpp) REVERT: Af 96 LYS cc_start: 0.8885 (mttm) cc_final: 0.8651 (mttm) REVERT: Af 107 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8547 (tm-30) REVERT: Ag 29 SER cc_start: 0.8893 (m) cc_final: 0.8454 (t) REVERT: Ag 66 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8420 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8833 (mt0) cc_final: 0.8559 (mt0) REVERT: Ah 45 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7899 (ptm160) REVERT: Aj 23 LEU cc_start: 0.9249 (tp) cc_final: 0.8970 (tp) REVERT: Aj 53 TRP cc_start: 0.8322 (t-100) cc_final: 0.7622 (t-100) REVERT: Ak 23 MET cc_start: 0.7436 (mmt) cc_final: 0.6737 (tpp) outliers start: 137 outliers final: 97 residues processed: 788 average time/residue: 0.1828 time to fit residues: 236.0492 Evaluate side-chains 781 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 674 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 79 SER Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 424 VAL Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 119 GLN Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AE residue 270 VAL Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 77 ASP Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 92 PHE Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 243 LEU Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 379 LEU Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 169 SER Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 146 ILE Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 56 VAL Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 107 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 281 optimal weight: 0.9990 chunk 324 optimal weight: 0.0270 chunk 286 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 316 optimal weight: 0.0370 chunk 278 optimal weight: 7.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 249 HIS AC 196 HIS ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 341 GLN ** AD 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 78 HIS ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 175 ASN Aa 223 HIS Aa 373 GLN Aa 393 ASN Ac 331 ASN Ac 352 GLN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 242 HIS Ah 78 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.121142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092459 restraints weight = 75264.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095639 restraints weight = 36089.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.097762 restraints weight = 23118.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099115 restraints weight = 17499.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099835 restraints weight = 14658.386| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.469 32218 Z= 0.150 Angle : 0.700 14.546 43733 Z= 0.339 Chirality : 0.044 0.334 4746 Planarity : 0.004 0.064 5552 Dihedral : 8.752 87.740 4583 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.00 % Allowed : 23.46 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3849 helix: 1.26 (0.11), residues: 2049 sheet: -0.08 (0.27), residues: 378 loop : -0.21 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAH 54 TYR 0.027 0.001 TYRAD 140 PHE 0.028 0.001 PHEAg 67 TRP 0.035 0.001 TRPAC 113 HIS 0.011 0.001 HISAd 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (32203) covalent geometry : angle 0.69712 / 0.34 (43717) SS BOND : bond 0.00393 / 0.19 ( 8) SS BOND : angle 3.19469 / 1.29 ( 16) hydrogen bonds : bond 0.04144 / 2.80 ( 1796) hydrogen bonds : angle 4.72155 / 3.32 ( 5166) Misc. bond : bond 0.27149 / 11.78 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 730 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 74 TRP cc_start: 0.8444 (m100) cc_final: 0.7539 (m-10) REVERT: AA 114 GLU cc_start: 0.8338 (tp30) cc_final: 0.8035 (mm-30) REVERT: AA 131 TYR cc_start: 0.8741 (m-80) cc_final: 0.8302 (m-80) REVERT: AA 140 LEU cc_start: 0.7784 (mt) cc_final: 0.7409 (mt) REVERT: AA 240 GLN cc_start: 0.8666 (tp40) cc_final: 0.8374 (tp-100) REVERT: AA 292 GLU cc_start: 0.8416 (pp20) cc_final: 0.8151 (pp20) REVERT: AA 385 GLU cc_start: 0.8939 (pm20) cc_final: 0.8223 (pm20) REVERT: AB 166 PHE cc_start: 0.8318 (m-10) cc_final: 0.7896 (m-10) REVERT: AB 180 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8177 (p) REVERT: AB 197 MET cc_start: 0.7819 (mtp) cc_final: 0.7341 (ttm) REVERT: AB 235 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: AC 163 TRP cc_start: 0.8851 (t60) cc_final: 0.7928 (t60) REVERT: AC 216 ASP cc_start: 0.8595 (t0) cc_final: 0.8041 (t70) REVERT: AC 316 MET cc_start: 0.8980 (ttm) cc_final: 0.8335 (ttm) REVERT: AC 337 TRP cc_start: 0.9035 (t60) cc_final: 0.8824 (t60) REVERT: AD 96 TRP cc_start: 0.7493 (m100) cc_final: 0.7088 (m100) REVERT: AD 164 MET cc_start: 0.6992 (tmm) cc_final: 0.6489 (tmm) REVERT: AD 244 MET cc_start: 0.7874 (ttp) cc_final: 0.7441 (ttp) REVERT: AE 165 MET cc_start: 0.5523 (tpp) cc_final: 0.5208 (tpp) REVERT: AE 167 PHE cc_start: 0.8155 (m-80) cc_final: 0.7679 (m-10) REVERT: AE 231 PHE cc_start: 0.7185 (t80) cc_final: 0.5922 (t80) REVERT: AE 248 ARG cc_start: 0.7101 (mtp85) cc_final: 0.6541 (mtp85) REVERT: AF 33 MET cc_start: 0.7699 (mmt) cc_final: 0.6894 (mmt) REVERT: AG 17 TYR cc_start: 0.8110 (m-80) cc_final: 0.7787 (m-80) REVERT: AG 71 LYS cc_start: 0.7925 (tptp) cc_final: 0.7702 (ptmm) REVERT: AG 78 TYR cc_start: 0.7118 (m-80) cc_final: 0.6705 (m-80) REVERT: AH 39 GLU cc_start: 0.9011 (pm20) cc_final: 0.8657 (pp20) REVERT: AH 48 LEU cc_start: 0.8884 (tt) cc_final: 0.8672 (mm) REVERT: AH 50 LEU cc_start: 0.8237 (mm) cc_final: 0.7783 (pp) REVERT: AH 66 THR cc_start: 0.6863 (m) cc_final: 0.6527 (t) REVERT: Aa 49 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: Aa 76 ASP cc_start: 0.8220 (t0) cc_final: 0.7936 (t0) REVERT: Aa 84 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8561 (pm20) REVERT: Aa 91 TYR cc_start: 0.9012 (t80) cc_final: 0.7528 (t80) REVERT: Aa 149 ASP cc_start: 0.8901 (t0) cc_final: 0.8417 (t0) REVERT: Aa 197 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9057 (mp) REVERT: Aa 249 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7445 (m-70) REVERT: Aa 368 MET cc_start: 0.8855 (mmm) cc_final: 0.8516 (tpt) REVERT: Aa 377 MET cc_start: 0.9457 (tpp) cc_final: 0.9061 (mmm) REVERT: Aa 379 LEU cc_start: 0.8699 (mm) cc_final: 0.8261 (tp) REVERT: Aa 435 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8304 (tm-30) REVERT: Aa 440 MET cc_start: 0.8472 (ptp) cc_final: 0.8186 (ptp) REVERT: Aa 445 CYS cc_start: 0.8481 (m) cc_final: 0.7370 (t) REVERT: Aa 473 SER cc_start: 0.8535 (m) cc_final: 0.8300 (p) REVERT: Ab 82 LEU cc_start: 0.8962 (tp) cc_final: 0.8716 (tp) REVERT: Ab 84 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7301 (ttp-110) REVERT: Ab 173 ILE cc_start: 0.8757 (tp) cc_final: 0.8446 (tp) REVERT: Ab 199 LYS cc_start: 0.8350 (tttm) cc_final: 0.7971 (tttm) REVERT: Ab 377 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8528 (ttmm) REVERT: Ab 387 GLU cc_start: 0.8630 (tm-30) cc_final: 0.7851 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8906 (pp20) cc_final: 0.8329 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8657 (tp30) cc_final: 0.8241 (tp30) REVERT: Ac 12 LYS cc_start: 0.8106 (tmtt) cc_final: 0.7533 (mptt) REVERT: Ac 121 PHE cc_start: 0.8858 (m-80) cc_final: 0.8551 (m-10) REVERT: Ac 165 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: Ac 202 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8264 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8707 (t0) cc_final: 0.8316 (t0) REVERT: Ac 235 MET cc_start: 0.8416 (tmm) cc_final: 0.7941 (tpp) REVERT: Ac 271 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7632 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8777 (mt) cc_final: 0.8476 (mt) REVERT: Ac 344 GLU cc_start: 0.8549 (tp30) cc_final: 0.8218 (tp30) REVERT: Ac 358 TYR cc_start: 0.8649 (t80) cc_final: 0.7861 (t80) REVERT: Ad 119 GLN cc_start: 0.8683 (mt0) cc_final: 0.8262 (mt0) REVERT: Ad 164 MET cc_start: 0.8218 (ptp) cc_final: 0.7823 (ppp) REVERT: Ad 177 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9029 (mttm) REVERT: Ad 189 ASN cc_start: 0.7564 (m-40) cc_final: 0.7113 (m-40) REVERT: Ae 140 MET cc_start: 0.8392 (mtp) cc_final: 0.7289 (ttm) REVERT: Ae 248 ARG cc_start: 0.7029 (mtm180) cc_final: 0.5694 (mtm180) REVERT: Af 33 MET cc_start: 0.8484 (mtm) cc_final: 0.7959 (mtt) REVERT: Af 60 MET cc_start: 0.8910 (tpp) cc_final: 0.7893 (mpp) REVERT: Af 86 GLU cc_start: 0.8896 (pm20) cc_final: 0.8688 (pm20) REVERT: Af 107 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8530 (tm-30) REVERT: Ag 20 SER cc_start: 0.9027 (p) cc_final: 0.8652 (p) REVERT: Ag 29 SER cc_start: 0.8884 (m) cc_final: 0.8438 (t) REVERT: Ag 66 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8296 (tm-30) REVERT: Ah 45 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7822 (ptm160) REVERT: Aj 23 LEU cc_start: 0.9203 (tp) cc_final: 0.8918 (tp) REVERT: Aj 53 TRP cc_start: 0.8351 (t-100) cc_final: 0.7670 (t-100) REVERT: Ak 23 MET cc_start: 0.7452 (mmt) cc_final: 0.6744 (tpp) REVERT: Ak 32 LEU cc_start: 0.8752 (tt) cc_final: 0.8518 (mp) REVERT: Ak 39 ARG cc_start: 0.7400 (tpt90) cc_final: 0.6631 (ptp-170) outliers start: 132 outliers final: 99 residues processed: 800 average time/residue: 0.1778 time to fit residues: 232.0674 Evaluate side-chains 779 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 670 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 249 HIS Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 357 HIS Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 424 VAL Chi-restraints excluded: chain AC residue 27 ILE Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 310 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AE residue 87 ASP Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 35 CYS Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 49 GLN Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 179 MET Chi-restraints excluded: chain Aa residue 197 