Starting phenix.real_space_refine on Sun Jul 5 21:07:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibg_35343/07_2026/8ibg_35343_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibg_35343/07_2026/8ibg_35343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ibg_35343/07_2026/8ibg_35343_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibg_35343/07_2026/8ibg_35343_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ibg_35343/07_2026/8ibg_35343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibg_35343/07_2026/8ibg_35343.map" } resolution = 3.8 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= 0.053 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 151 5.16 5 C 19524 2.51 5 N 5165 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s 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: 30396 Number of models: 1 Model: "" Number of chains: 28 Chain: "AA" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3077 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 15, 'TRANS': 379} Chain breaks: 2 Chain: "AB" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3137 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} 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: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1878 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 22, 'TRANS': 213} Chain: "AE" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 830 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 3 Chain: "AF" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 855 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 200 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "AJ" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "AK" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 118 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "Aa" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3076 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain breaks: 3 Chain: "Ab" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3137 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} 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: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1903 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} 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: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 622 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "Ah" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 512 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 1 Chain: "Ai" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 204 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "Aj" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 345 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Ak" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "AC" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 15 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: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "Ac" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PE': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 76 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: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PH': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "Ag" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 115 Time building chain proxies: 6.06, per 1000 atoms: 0.20 Number of scatterers: 30396 At special positions: 0 Unit cell: (145.2, 144.1, 169.4, 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 151 16.00 P 8 15.00 O 5542 8.00 N 5165 7.00 C 19524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYSAA 338 " - pdb=" SG CYSAA 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 222 " - pdb=" SG CYSAE 238 " distance=2.05 Simple disulfide: pdb=" SG CYSAH 51 " - pdb=" SG CYSAH 65 " distance=2.02 Simple disulfide: pdb=" SG CYSAa 338 " - pdb=" SG CYSAa 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAe 222 " - pdb=" SG CYSAe 238 " distance=2.05 Simple disulfide: pdb=" SG CYSAh 35 " - pdb=" SG CYSAh 79 " distance=1.85 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7060 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 14 sheets defined 58.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 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: 3.566A pdb=" N GLUAA 145 " --> pdb=" O PROAA 141 " (cutoff:3.500A) Processing helix chain 'AA' and resid 157 through 176 removed outlier: 3.716A pdb=" N ASPAA 176 " --> pdb=" O METAA 172 " (cutoff:3.500A) Processing helix chain 'AA' and resid 178 through 192 removed outlier: 3.811A pdb=" N ALAAA 189 " --> pdb=" O ASPAA 185 " (cutoff:3.500A) Processing helix chain 'AA' and resid 195 through 199 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 380 Processing helix chain 'AA' and resid 384 through 397 Processing helix chain 'AA' and resid 401 through 404 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 473 Processing helix chain 'AB' and resid 68 through 72 removed outlier: 3.542A 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: 4.714A pdb=" N SERAB 156 " --> pdb=" O ALAAB 152 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLNAB 157 " --> pdb=" O ALAAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 168 through 182 removed outlier: 3.931A 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 293 removed outlier: 3.829A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 307 through 317 removed outlier: 3.563A pdb=" N ALAAB 314 " --> pdb=" O SERAB 310 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYSAB 315 " --> pdb=" O GLNAB 311 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLYAB 316 " --> pdb=" O SERAB 312 " (cutoff:3.500A) 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: 3.607A pdb=" N ILEAC 14 " --> pdb=" O LEUAC 10 " (cutoff:3.500A) Processing helix chain 'AC' and resid 29 through 31 No H-bonds generated for 'chain 'AC' and resid 29 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: 3.577A 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: 3.508A pdb=" N LEUAC 150 " --> pdb=" O ILEAC 146 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SERAC 151 " --> pdb=" O THRAC 147 " (cutoff:3.500A) removed outlier: 3.764A 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: 3.552A 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 Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 284 removed outlier: 4.428A pdb=" N PHEAC 276 " --> pdb=" O TRPAC 272 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALAAC 277 " --> pdb=" O TYRAC 273 " (cutoff:3.500A) Processing helix chain 'AC' and resid 286 through 304 removed outlier: 3.506A 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: 4.282A 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: 3.759A 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 106 through 120 Processing helix chain 'AD' and resid 121 through 124 Processing helix chain 'AD' and resid 131 through 136 Processing helix chain 'AD' and resid 141 through 151 Processing helix chain 'AD' and resid 181 through 188 Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 206 through 216 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: 3.866A pdb=" N VALAD 313 " --> pdb=" O HISAD 309 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEUAD 314 " --> pdb=" O LYSAD 310 " (cutoff:3.500A) Processing helix chain 'AE' and resid 108 through 139 Processing helix chain 'AE' and resid 168 through 172 Processing helix chain 'AF' and resid 15 through 26 Processing helix chain 'AF' and resid 26 through 31 removed outlier: 3.501A pdb=" N LEUAF 30 " --> pdb=" O GLYAF 26 " (cutoff:3.500A) Processing helix chain 'AF' and resid 33 through 38 removed outlier: 3.668A pdb=" N THRAF 37 " --> pdb=" O METAF 33 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEUAF 38 " --> pdb=" O ARGAF 34 " (cutoff:3.500A) No H-bonds generated for '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 90 through 110 removed outlier: 4.160A pdb=" N TYRAF 94 " --> pdb=" O TYRAF 90 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLUAF 97 " --> pdb=" O PROAF 93 " (cutoff:3.500A) Processing helix chain 'AG' and resid 33 through 72 removed outlier: 3.985A pdb=" N ASNAG 37 " --> pdb=" O LYSAG 33 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARGAG 48 " --> pdb=" O GLUAG 44 " (cutoff:3.500A) Proline residue: AG 51 - end of helix removed outlier: 3.535A pdb=" N LEUAG 58 " --> pdb=" O VALAG 54 " (cutoff:3.500A) Processing helix chain 'AH' and resid 26 through 38 Processing helix chain 'AH' and resid 38 through 58 removed outlier: 3.631A pdb=" N ARGAH 58 " --> pdb=" O ARGAH 54 " (cutoff:3.500A) Processing helix chain 'AH' and resid 65 through 84 Processing helix chain 'AJ' and resid 18 through 37 removed outlier: 3.843A pdb=" N ARGAJ 34 " --> pdb=" O LEUAJ 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 22 through 37 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 117 Processing helix chain 'Aa' and resid 139 through 152 removed outlier: 3.535A pdb=" N GLUAa 145 " --> pdb=" O PROAa 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEUAa 147 " --> pdb=" O VALAa 143 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 161 through 176 removed outlier: 3.717A 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 397 Processing helix chain 'Aa' and resid 401 through 404 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 Processing helix chain 'Ab' and resid 78 through 86 Processing helix chain 'Ab' and resid 95 through 107 Processing helix chain 'Ab' and resid 129 through 143 Processing helix chain 'Ab' and resid 147 through 165 removed outlier: 4.667A pdb=" N SERAb 156 " --> pdb=" O ALAAb 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLNAb 157 " --> pdb=" O ALAAb 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILEAb 160 " --> pdb=" O SERAb 156 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 168 through 182 removed outlier: 3.895A 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 238 removed outlier: 5.188A pdb=" N GLNAb 236 " --> pdb=" O GLNAb 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHEAb 237 " --> pdb=" O VALAb 233 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 239 through 241 No H-bonds generated for 'chain 'Ab' and resid 239 through 241' Processing helix chain 'Ab' and resid 280 through 294 removed outlier: 3.829A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 307 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: 3.609A 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: 3.578A 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: 3.508A pdb=" N LEUAc 150 " --> pdb=" O ILEAc 146 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.550A 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: 4.575A 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 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 removed outlier: 3.502A pdb=" N TYRAc 278 " --> pdb=" O PHEAc 274 " (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: 4.600A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 307 No H-bonds generated for 'chain 'Ac' and resid 305 through 307' 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 378 Processing helix chain 'Ad' and resid 106 through 120 Processing helix chain 'Ad' and resid 121 through 124 Processing helix chain 'Ad' and resid 131 through 136 Processing helix chain 'Ad' and resid 141 through 152 Processing helix chain 'Ad' and resid 181 through 189 removed outlier: 3.568A pdb=" N ARGAd 186 " --> pdb=" O PROAd 182 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 199 through 204 Processing helix chain 'Ad' and resid 206 through 217 Processing helix chain 'Ad' and resid 237 through 241 removed outlier: 3.623A 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 313 Proline residue: Ad 301 - end of helix removed outlier: 4.503A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 314 through 316 No H-bonds generated for 'chain 'Ad' and resid 314 through 316' Processing helix chain 'Ae' and resid 104 through 140 removed outlier: 4.376A pdb=" N ALAAe 109 " --> pdb=" O GLUAe 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N METAe 140 " --> pdb=" O PHEAe 136 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 149 Processing helix chain 'Ae' and resid 155 through 159 removed outlier: 3.513A pdb=" N ASPAe 158 " --> pdb=" O LYSAe 155 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILEAe 159 " --> pdb=" O LEUAe 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 