LEU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 216 LEU Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 84 ARG Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 335 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 85 PHE Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 8 SER Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 37 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 281 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 343 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 308 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 350 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 259 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 137 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 119 GLN ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 376 ASN Ac 331 ASN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 78 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.120410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091607 restraints weight = 75070.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094719 restraints weight = 36282.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096787 restraints weight = 23344.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098063 restraints weight = 17756.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098926 restraints weight = 15000.090| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.507 32218 Z= 0.164 Angle : 0.712 14.139 43733 Z= 0.346 Chirality : 0.044 0.291 4746 Planarity : 0.004 0.062 5552 Dihedral : 8.706 89.513 4583 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.15 % Allowed : 23.52 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3849 helix: 1.26 (0.11), residues: 2049 sheet: -0.11 (0.27), residues: 375 loop : -0.23 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAk 39 TYR 0.024 0.002 TYRAd 117 PHE 0.033 0.002 PHEAa 370 TRP 0.036 0.001 TRPAG 62 HIS 0.012 0.001 HISAA 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (32203) covalent geometry : angle 0.71036 / 0.35 (43717) SS BOND : bond 0.00689 / 0.35 ( 8) SS BOND : angle 2.48437 / 1.12 ( 16) hydrogen bonds : bond 0.04162 / 2.82 ( 1796) hydrogen bonds : angle 4.72841 / 3.33 ( 5166) Misc. bond : bond 0.28241 / 12.13 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 699 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 74 TRP cc_start: 0.8382 (m100) cc_final: 0.7432 (m-10) REVERT: AA 114 GLU cc_start: 0.8276 (tp30) cc_final: 0.7904 (mm-30) REVERT: AA 131 TYR cc_start: 0.8755 (m-80) cc_final: 0.8292 (m-80) REVERT: AA 199 GLN cc_start: 0.8485 (pm20) cc_final: 0.8261 (pm20) REVERT: AA 240 GLN cc_start: 0.8680 (tp40) cc_final: 0.8366 (tp-100) REVERT: AA 292 GLU cc_start: 0.8413 (pp20) cc_final: 0.8155 (pp20) REVERT: AA 385 GLU cc_start: 0.8909 (pm20) cc_final: 0.8194 (pm20) REVERT: AB 166 PHE cc_start: 0.8328 (m-10) cc_final: 0.7887 (m-10) REVERT: AB 180 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8197 (p) REVERT: AB 197 MET cc_start: 0.7849 (mtp) cc_final: 0.7363 (ttm) REVERT: AB 203 GLU cc_start: 0.8433 (mp0) cc_final: 0.8216 (mp0) REVERT: AB 235 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: AC 118 LEU cc_start: 0.9293 (tp) cc_final: 0.8901 (tt) REVERT: AC 137 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6539 (tp40) REVERT: AC 163 TRP cc_start: 0.8879 (t60) cc_final: 0.8113 (t60) REVERT: AC 216 ASP cc_start: 0.8619 (t0) cc_final: 0.8045 (t70) REVERT: AC 344 GLU cc_start: 0.8078 (tp30) cc_final: 0.7820 (tp30) REVERT: AD 96 TRP cc_start: 0.7436 (m100) cc_final: 0.6978 (m100) REVERT: AD 164 MET cc_start: 0.7007 (tmm) cc_final: 0.6542 (tmm) REVERT: AD 244 MET cc_start: 0.7853 (ttp) cc_final: 0.7373 (ttp) REVERT: AD 265 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7679 (tp40) REVERT: AD 295 MET cc_start: 0.7545 (ptp) cc_final: 0.7213 (ptt) REVERT: AE 165 MET cc_start: 0.5465 (tpp) cc_final: 0.5128 (tpp) REVERT: AE 167 PHE cc_start: 0.8162 (m-80) cc_final: 0.7685 (m-10) REVERT: AE 231 PHE cc_start: 0.7204 (t80) cc_final: 0.5924 (t80) REVERT: AE 248 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6591 (mtp85) REVERT: AF 33 MET cc_start: 0.7715 (mmt) cc_final: 0.6901 (mmt) REVERT: AG 17 TYR cc_start: 0.8042 (m-80) cc_final: 0.7703 (m-80) REVERT: AG 48 ARG cc_start: 0.8259 (mpt-90) cc_final: 0.7370 (mpt180) REVERT: AG 78 TYR cc_start: 0.7321 (m-80) cc_final: 0.6911 (m-80) REVERT: AH 39 GLU cc_start: 0.9008 (pm20) cc_final: 0.8662 (pp20) REVERT: AH 48 LEU cc_start: 0.8934 (tt) cc_final: 0.8674 (mm) REVERT: AK 24 TRP cc_start: 0.6650 (m100) cc_final: 0.6357 (m100) REVERT: Aa 49 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: Aa 76 ASP cc_start: 0.8213 (t0) cc_final: 0.7913 (t0) REVERT: Aa 79 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7699 (t) REVERT: Aa 84 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: Aa 91 TYR cc_start: 0.8868 (t80) cc_final: 0.8337 (t80) REVERT: Aa 149 ASP cc_start: 0.8871 (t0) cc_final: 0.8394 (t0) REVERT: Aa 172 MET cc_start: 0.8387 (ttt) cc_final: 0.8107 (ttt) REVERT: Aa 197 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9058 (mp) REVERT: Aa 249 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7440 (m-70) REVERT: Aa 292 GLU cc_start: 0.8410 (pp20) cc_final: 0.8158 (tp30) REVERT: Aa 368 MET cc_start: 0.8890 (mmm) cc_final: 0.8503 (tpt) REVERT: Aa 377 MET cc_start: 0.9469 (tpp) cc_final: 0.9081 (mmm) REVERT: Aa 379 LEU cc_start: 0.8694 (mm) cc_final: 0.8304 (tp) REVERT: Aa 435 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8314 (tm-30) REVERT: Aa 445 CYS cc_start: 0.8495 (m) cc_final: 0.7307 (t) REVERT: Aa 473 SER cc_start: 0.8462 (m) cc_final: 0.8222 (p) REVERT: Ab 84 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7300 (ttp-110) REVERT: Ab 172 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7677 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8786 (tp) cc_final: 0.8479 (tp) REVERT: Ab 199 LYS cc_start: 0.8397 (tttm) cc_final: 0.8012 (tttm) REVERT: Ab 311 GLN cc_start: 0.7671 (mt0) cc_final: 0.7357 (mm-40) REVERT: Ab 377 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (ttmm) REVERT: Ab 387 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8001 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8895 (pp20) cc_final: 0.8354 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8635 (tp30) cc_final: 0.8136 (tp30) REVERT: Ac 12 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7476 (mptt) REVERT: Ac 118 LEU cc_start: 0.8881 (tp) cc_final: 0.8328 (tt) REVERT: Ac 121 PHE cc_start: 0.8813 (m-80) cc_final: 0.8532 (m-10) REVERT: Ac 165 TRP cc_start: 0.7491 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: Ac 202 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8296 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8722 (t0) cc_final: 0.8366 (t0) REVERT: Ac 260 ASN cc_start: 0.8892 (t0) cc_final: 0.8566 (t0) REVERT: Ac 271 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7676 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8800 (mt) cc_final: 0.8481 (mt) REVERT: Ac 344 GLU cc_start: 0.8578 (tp30) cc_final: 0.8228 (tp30) REVERT: Ac 358 TYR cc_start: 0.8649 (t80) cc_final: 0.7880 (t80) REVERT: Ad 119 GLN cc_start: 0.8753 (mt0) cc_final: 0.8341 (mt0) REVERT: Ad 164 MET cc_start: 0.8310 (ptp) cc_final: 0.7830 (ppp) REVERT: Ad 177 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9001 (mttm) REVERT: Ad 189 ASN cc_start: 0.7583 (m-40) cc_final: 0.7149 (m-40) REVERT: Ae 140 MET cc_start: 0.8452 (mtp) cc_final: 0.7529 (ttm) REVERT: Af 33 MET cc_start: 0.8508 (mtm) cc_final: 0.8018 (mtt) REVERT: Af 60 MET cc_start: 0.8919 (tpp) cc_final: 0.7913 (mpp) REVERT: Af 86 GLU cc_start: 0.8910 (pm20) cc_final: 0.8647 (pm20) REVERT: Af 106 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8195 (mt-10) REVERT: Ag 29 SER cc_start: 0.8909 (m) cc_final: 0.8449 (t) REVERT: Ag 57 TYR cc_start: 0.8723 (t80) cc_final: 0.8244 (t80) REVERT: Ag 66 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8351 (tm-30) REVERT: Ah 45 ARG cc_start: 0.8049 (ptm160) cc_final: 0.7761 (ptm160) REVERT: Ah 66 THR cc_start: 0.7730 (m) cc_final: 0.7485 (t) REVERT: Aj 23 LEU cc_start: 0.9218 (tp) cc_final: 0.8906 (tp) REVERT: Aj 53 TRP cc_start: 0.8369 (t-100) cc_final: 0.7594 (t-100) REVERT: Ak 23 MET cc_start: 0.7497 (mmt) cc_final: 0.6770 (tpp) REVERT: Ak 32 LEU cc_start: 0.8719 (tt) cc_final: 0.8462 (mp) REVERT: Ak 39 ARG cc_start: 0.7379 (tpt90) cc_final: 0.6669 (ptp-170) outliers start: 137 outliers final: 100 residues processed: 773 average time/residue: 0.1836 time to fit residues: 233.1346 Evaluate side-chains 773 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 659 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 LEU Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 229 MET Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 357 HIS Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 424 VAL Chi-restraints excluded: chain AC residue 27 ILE Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 137 GLN Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 188 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 310 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AD residue 265 GLN Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 34 TRP Chi-restraints excluded: chain Aa residue 49 GLN Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 179 MET Chi-restraints excluded: chain Aa residue 197 LEU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 216 LEU Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 84 ARG Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 169 SER Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 335 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 85 PHE Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Aj residue 8 SER Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 41 optimal weight: 5.9990 chunk 263 optimal weight: 0.0030 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 234 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AC 137 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN Ad 309 HIS Ag 69 GLN ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.119524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090672 restraints weight = 75548.