155 through 159' 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 removed outlier: 3.721A pdb=" N GLYAf 26 " --> pdb=" O TYRAf 22 " (cutoff:3.500A) Processing helix chain 'Af' and resid 34 through 38 removed outlier: 3.686A 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: 4.178A 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: 3.851A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 4.959A pdb=" N LEUAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) removed outlier: 5.655A 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 37 removed outlier: 3.526A pdb=" N THRAh 30 " --> pdb=" O ASPAh 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLUAh 33 " --> pdb=" O THRAh 29 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 38 through 54 Processing helix chain 'Ah' and resid 64 through 84 removed outlier: 4.350A pdb=" N GLUAh 68 " --> pdb=" O ASPAh 64 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHEAh 70 " --> pdb=" O THRAh 66 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHEAh 72 " --> pdb=" O GLUAh 68 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAh 75 " --> pdb=" O ASPAh 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYSAh 83 " --> pdb=" O CYSAh 79 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 9 through 15 Processing helix chain 'Aj' and resid 17 through 48 removed outlier: 4.276A pdb=" N ARGAj 34 " --> pdb=" O LEUAj 30 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 37 Proline residue: Ak 19 - end of helix Processing sheet with id=AA1, first strand: chain 'AA' and resid 49 through 52 removed outlier: 3.536A pdb=" N SERAA 51 " --> pdb=" O VALAA 59 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARGAA 58 " --> pdb=" O LEUAA 231 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALAAA 233 " --> pdb=" O ARGAA 58 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALAAA 60 " --> pdb=" O ALAAA 233 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLYAA 235 " --> pdb=" O ALAAA 60 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLUAA 62 " --> pdb=" O GLYAA 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 342 through 348 removed outlier: 3.546A pdb=" N ARGAA 276 " --> pdb=" O SERAG 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SERAG 16 " --> pdb=" O ARGAA 276 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARGAA 278 " --> pdb=" O VALAG 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 39 through 42 removed outlier: 6.529A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARGAI 77 " --> pdb=" O VALAI 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.737A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.549A 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 'AE' and resid 163 through 165 Processing sheet with id=AA7, first strand: chain 'AE' and resid 225 through 226 removed outlier: 6.660A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Aa' and resid 50 through 52 removed outlier: 6.418A pdb=" N ARGAa 58 " --> pdb=" O LEUAa 231 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALAAa 233 " --> pdb=" O ARGAa 58 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALAAa 60 " --> pdb=" O ALAAa 233 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLYAa 235 " --> pdb=" O ALAAa 60 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLUAa 62 " --> pdb=" O GLYAa 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Aa' and resid 342 through 348 Processing sheet with id=AB1, first strand: chain 'Ab' and resid 41 through 42 removed outlier: 6.311A pdb=" N VALAb 48 " --> pdb=" O LEUAb 220 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLYAb 222 " --> pdb=" O VALAb 48 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALAAb 50 " --> pdb=" O GLYAb 222 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALAi 68 " --> pdb=" O VALAb 112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARGAi 77 " --> pdb=" O VALAi 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ab' and resid 256 through 261 removed outlier: 6.893A pdb=" N GLYAb 256 " --> pdb=" O METAb 438 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ALAAb 440 " --> pdb=" O GLYAb 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILEAb 258 " --> pdb=" O ALAAb 440 " (cutoff:3.500A) removed outlier: 8.546A 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: 3.638A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ac' and resid 23 through 24 Processing sheet with id=AB4, first strand: chain 'Ae' and resid 174 through 175 Processing sheet with id=AB5, first strand: chain 'Ae' and resid 225 through 226 1735 hydrogen bonds defined for protein. 4980 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: 5.97 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 10061 1.37 - 1.55: 20761 1.55 - 1.74: 39 1.74 - 1.93: 255 1.93 - 2.11: 21 Bond restraints: 31137 Sorted by residual: bond pdb=" C ASPAI 44 " pdb=" N VALAI 45 " ideal model delta sigma weight residual 1.332 1.517 -0.186 9.20e-03 1.18e+04 4.07e+02 bond pdb=" C ASPAi 44 " pdb=" N VALAi 45 " ideal model delta sigma weight residual 1.332 1.516 -0.184 9.20e-03 1.18e+04 3.99e+02 bond pdb=" N PROAd 221 " pdb=" CD PROAd 221 " ideal model delta sigma weight residual 1.473 1.732 -0.259 1.40e-02 5.10e+03 3.43e+02 bond pdb=" C VALAi 45 " pdb=" N LYSAi 46 " ideal model delta sigma weight residual 1.331 1.533 -0.203 1.29e-02 6.01e+03 2.47e+02 bond pdb=" C VALAI 45 " pdb=" N LYSAI 46 " ideal model delta sigma weight residual 1.329 1.532 -0.203 1.40e-02 5.10e+03 2.10e+02 ... (remaining 31132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 40670 3.21 - 6.43: 1313 6.43 - 9.64: 224 9.64 - 12.85: 36 12.85 - 16.07: 9 Bond angle restraints: 42252 Sorted by residual: angle pdb=" CA ASPAI 44 " pdb=" C ASPAI 44 " pdb=" N VALAI 45 " ideal model delta sigma weight residual 119.52 106.97 12.55 7.90e-01 1.60e+00 2.52e+02 angle pdb=" N ILEAC 115 " pdb=" CA ILEAC 115 " pdb=" C ILEAC 115 " ideal model delta sigma weight residual 110.62 99.16 11.46 1.02e+00 9.61e-01 1.26e+02 angle pdb=" N TRPAk 38 " pdb=" CA TRPAk 38 " pdb=" C TRPAk 38 " ideal model delta sigma weight residual 110.24 126.05 -15.81 1.47e+00 4.63e-01 1.16e+02 angle pdb=" N ASNAb 303 " pdb=" CA ASNAb 303 " pdb=" C ASNAb 303 " ideal model