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093716 restraints weight = 36585.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095756 restraints weight = 23658.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.096886 restraints weight = 18020.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.097855 restraints weight = 15365.415| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.558 32218 Z= 0.195 Angle : 0.740 14.348 43733 Z= 0.359 Chirality : 0.045 0.281 4746 Planarity : 0.004 0.057 5552 Dihedral : 8.755 87.875 4583 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.00 % Allowed : 24.01 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3849 helix: 1.19 (0.11), residues: 2054 sheet: -0.08 (0.27), residues: 366 loop : -0.27 (0.18), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARGAH 54 TYR 0.028 0.002 TYRAD 140 PHE 0.033 0.002 PHEAh 70 TRP 0.061 0.002 TRPAC 337 HIS 0.009 0.001 HISAC 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (32203) covalent geometry : angle 0.73969 / 0.36 (43717) SS BOND : bond 0.00624 / 0.32 ( 8) SS BOND : angle 1.94616 / 0.92 ( 16) hydrogen bonds : bond 0.04253 / 2.88 ( 1796) hydrogen bonds : angle 4.79344 / 3.38 ( 5166) Misc. bond : bond 0.30675 / 13.35 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 685 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 74 TRP cc_start: 0.8407 (m100) cc_final: 0.7490 (m-10) REVERT: AA 114 GLU cc_start: 0.8498 (tp30) cc_final: 0.8100 (mm-30) REVERT: AA 131 TYR cc_start: 0.8766 (m-80) cc_final: 0.8267 (m-80) REVERT: AA 240 GLN cc_start: 0.8722 (tp40) cc_final: 0.8298 (tp-100) REVERT: AA 244 ASP cc_start: 0.8343 (m-30) cc_final: 0.8078 (m-30) REVERT: AA 292 GLU cc_start: 0.8431 (pp20) cc_final: 0.8204 (pp20) REVERT: AA 377 MET cc_start: 0.8386 (mmm) cc_final: 0.7688 (mmm) REVERT: AA 385 GLU cc_start: 0.8906 (pm20) cc_final: 0.8208 (pm20) REVERT: AB 180 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8276 (p) REVERT: AB 197 MET cc_start: 0.7846 (mtp) cc_final: 0.7377 (ttm) REVERT: AB 235 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: AC 118 LEU cc_start: 0.9300 (tp) cc_final: 0.8899 (tt) REVERT: AC 137 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6560 (tp40) REVERT: AC 163 TRP cc_start: 0.8950 (t60) cc_final: 0.8107 (t60) REVERT: AC 216 ASP cc_start: 0.8641 (t0) cc_final: 0.8089 (t70) REVERT: AC 246 PHE cc_start: 0.8559 (m-80) cc_final: 0.8293 (m-80) REVERT: AD 96 TRP cc_start: 0.7367 (m100) cc_final: 0.6886 (m100) REVERT: AD 164 MET cc_start: 0.7095 (tmm) cc_final: 0.5691 (tmm) REVERT: AD 212 PHE cc_start: 0.8253 (t80) cc_final: 0.7989 (t80) REVERT: AD 244 MET cc_start: 0.7853 (ttp) cc_final: 0.7364 (ttp) REVERT: AD 265 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7739 (tp40) REVERT: AD 295 MET cc_start: 0.7515 (ptp) cc_final: 0.7243 (ptt) REVERT: AE 113 PHE cc_start: 0.7987 (t80) cc_final: 0.7661 (t80) REVERT: AE 165 MET cc_start: 0.5568 (tpp) cc_final: 0.5153 (tpp) REVERT: AE 167 PHE cc_start: 0.8184 (m-80) cc_final: 0.7733 (m-10) REVERT: AE 231 PHE cc_start: 0.7137 (t80) cc_final: 0.5814 (t80) REVERT: AF 33 MET cc_start: 0.7735 (mmt) cc_final: 0.6883 (mmt) REVERT: AF 40 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7279 (tm-30) REVERT: AG 17 TYR cc_start: 0.8120 (m-80) cc_final: 0.7794 (m-80) REVERT: AG 23 GLU cc_start: 0.8618 (mp0) cc_final: 0.8361 (mp0) REVERT: AG 48 ARG cc_start: 0.8271 (mpt-90) cc_final: 0.7395 (mpt180) REVERT: AG 78 TYR cc_start: 0.7280 (m-80) cc_final: 0.7013 (m-80) REVERT: AH 39 GLU cc_start: 0.9031 (pm20) cc_final: 0.8673 (pp20) REVERT: AH 48 LEU cc_start: 0.8911 (tt) cc_final: 0.8634 (mm) REVERT: AJ 34 ARG cc_start: 0.6270 (mmp80) cc_final: 0.5763 (tpm170) REVERT: AK 24 TRP cc_start: 0.6501 (m100) cc_final: 0.6199 (m100) REVERT: Aa 76 ASP cc_start: 0.8233 (t0) cc_final: 0.7972 (t0) REVERT: Aa 79 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7738 (t) REVERT: Aa 84 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: Aa 149 ASP cc_start: 0.8885 (t0) cc_final: 0.8530 (t0) REVERT: Aa 172 MET cc_start: 0.8511 (ttt) cc_final: 0.8234 (ttt) REVERT: Aa 249 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7559 (m-70) REVERT: Aa 292 GLU cc_start: 0.8441 (pp20) cc_final: 0.8199 (tp30) REVERT: Aa 368 MET cc_start: 0.8936 (mmm) cc_final: 0.8538 (tpt) REVERT: Aa 371 PHE cc_start: 0.9137 (t80) cc_final: 0.8853 (t80) REVERT: Aa 377 MET cc_start: 0.9479 (tpp) cc_final: 0.9124 (mmm) REVERT: Aa 379 LEU cc_start: 0.8721 (mm) cc_final: 0.8325 (tp) REVERT: Aa 435 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8176 (tm-30) REVERT: Aa 440 MET cc_start: 0.8524 (ptp) cc_final: 0.7994 (ptp) REVERT: Aa 445 CYS cc_start: 0.8525 (m) cc_final: 0.7270 (t) REVERT: Aa 473 SER cc_start: 0.8498 (m) cc_final: 0.8241 (p) REVERT: Ab 82 LEU cc_start: 