delta sigma weight residual 112.88 100.17 12.71 1.29e+00 6.01e-01 9.71e+01 angle pdb=" N THRAb 306 " pdb=" CA THRAb 306 " pdb=" C THRAb 306 " ideal model delta sigma weight residual 111.33 123.22 -11.89 1.21e+00 6.83e-01 9.66e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.38: 17857 25.38 - 50.75: 526 50.75 - 76.13: 82 76.13 - 101.50: 28 101.50 - 126.88: 1 Dihedral angle restraints: 18494 sinusoidal: 7526 harmonic: 10968 Sorted by residual: dihedral pdb=" CB CYSAh 35 " pdb=" SG CYSAh 35 " pdb=" SG CYSAh 79 " pdb=" CB CYSAh 79 " ideal model delta sinusoidal sigma weight residual 93.00 176.19 -83.19 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYSAH 51 " pdb=" SG CYSAH 51 " pdb=" SG CYSAH 65 " pdb=" CB CYSAH 65 " ideal model delta sinusoidal sigma weight residual 93.00 154.47 -61.47 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" N ARGAk 39 " pdb=" C ARGAk 39 " pdb=" CA ARGAk 39 " pdb=" CB ARGAk 39 " ideal model delta harmonic sigma weight residual 122.80 139.73 -16.93 0 2.50e+00 1.60e-01 4.59e+01 ... (remaining 18491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 4341 0.119 - 0.238: 217 0.238 - 0.358: 28 0.358 - 0.477: 3 0.477 - 0.596: 1 Chirality restraints: 4590 Sorted by residual: chirality pdb=" CA ARGAk 39 " pdb=" N ARGAk 39 " pdb=" C ARGAk 39 " pdb=" CB ARGAk 39 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA GLUAa 47 " pdb=" N GLUAa 47 " pdb=" C GLUAa 47 " pdb=" CB GLUAa 47 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA HISAe 200 " pdb=" N HISAe 200 " pdb=" C HISAe 200 " pdb=" CB HISAe 200 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 4587 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10Ac 404 " -0.018 2.00e-02 2.50e+03 2.41e-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 " 0.061 2.00e-02 2.50e+03 pdb=" C5 U10Ac 404 " -0.087 2.00e-02 2.50e+03 pdb=" C6 U10Ac 404 " 0.088 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 " -0.526 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 U10Ac 404 " 0.319 2.00e-02 2.50e+03 2.72e-01 9.25e+02 pdb=" C13 U10Ac 404 " -0.472 2.00e-02 2.50e+03 pdb=" C14 U10Ac 404 " -0.097 2.00e-02 2.50e+03 pdb=" C15 U10Ac 404 " 0.074 2.00e-02 2.50e+03 pdb=" C16 U10Ac 404 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10Ac 404 " 0.192 2.00e-02 2.50e+03 2.56e-01 8.20e+02 pdb=" C11 U10Ac 404 " 0.035 2.00e-02 2.50e+03 pdb=" C7 U10Ac 404 " 0.303 2.00e-02 2.50e+03 pdb=" C8 U10Ac 404 " -0.435 2.00e-02 2.50e+03 pdb=" C9 U10Ac 404 " -0.095 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 671 2.61 - 3.19: 31455 3.19 - 3.76: 51879 3.76 - 4.33: 73863 4.33 - 4.90: 112625 Nonbonded interactions: 270493 Sorted by model distance: nonbonded pdb=" OG1 THRAa 68 " pdb=" OE1 GLUAb 387 " model vdw 2.042 3.040 nonbonded pdb=" N LEUAa 120 " pdb=" O HISAb 298 " model vdw 2.043 3.120 nonbonded pdb=" NE2 HISAC 83 " pdb="FE HEMAC 401 " model vdw 2.062 3.080 nonbonded pdb=" O PROAC 266 " pdb=" CB PROAe 237 " model vdw 2.065 3.440 nonbonded pdb=" O METAE 140 " pdb=" NH2 ARGAc 177 " model vdw 2.069 3.120 ... (remaining 270488 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 45 through 156 or resid 160 through 253 or resid 267 thro \ ugh 476)) selection = (chain 'Aa' and resid 45 through 476) } ncs_group { reference = chain 'AB' selection = chain 'Ab' } ncs_group { reference = (chain 'AC' and resid 8 through 402) selection = (chain 'Ac' and resid 8 through 402) } ncs_group { reference = chain 'AD' selection = (chain 'Ad' and resid 89 through 401) } ncs_group { reference = chain 'AF' selection = (chain 'Af' and resid 14 through 110) } ncs_group { reference = (chain 'AG' and resid 4 through 77) selection = (chain 'Ag' and resid 4 through 77) } ncs_group { reference = (chain 'AH' and (resid 25 through 56 or resid 61 through 88)) selection = (chain 'Ah' and resid 25 through 88) } ncs_group { reference = (chain 'AI' and resid 42 through 78) selection = (chain 'Ai' and (resid 42 through 46 or resid 57 through 78)) } 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: 3.510 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.350 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 0.288 31150 Z= 0.659 Angle : 1.375 46.163 42266 Z= 0.893 Chirality : 0.061 0.596 4590 Planarity : 0.009 0.272 5364 Dihedral : 12.615 126.878 11413 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 41.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 0.41 % Allowed : 2.82 % Favored : 96.77 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.12 % 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: -2.01 (0.12), residues: 3721 helix: -1.09 (0.10), residues: 1960 sheet: -0.59 (0.27), residues: 362 loop : -1.70 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAE 250 TYR 0.049 0.002 TYRAE 235 PHE 0.049 0.002 PHEAc 183 TRP 0.021 0.002 TRPAC 141 HIS 0.015 0.001 HISAe 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00982 / 0.65 (31137) covalent geometry : angle 1.35171 / 0.89 (42252) SS BOND : bond 0.07077 / 2.31 ( 7) SS BOND : angle 13.96925 / 10.65 ( 14) hydrogen bonds : bond 0.20000 / 13.32 ( 1735) hydrogen bonds : angle 7.90660 / 5.60 ( 4980) Misc. bond : bond 0.15350 / 7.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1312 time to evaluate : 1.080 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 358 PHE cc_start: 0.9001 (p90) cc_final: 0.8669 (p90) REVERT: AA 440 MET cc_start: 0.7721 (ptp) cc_final: 0.7430 (ptp) REVERT: AB 69 SER cc_start: 0.7927 (p) cc_final: 0.7695 (t) REVERT: AB 172 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7684 (ttm-80) REVERT: AB 231 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8420 (mtpt) REVERT: AB 309 LEU cc_start: 0.7562 (mt) cc_final: 0.7256 (mt) REVERT: AB 438 MET cc_start: 0.8679 (ttt) cc_final: 0.8400 (ttt) REVERT: AB 443 ASN cc_start: 0.7970 (t0) cc_final: 0.7770 (m-40) REVERT: AC 35 SER cc_start: 0.8194 (p) cc_final: 0.7851 (p) REVERT: AC 121 PHE cc_start: 0.7608 (m-80) cc_final: 0.7351 (m-80) REVERT: AC 240 MET cc_start: 0.8212 (mmm) cc_final: 0.7886 (mmt) REVERT: AC 294 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7952 (tt) REVERT: AC 343 VAL cc_start: 0.7823 (t) cc_final: 0.7478 (m) REVERT: AC 347 PHE cc_start: 0.7321 (m-80) cc_final: 0.6969 (m-10) REVERT: AF 43 ASP cc_start: 0.8526 (m-30) cc_final: 0.8299 (m-30) REVERT: AF 89 PHE cc_start: 0.7848 (m-10) cc_final: 0.7310 (m-80) REVERT: AG 60 TYR cc_start: 0.7824 (t80) cc_final: 0.7589 (t80) REVERT: AG 64 ASN cc_start: 0.8067 (m-40) cc_final: 0.7750 (m-40) REVERT: AH 42 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.6920 (t) REVERT: AH 61 THR cc_start: 0.4609 (t) cc_final: 0.4287 (t) REVERT: AH 86 LYS cc_start: 0.7792 (pttp) cc_final: 0.7377 (mtmm) REVERT: AI 67 THR cc_start: 0.8744 (m) cc_final: 0.8425 (t) REVERT: Aa 449 PHE cc_start: 0.8398 (m-80) cc_final: 0.8073 (m-80) REVERT: Aa 475 MET cc_start: 0.7436 (mmm) cc_final: 0.7013 (tpp) REVERT: Aa 477 TRP cc_start: 0.6875 (m-10) cc_final: 0.6100 (t60) REVERT: Ab 170 GLN cc_start: 0.8114 (mp10) cc_final: 0.7840 (mp10) REVERT: Ab 213 PHE cc_start: 0.7977 (t80) cc_final: 0.7740 (t80) REVERT: Ac 20 ASP cc_start: 0.7927 (m-30) cc_final: 0.7654 (m-30) REVERT: Ac 94 LEU cc_start: 0.8684 (tp) cc_final: 0.8294 (tt) REVERT: Ac 138 MET cc_start: 0.5224 (tpt) cc_final: 0.4753 (mmm) REVERT: Ac 212 ASN cc_start: 0.6851 (t0) cc_final: 0.6336 (t0) REVERT: Ac 223 TYR cc_start: 0.7542 (m-80) cc_final: 0.7289 (m-80) REVERT: Ac 256 TYR cc_start: 0.6740 (m-80) cc_final: 0.6491 (m-80) REVERT: Ac 265 PRO cc_start: 0.7753 (Cg_endo) cc_final: 0.7461 (Cg_exo) REVERT: Ac 333 LEU cc_start: 0.9014 (mt) cc_final: 0.8773 (tt) REVERT: Ac 376 MET cc_start: 0.8706 (mmm) cc_final: 0.8389 (mmm) REVERT: Ad 134 HIS cc_start: 0.5769 (m170) cc_final: 0.5545 (m-70) REVERT: Ad 202 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7604 (mtt180) REVERT: Ad 278 SER cc_start: 0.9002 (m) cc_final: 0.8519 (t) REVERT: Ad 288 MET cc_start: 0.8070 (mmt) cc_final: 0.7502 (mmt) REVERT: Ae 91 TYR cc_start: 0.7128 (m-80) cc_final: 0.6756 (m-80) REVERT: Ae 182 LYS cc_start: 0.6216 (tttt) cc_final: 0.5885 (mtmm) REVERT: Ae 244 ASP cc_start: 0.2798 (p0) cc_final: 0.1737 (t70) REVERT: Ae 248 ARG cc_start: 0.3593 (mtm180) cc_final: 0.3333 (ptp90) REVERT: Af 69 LEU cc_start: 0.9146 (mt) cc_final: 0.8879 (mt) REVERT: Af 74 GLN cc_start: 0.8567 (mm110) cc_final: 0.7970 (mm-40) outliers start: 13 outliers final: 5 residues processed: 1319 average time/residue: 0.1954 time to fit residues: 397.3717 Evaluate side-chains 753 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 746 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 294 LEU Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain Ab residue 168 ASN Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 252 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... AA 103 ASN AA 173 GLN ** AA 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 397 ASN AB 167 GLN AB 210 GLN ** AB 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 44 GLN ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 240 GLN AD 282 HIS ** AD 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 HIS AE 135 GLN ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 227 ASN AE 242 HIS AF 23 ASN AF 80 GLN AH 74 HIS Aa 49 GLN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 128 HIS Aa 397 ASN Aa 402 HIS Ab 118 ASN ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 211 ASN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 261 GLN Ab 298 HIS Ab 311 GLN Ab 365 ASN Ab 415 GLN Ac 44 GLN Ac 267 HIS Ac 308 HIS ** Ac 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 309 HIS ** Ae 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Ag 37 ASN Ah 34 HIS Ah 87 ASN Ak 16 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.133013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103635 restraints weight = 73353.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105361 restraints weight = 40436.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.107274 restraints weight = 27886.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.107655 restraints weight = 22495.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.107550 restraints weight = 20067.550| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.567 31150 Z= 0.182 Angle : 0.751 14.791 42266 Z= 0.380 Chirality : 0.046 0.193 4590 Planarity : 0.006 0.096 5364 Dihedral : 9.518 121.550 4440 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.74 % Allowed : 15.66 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.05 (0.14), residues: 3721 helix: 0.69 (0.11), residues: 1995 sheet: -0.13 (0.28), residues: 364 loop : -0.78 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAa 104 TYR 0.024 0.002 TYRAD 255 PHE 0.038 0.002 PHEAC 95 TRP 0.028 0.002 TRPAC 165 HIS 0.012 0.002 HISAA 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (31137) covalent geometry : angle 0.74910 / 0.38 (42252) SS BOND : bond 0.01235 / 0.39 ( 7) SS BOND : angle 2.99589 / 2.08 ( 14) hydrogen bonds : bond 0.05288 / 3.61 ( 1735) hydrogen bonds : angle 5.41294 / 3.87 ( 4980) Misc. bond : bond 0.36996 / 15.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 866 time to evaluate : 1.172 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: AA 134 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8455 (mtpp) REVERT: AA 142 LYS cc_start: 0.9286 (tppt) cc_final: 0.8946 (tppt) REVERT: AA 145 GLU cc_start: 0.8720 (tt0) cc_final: 0.8500 (tp30) REVERT: AA 172 MET cc_start: 0.9041 (mtm) cc_final: 0.8827 (mtm) REVERT: AA 190 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.9035 (t) REVERT: AA 229 MET cc_start: 0.8644 (mtp) cc_final: 0.8334 (mtp) REVERT: AA 341 PHE cc_start: 0.7878 (t80) cc_final: 0.7608 (t80) REVERT: AA 358 PHE cc_start: 0.9006 (p90) cc_final: 0.8566 (p90) REVERT: AA 376 TRP cc_start: 0.9188 (m-10) cc_final: 0.8916 (m-10) REVERT: AA 412 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8623 (t0) REVERT: AA 440 MET cc_start: 0.8444 (ptp) cc_final: 0.8221 (ptp) REVERT: AA 463 GLU cc_start: 0.7267 (tt0) cc_final: 0.7036 (tt0) REVERT: AB 77 LEU cc_start: 0.9360 (mt) cc_final: 0.9113 (mp) REVERT: AB 271 ILE cc_start: 0.8454 (mt) cc_final: 0.8125 (pt) REVERT: AB 407 MET cc_start: 0.8068 (mpp) cc_final: 0.7797 (mpp) REVERT: AB 443 ASN cc_start: 0.8403 (t0) cc_final: 0.7823 (m-40) REVERT: AC 82 MET cc_start: 0.8289 (tpp) cc_final: 0.8019 (tpp) REVERT: AC 95 PHE cc_start: 0.7269 (m-80) cc_final: 0.6418 (m-80) REVERT: AC 216 ASP cc_start: 0.8554 (t0) cc_final: 0.8098 (t70) REVERT: AC 223 TYR cc_start: 0.8209 (m-80) cc_final: 0.7757 (m-80) REVERT: AC 376 MET cc_start: 0.8680 (mmm) cc_final: 0.8386 (tpp) REVERT: AD 134 HIS cc_start: 0.5925 (m90) cc_final: 0.5635 (m90) REVERT: AD 174 TYR cc_start: 0.7697 (m-80) cc_final: 0.7265 (m-80) REVERT: AD 244 MET cc_start: 0.7615 (tmm) cc_final: 0.7182 (tmm) REVERT: AD 288 MET cc_start: 0.7978 (mmm) cc_final: 0.7619 (mmm) REVERT: AD 292 MET cc_start: 0.7302 (mmp) cc_final: 0.6988 (mmp) REVERT: AE 87 ASP cc_start: 0.8367 (t0) cc_final: 0.8039 (t0) REVERT: AE 89 SER cc_start: 0.8375 (m) cc_final: 0.8102 (p) REVERT: AF 45 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9165 (mtpp) REVERT: AF 79 ASP cc_start: 0.8615 (p0) cc_final: 0.8387 (p0) REVERT: AF 91 LEU cc_start: 0.9024 (tp) cc_final: 0.8778 (tt) REVERT: AF 92 GLU cc_start: 0.8080 (tp30) cc_final: 0.7796 (tp30) REVERT: AF 103 LYS cc_start: 0.9310 (mtmm) cc_final: 0.8956 (mtmm) REVERT: AF 104 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8250 (mt-10) REVERT: AF 110 LYS cc_start: 0.6719 (mtmt) cc_final: 0.6470 (mtmt) REVERT: AG 60 TYR cc_start: 0.7910 (t80) cc_final: 0.7639 (t80) REVERT: AG 64 ASN cc_start: 0.8574 (m-40) cc_final: 0.8050 (m-40) REVERT: AH 86 LYS cc_start: 0.8850 (pttp) cc_final: 0.8204 (mtmm) REVERT: Aa 76 ASP cc_start: 0.7670 (t0) cc_final: 0.7446 (t0) REVERT: Aa 165 ARG cc_start: 0.9151 (ttm110) cc_final: 0.8723 (ttm110) REVERT: Aa 209 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7564 (mtm180) REVERT: Aa 270 PHE cc_start: 0.7997 (t80) cc_final: 0.7689 (t80) REVERT: Aa 274 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: Aa 392 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8255 (mtmm) REVERT: Aa 449 PHE cc_start: 0.8600 (m-80) cc_final: 0.8231 (m-80) REVERT: Aa 450 TYR cc_start: 0.8237 (t80) cc_final: 0.7286 (t80) REVERT: Ab 135 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7439 (tp30) REVERT: Ab 161 ASP cc_start: 0.8851 (t0) cc_final: 0.8509 (t70) REVERT: Ab 218 MET cc_start: 0.8783 (mtm) cc_final: 0.8578 (mtp) REVERT: Ab 384 MET cc_start: 0.7950 (mtm) cc_final: 0.7617 (mtm) REVERT: Ac 20 ASP cc_start: 0.8326 (m-30) cc_final: 0.8044 (m-30) REVERT: Ac 89 MET cc_start: 0.8468 (tpp) cc_final: 0.8171 (tpp) REVERT: Ac 138 MET cc_start: 0.6485 (tpt) cc_final: 0.5457 (tpt) REVERT: Ac 200 LEU cc_start: 0.9277 (tp) cc_final: 0.9056 (tt) REVERT: Ac 212 ASN cc_start: 0.7778 (t0) cc_final: 0.7189 (t0) REVERT: Ac 265 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8371 (Cg_exo) REVERT: Ac 369 SER cc_start: 0.8959 (p) cc_final: 0.8395 (t) REVERT: Ac 373 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7144 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8933 (tt) REVERT: Ad 114 PHE cc_start: 0.9010 (t80) cc_final: 0.8715 (t80) REVERT: Ad 255 TYR cc_start: 0.7914 (m-80) cc_final: 0.7638 (m-80) REVERT: Ad 273 PHE cc_start: 0.9060 (t80) cc_final: 0.8573 (t80) REVERT: Ad 288 MET cc_start: 0.8252 (mmt) cc_final: 0.7752 (mmt) REVERT: Ae 156 LEU cc_start: 0.5591 (tp) cc_final: 0.5288 (tp) REVERT: Ae 244 ASP cc_start: 0.3044 (p0) cc_final: 0.2130 (t0) REVERT: Af 33 MET cc_start: 0.8385 (mmm) cc_final: 0.7828 (mmm) REVERT: Af 60 MET cc_start: 0.8819 (tpp) cc_final: 0.8326 (mpp) REVERT: Af 83 LYS cc_start: 0.8423 (mptt) cc_final: 0.8043 (mptt) REVERT: Af 89 PHE cc_start: 0.7718 (m-10) cc_final: 0.7438 (m-10) REVERT: Ah 70 PHE cc_start: 0.8298 (m-80) cc_final: 0.7781 (m-80) REVERT: Ah 80 VAL cc_start: 0.8941 (t) cc_final: 0.8331 (t) REVERT: Ah 87 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8851 (t0) REVERT: Ai 78 PHE cc_start: 0.6351 (m-80) cc_final: 0.6125 (m-80) REVERT: Ak 23 MET cc_start: 0.7612 (mmp) cc_final: 0.6621 (mtm) outliers start: 119 outliers final: 60 residues processed: 931 average time/residue: 0.1878 time to fit residues: 276.7499 Evaluate side-chains 765 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 700 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 143 VAL Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 208 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 306 VAL Chi-restraints excluded: chain AA residue 311 ILE Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 412 ASP Chi-restraints excluded: chain AB residue 38 LEU Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 126 THR Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 161 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 211 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 75 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AG residue 38 VAL Chi-restraints excluded: chain AG residue 54 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 274 GLU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 435 GLU Chi-restraints excluded: chain Aa residue 442 ARG Chi-restraints excluded: chain Ab residue 47 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 194 ILE Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 102 LEU Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ae residue 122 THR Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 65 CYS Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Ai residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 324 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN AD 240 GLN AD 309 HIS ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 175 ASN Aa 207 ASN Aa 240 GLN Aa 249 HIS Ab 45 ASN ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 227 HIS Ab 365 ASN Ac 68 HIS Ac 267 HIS Ac 308 HIS Ac 345 HIS ** Ae 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.126743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096682 restraints weight = 74481.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097867 restraints weight = 43782.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099327 restraints weight = 31069.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099689 restraints weight = 26028.