0.9086 (tp) cc_final: 0.8846 (tp) REVERT: Ab 84 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7269 (ttp-110) REVERT: Ab 172 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7721 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8892 (tp) cc_final: 0.8514 (tp) REVERT: Ab 199 LYS cc_start: 0.8427 (tttm) cc_final: 0.8037 (tttm) REVERT: Ab 311 GLN cc_start: 0.7634 (mt0) cc_final: 0.7305 (mm-40) REVERT: Ab 377 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8606 (ttmm) REVERT: Ab 390 GLU cc_start: 0.8909 (pp20) cc_final: 0.8367 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8688 (tp30) cc_final: 0.8201 (tp30) REVERT: Ac 12 LYS cc_start: 0.8045 (tmtt) cc_final: 0.7490 (mptt) REVERT: Ac 121 PHE cc_start: 0.8836 (m-80) cc_final: 0.8599 (m-10) REVERT: Ac 165 TRP cc_start: 0.7553 (OUTLIER) cc_final: 0.7167 (m-10) REVERT: Ac 202 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8343 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8759 (t0) cc_final: 0.8366 (t0) REVERT: Ac 260 ASN cc_start: 0.8892 (t0) cc_final: 0.8585 (t0) REVERT: Ac 271 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7677 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8817 (mt) cc_final: 0.8498 (mt) REVERT: Ac 344 GLU cc_start: 0.8555 (tp30) cc_final: 0.8217 (tp30) REVERT: Ac 358 TYR cc_start: 0.8705 (t80) cc_final: 0.7954 (t80) REVERT: Ad 119 GLN cc_start: 0.8777 (mt0) cc_final: 0.8365 (mt0) REVERT: Ad 164 MET cc_start: 0.8342 (ptp) cc_final: 0.7842 (ppp) REVERT: Ad 177 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8980 (mttm) REVERT: Ad 189 ASN cc_start: 0.7428 (m-40) cc_final: 0.6938 (m-40) REVERT: Ad 295 MET cc_start: 0.7615 (mmp) cc_final: 0.7391 (mmp) REVERT: Ae 140 MET cc_start: 0.8520 (mtp) cc_final: 0.7576 (ttm) REVERT: Af 33 MET cc_start: 0.8537 (mtm) cc_final: 0.8053 (mtt) REVERT: Af 60 MET cc_start: 0.8930 (tpp) cc_final: 0.7920 (mpp) REVERT: Af 86 GLU cc_start: 0.8922 (pm20) cc_final: 0.8648 (pm20) REVERT: Af 106 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8247 (mt-10) REVERT: Ag 29 SER cc_start: 0.8925 (m) cc_final: 0.8459 (t) REVERT: Ag 57 TYR cc_start: 0.8729 (t80) cc_final: 0.8197 (t80) REVERT: Ag 66 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8354 (tm-30) REVERT: Ah 45 ARG cc_start: 0.8104 (ptm160) cc_final: 0.7785 (ptm160) REVERT: Aj 53 TRP cc_start: 0.8366 (t-100) cc_final: 0.7647 (t-100) REVERT: Ak 32 LEU cc_start: 0.8723 (tt) cc_final: 0.8489 (mp) REVERT: Ak 39 ARG cc_start: 0.7340 (tpt90) cc_final: 0.6619 (ptp-170) outliers start: 132 outliers final: 101 residues processed: 753 average time/residue: 0.1803 time to fit residues: 223.5355 Evaluate side-chains 769 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 656 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 220 LEU Chi-restraints excluded: chain AA residue 229 MET Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 357 HIS Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 424 VAL Chi-restraints excluded: chain AC residue 27 ILE Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 137 GLN Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 188 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 310 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AD residue 265 GLN Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AE residue 87 ASP Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 179 MET Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 84 ARG Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 169 SER Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 53 MET Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 323 ILE Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 335 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ac residue 376 MET Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 8 SER Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 214 optimal weight: 0.4980 chunk 377 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 287 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 103 optimal weight: 0.0060 chunk 345 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 137 GLN AC 196 HIS AC 331 ASN ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 37 GLN ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.122028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.093313 restraints weight = 74784.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096441 restraints weight = 35893.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098569 restraints weight = 23011.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.099940 restraints weight = 17403.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100645 restraints weight = 14575.805| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.7324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.413 32218 Z= 0.140 Angle : 0.718 15.505 43733 Z= 0.348 Chirality : 0.044 0.277 4746 Planarity : 0.004 0.056 5552 Dihedral : 8.612 89.197 4583 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.33 % Allowed : 25.07 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3849 helix: 1.24 (0.11), residues: 2047 sheet: 0.03 (0.27), residues: 366 loop : -0.23 (0.18), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARGAE 248 TYR 0.021 0.001 TYRAE 235 PHE 0.054 0.002 PHEAh 70 TRP 0.063 0.002 TRPAC 337 HIS 0.010 0.001 HISAC 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (32203) covalent geometry : angle 0.71767 / 0.35 (43717) SS BOND : bond 0.00591 / 0.30 ( 8) SS BOND : angle 1.80354 / 0.91 ( 16) hydrogen bonds : bond 0.04032 / 2.72 ( 1796) hydrogen bonds : angle 4.70640 / 3.32 ( 5166) Misc. bond : bond 0.23609 / 10.38 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 701 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 74 TRP cc_start: 0.8316 (m100) cc_final: 0.7277 (m-10) REVERT: AA 114 GLU cc_start: 0.8356 (tp30) cc_final: 0.8089 (mt-10) REVERT: AA 131 TYR cc_start: 0.8748 (m-80) cc_final: 0.8261 (m-80) REVERT: AA 140 LEU cc_start: 0.7787 (mt) cc_final: 0.7434 (mt) REVERT: AA 240 GLN cc_start: 0.8658 (tp40) cc_final: 0.8376 (tp-100) REVERT: AA 377 MET cc_start: 0.8271 (mmm) cc_final: 0.7693 (mmm) REVERT: AA 385 GLU cc_start: 0.8858 (pm20) cc_final: 0.8134 (pm20) REVERT: AB 180 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8175 (p) REVERT: AB 197 MET cc_start: 0.7809 (mtp) cc_final: 0.7295 (ttm) REVERT: AB 235 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: AB 384 MET cc_start: 0.8751 (mtm) cc_final: 0.8530 (ptm) REVERT: AC 36 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7982 (mp) REVERT: AC 118 LEU cc_start: 0.9276 (tp) cc_final: 0.8905 (tt) REVERT: AC 123 VAL cc_start: 0.9237 (t) cc_final: 0.9005 (p) REVERT: AC 137 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6612 (tp40) REVERT: AC 163 TRP cc_start: 0.8923 (t60) cc_final: 0.8000 (t60) REVERT: AC 183 PHE cc_start: 0.8631 (t80) cc_final: 0.8423 (t80) REVERT: AC 216 ASP cc_start: 0.8551 (t0) cc_final: 0.8055 (t70) REVERT: AC 246 PHE cc_start: 0.8530 (m-80) cc_final: 0.8289 (m-80) REVERT: AD 96 TRP cc_start: 0.7278 (m100) cc_final: 0.6877 (m100) REVERT: AD 101 LEU cc_start: 0.8604 (tp) cc_final: 0.8223 (mp) REVERT: AD 119 GLN cc_start: 0.8285 (mm110) cc_final: 0.8043 (mm-40) REVERT: AD 164 MET cc_start: 0.7112 (tmm) cc_final: 0.6591 (tmm) REVERT: AD 212 PHE cc_start: 0.8335 (t80) cc_final: 0.7694 (t80) REVERT: AD 244 MET cc_start: 0.7857 (ttp) cc_final: 0.7245 (ttp) REVERT: AD 265 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7707 (tp40) REVERT: AE 113 PHE cc_start: 0.7910 (t80) cc_final: 0.7602 (t80) REVERT: AE 165 MET cc_start: 0.5289 (tpp) cc_final: 0.5045 (tpp) REVERT: AE 167 PHE cc_start: 0.8149 (m-80) cc_final: 0.7697 (m-10) REVERT: AE 231 PHE cc_start: 0.7149 (t80) cc_final: 0.5841 (t80) REVERT: AF 33 MET cc_start: 0.7742 (mmt) cc_final: 0.6873 (mmt) REVERT: AG 17 TYR cc_start: 0.7999 (m-80) cc_final: 0.7785 (m-80) REVERT: AG 23 GLU cc_start: 0.8641 (mp0) cc_final: 0.8369 (mp0) REVERT: AG 48 ARG cc_start: 0.8212 (mpt-90) cc_final: 0.7389 (mpt180) REVERT: AG 78 TYR cc_start: 0.7490 (m-80) cc_final: 0.7137 (m-80) REVERT: AH 39 GLU cc_start: 0.9065 (pm20) cc_final: 0.8848 (pp20) REVERT: AH 48 LEU cc_start: 0.8812 (tt) cc_final: 0.8579 (mm) REVERT: AJ 15 PHE cc_start: 0.7443 (m-80) cc_final: 0.7128 (m-80) REVERT: AJ 34 ARG cc_start: 0.6394 (mmp80) cc_final: 0.5919 (tpm170) REVERT: AK 24 TRP cc_start: 0.6577 (m100) cc_final: 0.6290 (m100) REVERT: Aa 76 ASP cc_start: 0.8169 (t0) cc_final: 0.7915 (t0) REVERT: Aa 79 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7506 (t) REVERT: Aa 84 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: Aa 149 ASP cc_start: 0.8809 (t0) cc_final: 0.8421 (t0) REVERT: Aa 172 MET cc_start: 0.8437 (ttt) cc_final: 0.8173 (ttt) REVERT: Aa 199 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: Aa 249 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7403 (m-70) REVERT: Aa 292 GLU cc_start: 0.8391 (pp20) cc_final: 0.8152 (tp30) REVERT: Aa 377 MET cc_start: 0.9458 (tpp) cc_final: 0.9139 (mmm) REVERT: Aa 379 LEU cc_start: 0.8618 (mm) cc_final: 0.8304 (tp) REVERT: Aa 435 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8157 (tm-30) REVERT: Aa 440 MET cc_start: 0.8467 (ptp) cc_final: 0.7939 (ptp) REVERT: Aa 445 CYS cc_start: 0.8521 (m) cc_final: 0.7221 (t) REVERT: Aa 473 SER cc_start: 0.8479 (m) cc_final: 0.8212 (p) REVERT: Ab 82 LEU cc_start: 0.8978 (tp) cc_final: 0.8756 (tp) REVERT: Ab 84 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7238 (ttp-110) REVERT: Ab 172 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7672 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8619 (tp) cc_final: 0.8280 (tp) REVERT: Ab 199 LYS cc_start: 0.8384 (tttm) cc_final: 0.8004 (mttt) REVERT: Ab 311 GLN cc_start: 0.7695 (mt0) cc_final: 0.7226 (mm-40) REVERT: Ab 390 GLU cc_start: 0.8928 (pp20) cc_final: 0.8353 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8709 (tp30) cc_final: 0.8330 (tp30) REVERT: Ac 12 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7591 (mptt) REVERT: Ac 121 PHE cc_start: 0.8756 (m-80) cc_final: 0.8494 (m-10) REVERT: Ac 165 TRP cc_start: 0.7269 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: Ac 202 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8309 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8667 (t0) cc_final: 0.8329 (t0) REVERT: Ac 260 ASN cc_start: 0.8899 (t0) cc_final: 0.8598 (t0) REVERT: Ac 271 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7563 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8639 (mt) cc_final: 0.8326 (mt) REVERT: Ac 312 GLN cc_start: 0.8829 (mt0) cc_final: 0.8314 (mt0) REVERT: Ac 316 MET cc_start: 0.8802 (tpp) cc_final: 0.8436 (tpp) REVERT: Ac 344 GLU cc_start: 0.8530 (tp30) cc_final: 0.8197 (tp30) REVERT: Ac 358 TYR cc_start: 0.8609 (t80) cc_final: 0.7838 (t80) REVERT: Ad 119 GLN cc_start: 0.8700 (mt0) cc_final: 0.8298 (mt0) REVERT: Ad 164 MET cc_start: 0.8155 (ptp) cc_final: 0.7751 (ppp) REVERT: Ad 166 MET cc_start: 0.7457 (mmm) cc_final: 0.6940 (mmm) REVERT: Ad 189 ASN cc_start: 0.7501 (m-40) cc_final: 0.7043 (m-40) REVERT: Ad 236 TYR cc_start: 0.8792 (m-80) cc_final: 0.8514 (m-10) REVERT: Ad 273 PHE cc_start: 0.9173 (t80) cc_final: 0.8967 (t80) REVERT: Ae 140 MET cc_start: 0.8418 (mtp) cc_final: 0.7390 (ttm) REVERT: Af 33 MET cc_start: 0.8485 (mtm) cc_final: 0.8055 (mtt) REVERT: Af 60 MET cc_start: 0.8877 (tpp) cc_final: 0.7845 (mpp) REVERT: Af 106 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8167 (mt-10) REVERT: Ag 12 ARG cc_start: 0.8293 (mmm160) cc_final: 0.7999 (mmm160) REVERT: Ag 29 SER cc_start: 0.8881 (m) cc_final: 0.8479 (t) REVERT: Ag 57 TYR cc_start: 0.8712 (t80) cc_final: 0.8195 (t80) REVERT: Ag 66 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8459 (tm-30) REVERT: Ah 26 ASP cc_start: 0.8252 (m-30) cc_final: 0.7906 (t70) REVERT: Ah 45 ARG cc_start: 0.8098 (ptm160) cc_final: 0.7841 (ptm160) REVERT: Aj 53 TRP cc_start: 0.8285 (t-100) cc_final: 0.7513 (t-100) REVERT: Ak 23 MET cc_start: 0.7461 (mmt) cc_final: 0.6756 (tpp) REVERT: Ak 32 LEU cc_start: 0.8671 (tt) cc_final: 0.8429 (mp) REVERT: Ak 39 ARG cc_start: 0.7130 (tpt90) cc_final: 0.6433 (ptp-170) outliers start: 110 outliers final: 78 residues processed: 757 average time/residue: 0.1834 time to fit residues: 228.3288 Evaluate side-chains 760 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 670 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 229 MET Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 424 VAL Chi-restraints excluded: chain AC residue 27 ILE Chi-restraints excluded: chain AC residue 36 LEU Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 137 GLN Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 188 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 310 SER Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AD residue 265 GLN Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AG residue 11 ILE Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain AK residue 34 TRP Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 179 MET Chi-restraints excluded: chain Aa residue 182 VAL Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 237 VAL Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 84 ARG Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Aj residue 8 SER Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 176 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 302 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 137 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 49 GLN Aa 393 ASN Aa 434 GLN Ac 207 ASN Ac 352 GLN Ad 309 HIS ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.089339 restraints weight = 76416.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092400 restraints weight = 37430.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094446 restraints weight = 24266.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095692 restraints weight = 18513.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096357 restraints weight = 15682.348| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.614 32218 Z= 0.231 Angle : 0.781 15.593 43733 Z= 0.380 Chirality : 0.047 0.366 4746 Planarity : 0.005 0.061 5552 Dihedral : 8.809 88.708 4583 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.55 % Allowed : 24.73 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3849 helix: 1.14 (0.11), residues: 2051 sheet: -0.06 (0.27), residues: 366 loop : -0.33 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARGAH 54 TYR 0.028 0.002 TYRAf 21 PHE 0.052 0.002 PHEAh 70 TRP 0.062 0.002 TRPAC 337 HIS 0.011 0.001 HISAc 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (32203) covalent geometry : angle 0.78055 / 0.38 (43717) SS BOND : bond 0.00608 / 0.32 ( 8) SS BOND : angle 1.69883 / 0.84 ( 16) hydrogen bonds : bond 0.04383 / 2.96 ( 1796) hydrogen bonds : angle 4.89057 / 3.44 ( 5166) Misc. bond : bond 0.32718 / 14.54 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8044.79 seconds wall clock time: 138 minutes 59.29 seconds (8339.29 seconds total)