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099904 restraints weight = 23188.055| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.590 31150 Z= 0.256 Angle : 0.762 15.682 42266 Z= 0.380 Chirality : 0.045 0.190 4590 Planarity : 0.005 0.072 5364 Dihedral : 9.123 125.480 4431 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.12 % Allowed : 17.86 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.39 (0.14), residues: 3721 helix: 0.90 (0.12), residues: 2002 sheet: -0.28 (0.27), residues: 381 loop : -0.41 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAa 396 TYR 0.023 0.002 TYRAC 278 PHE 0.029 0.002 PHEAC 128 TRP 0.026 0.002 TRPAD 96 HIS 0.011 0.002 HISAc 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (31137) covalent geometry : angle 0.76106 / 0.38 (42252) SS BOND : bond 0.00658 / 0.29 ( 7) SS BOND : angle 2.07663 / 1.35 ( 14) hydrogen bonds : bond 0.04826 / 3.31 ( 1735) hydrogen bonds : angle 5.18241 / 3.72 ( 4980) Misc. bond : bond 0.41226 / 18.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 714 time to evaluate : 0.807 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: AA 91 TYR cc_start: 0.8672 (t80) cc_final: 0.8206 (t80) REVERT: AA 134 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8347 (mtpp) REVERT: AA 149 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: AA 363 MET cc_start: 0.8942 (mmt) cc_final: 0.8720 (mmt) REVERT: AA 440 MET cc_start: 0.8601 (ptp) cc_final: 0.8371 (ptp) REVERT: AB 77 LEU cc_start: 0.9442 (mt) cc_final: 0.9202 (mp) REVERT: AB 197 MET cc_start: 0.7107 (ttm) cc_final: 0.6878 (ttm) REVERT: AB 203 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: AB 271 ILE cc_start: 0.8603 (mt) cc_final: 0.8224 (pt) REVERT: AB 443 ASN cc_start: 0.8264 (t0) cc_final: 0.7784 (m-40) REVERT: AC 82 MET cc_start: 0.8523 (tpp) cc_final: 0.8230 (tpt) REVERT: AC 90 PHE cc_start: 0.8381 (t80) cc_final: 0.8118 (t80) REVERT: AC 91 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7464 (t80) REVERT: AC 95 PHE cc_start: 0.7466 (m-80) cc_final: 0.6634 (m-80) REVERT: AC 216 ASP cc_start: 0.8431 (t0) cc_final: 0.8191 (t0) REVERT: AC 282 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7052 (mmt-90) REVERT: AC 344 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7747 (tm-30) REVERT: AD 96 TRP cc_start: 0.7112 (m-90) cc_final: 0.6587 (m-90) REVERT: AD 174 TYR cc_start: 0.7624 (m-80) cc_final: 0.7099 (m-80) REVERT: AD 181 ASN cc_start: 0.7726 (t0) cc_final: 0.7406 (t0) REVERT: AD 244 MET cc_start: 0.7571 (tmm) cc_final: 0.7250 (tmm) REVERT: AE 93 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6944 (ttm-80) REVERT: AF 40 GLU cc_start: 0.8226 (mp0) cc_final: 0.8022 (mp0) REVERT: AF 45 LYS cc_start: 0.9423 (mtpp) cc_final: 0.8829 (mtmm) REVERT: AF 85 GLU cc_start: 0.8356 (pm20) cc_final: 0.7493 (pm20) REVERT: AF 110 LYS cc_start: 0.6923 (mtmt) cc_final: 0.6655 (mtmt) REVERT: AG 40 ARG cc_start: 0.8693 (tmm160) cc_final: 0.8169 (tmm160) REVERT: AG 60 TYR cc_start: 0.7865 (t80) cc_final: 0.7552 (t80) REVERT: AG 64 ASN cc_start: 0.8713 (m-40) cc_final: 0.8193 (m-40) REVERT: AH 45 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7162 (mtp85) REVERT: AH 86 LYS cc_start: 0.8803 (pttp) cc_final: 0.8140 (mtmm) REVERT: Aa 76 ASP cc_start: 0.7690 (t0) cc_final: 0.7486 (t0) REVERT: Aa 79 SER cc_start: 0.9184 (m) cc_final: 0.8202 (t) REVERT: Aa 274 GLU cc_start: 0.8436 (tt0) cc_final: 0.8201 (tt0) REVERT: Aa 450 TYR cc_start: 0.8296 (t80) cc_final: 0.7320 (t80) REVERT: Ab 112 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8870 (m) REVERT: Ab 309 LEU cc_start: 0.7598 (mt) cc_final: 0.7384 (mp) REVERT: Ac 20 ASP cc_start: 0.8543 (m-30) cc_final: 0.8168 (m-30) REVERT: Ac 121 PHE cc_start: 0.7833 (m-80) cc_final: 0.7619 (m-80) REVERT: Ac 217 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8499 (mtmm) REVERT: Ac 273 TYR cc_start: 0.8209 (p90) cc_final: 0.7979 (p90) REVERT: Ac 369 SER cc_start: 0.9066 (p) cc_final: 0.8691 (t) REVERT: Ac 373 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7313 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9284 (tt) REVERT: Ad 106 ASP cc_start: 0.8073 (t0) cc_final: 0.7801 (t0) REVERT: Ad 273 PHE cc_start: 0.9053 (t80) cc_final: 0.8470 (t80) REVERT: Ad 288 MET cc_start: 0.8395 (mmt) cc_final: 0.7871 (mmt) REVERT: Ae 93 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6875 (mtp85) REVERT: Af 33 MET cc_start: 0.8553 (mmm) cc_final: 0.7726 (mmm) REVERT: Af 58 ASP cc_start: 0.8944 (t0) cc_final: 0.8691 (t0) REVERT: Af 60 MET cc_start: 0.9151 (tpp) cc_final: 0.8714 (tpp) REVERT: Af 74 GLN cc_start: 0.8731 (mm110) cc_final: 0.8441 (mm110) REVERT: Af 83 LYS cc_start: 0.8649 (mptt) cc_final: 0.8343 (mptt) REVERT: Af 89 PHE cc_start: 0.7830 (m-10) cc_final: 0.7383 (m-10) REVERT: Ag 37 ASN cc_start: 0.8628 (m-40) cc_final: 0.8228 (t0) REVERT: Ag 40 ARG cc_start: 0.9148 (tmm-80) cc_final: 0.8755 (tmm-80) REVERT: Ah 70 PHE cc_start: 0.8402 (m-80) cc_final: 0.7972 (m-80) REVERT: Ai 67 THR cc_start: 0.8749 (m) cc_final: 0.8272 (p) REVERT: Ak 23 MET cc_start: 0.7596 (mmp) cc_final: 0.6720 (mtm) outliers start: 163 outliers final: 95 residues processed: 811 average time/residue: 0.1721 time to fit residues: 223.9188 Evaluate side-chains 720 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 617 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 109 LEU Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 143 VAL Chi-restraints excluded: chain AA residue 149 ASP Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 208 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AB residue 48 VAL Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 61 THR Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 242 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 48 ILE Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AG residue 38 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain Aa residue 52 ILE Chi-restraints excluded: chain Aa residue 75 ILE Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 379 LEU Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 272 VAL Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 102 LEU Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 154 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 252 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ad residue 300 LEU Chi-restraints excluded: chain Ad residue 303 THR Chi-restraints excluded: chain Ae residue 93 ARG Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 33 GLU Chi-restraints excluded: chain Ah residue 65 CYS Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 19 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 240 optimal weight: 7.9990 chunk 148 optimal weight: 30.0000 chunk 254 optimal weight: 0.8980 chunk 357 optimal weight: 0.2980 chunk 249 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 311 GLN ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 23 ASN AF 57 ASN ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 261 GLN Ab 365 ASN Ac 267 HIS Ac 308 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097130 restraints weight = 74154.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.098702 restraints weight = 43189.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100825 restraints weight = 29660.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101026 restraints weight = 23192.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100905 restraints weight = 21326.876| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.496 31150 Z= 0.179 Angle : 0.693 14.047 42266 Z= 0.339 Chirality : 0.043 0.220 4590 Planarity : 0.004 0.062 5364 Dihedral : 8.861 124.867 4431 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.30 % Allowed : 20.37 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.54 (0.14), residues: 3721 helix: 1.01 (0.12), residues: 2004 sheet: -0.30 (0.27), residues: 386 loop : -0.28 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAB 172 TYR 0.020 0.002 TYRAf 22 PHE 0.023 0.002 PHEAE 136 TRP 0.022 0.001 TRPAk 38 HIS 0.007 0.001 HISAD 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (31137) covalent geometry : angle 0.69196 / 0.34 (42252) SS BOND : bond 0.00495 / 0.21 ( 7) SS BOND : angle 1.67432 / 1.15 ( 14) hydrogen bonds : bond 0.04245 / 2.90 ( 1735) hydrogen bonds : angle 4.94773 / 3.56 ( 4980) Misc. bond : bond 0.31946 / 14.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 684 time to evaluate : 1.164 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: AA 91 TYR cc_start: 0.8698 (t80) cc_final: 0.8394 (t80) REVERT: AA 98 PHE cc_start: 0.8381 (m-80) cc_final: 0.8176 (m-80) REVERT: AA 363 MET cc_start: 0.8890 (mmt) cc_final: 0.8679 (mmt) REVERT: AA 440 MET cc_start: 0.8579 (ptp) cc_final: 0.8363 (ptp) REVERT: AB 77 LEU cc_start: 0.9406 (mt) cc_final: 0.9151 (mp) REVERT: AB 197 MET cc_start: 0.7091 (ttm) cc_final: 0.6808 (ttm) REVERT: AB 203 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: AB 271 ILE cc_start: 0.8511 (mt) cc_final: 0.8166 (pt) REVERT: AB 429 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8474 (ttmm) REVERT: AB 443 ASN cc_start: 0.8361 (t0) cc_final: 0.7701 (m-40) REVERT: AC 31 TRP cc_start: 0.8198 (m-90) cc_final: 0.7471 (m-90) REVERT: AC 82 MET cc_start: 0.8418 (tpp) cc_final: 0.8122 (tpp) REVERT: AC 90 PHE cc_start: 0.8394 (t80) cc_final: 0.8118 (t80) REVERT: AC 91 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7508 (t80) REVERT: AC 95 PHE cc_start: 0.7408 (m-80) cc_final: 0.6289 (m-80) REVERT: AC 181 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: AC 216 ASP cc_start: 0.8418 (t0) cc_final: 0.8181 (t0) REVERT: AC 226 ILE cc_start: 0.8576 (tp) cc_final: 0.8103 (tt) REVERT: AC 282 ARG cc_start: 0.7689 (mmm-85) cc_final: 0.7195 (mmt-90) REVERT: AD 174 TYR cc_start: 0.7517 (m-80) cc_final: 0.7231 (m-80) REVERT: AD 181 ASN cc_start: 0.7755 (t0) cc_final: 0.7354 (t0) REVERT: AD 244 MET cc_start: 0.7555 (tmm) cc_final: 0.7266 (tmm) REVERT: AE 92 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6957 (ttm110) REVERT: AF 40 GLU cc_start: 0.8209 (mp0) cc_final: 0.7976 (mp0) REVERT: AF 45 LYS cc_start: 0.9394 (mtpp) cc_final: 0.8816 (mtmm) REVERT: AF 71 MET cc_start: 0.8488 (tmm) cc_final: 0.8224 (tmm) REVERT: AF 79 ASP cc_start: 0.8669 (p0) cc_final: 0.8302 (p0) REVERT: AF 85 GLU cc_start: 0.8125 (pm20) cc_final: 0.7678 (pm20) REVERT: AF 102 ARG cc_start: 0.9208 (tmm-80) cc_final: 0.9006 (tmm-80) REVERT: AG 64 ASN cc_start: 0.8728 (m-40) cc_final: 0.8379 (m-40) REVERT: AH 45 ARG cc_start: 0.7586 (ttm110) cc_final: 0.7123 (mtp85) REVERT: Aa 76 ASP cc_start: 0.7621 (t0) cc_final: 0.7402 (t0) REVERT: Aa 79 SER cc_start: 0.9112 (m) cc_final: 0.8016 (t) REVERT: Aa 81 TYR cc_start: 0.8898 (m-80) cc_final: 0.8421 (m-80) REVERT: Aa 174 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7370 (tm-30) REVERT: Aa 199 GLN cc_start: 0.8230 (pt0) cc_final: 0.8008 (pt0) REVERT: Aa 274 GLU cc_start: 0.8438 (tt0) cc_final: 0.8158 (tt0) REVERT: Aa 468 TYR cc_start: 0.8472 (t80) cc_final: 0.8171 (t80) REVERT: Ab 407 MET cc_start: 0.8109 (mmp) cc_final: 0.7839 (tpp) REVERT: Ac 20 ASP cc_start: 0.8539 (m-30) cc_final: 0.8149 (m-30) REVERT: Ac 121 PHE cc_start: 0.7833 (m-80) cc_final: 0.7593 (m-80) REVERT: Ac 187 PHE cc_start: 0.7874 (m-80) cc_final: 0.7305 (m-80) REVERT: Ac 200 LEU cc_start: 0.9427 (tp) cc_final: 0.9195 (tt) REVERT: Ac 217 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8478 (mtmm) REVERT: Ac 282 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8390 (ptp90) REVERT: Ac 369 SER cc_start: 0.9094 (p) cc_final: 0.7794 (t) REVERT: Ac 373 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7078 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9337 (tt) REVERT: Ad 177 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8884 (mmtm) REVERT: Ad 273 PHE cc_start: 0.9020 (t80) cc_final: 0.8476 (t80) REVERT: Ad 288 MET cc_start: 0.8400 (mmt) cc_final: 0.7836 (mmt) REVERT: Ad 306 MET cc_start: 0.8841 (ttp) cc_final: 0.8440 (ttt) REVERT: Ae 131 ASN cc_start: 0.7098 (t0) cc_final: 0.6641 (t0) REVERT: Ae 156 LEU cc_start: 0.5302 (tp) cc_final: 0.5064 (tp) REVERT: Ae 244 ASP cc_start: 0.1409 (p0) cc_final: 0.0417 (t70) REVERT: Af 33 MET cc_start: 0.8493 (mmm) cc_final: 0.8002 (mtp) REVERT: Af 58 ASP cc_start: 0.8907 (t0) cc_final: 0.8521 (t0) REVERT: Af 60 MET cc_start: 0.9141 (tpp) cc_final: 0.8719 (tpp) REVERT: Af 83 LYS cc_start: 0.8668 (mptt) cc_final: 0.8409 (mptt) REVERT: Af 89 PHE cc_start: 0.7910 (m-10) cc_final: 0.7589 (m-10) REVERT: Ag 37 ASN cc_start: 0.8448 (m-40) cc_final: 0.8135 (t0) REVERT: Ag 40 ARG cc_start: 0.8924 (tmm-80) cc_final: 0.8610 (tmm-80) REVERT: Ag 60 TYR cc_start: 0.9155 (t80) cc_final: 0.8904 (t80) REVERT: Ah 70 PHE cc_start: 0.8278 (m-80) cc_final: 0.7751 (m-10) REVERT: Ai 67 THR cc_start: 0.8680 (m) cc_final: 0.8210 (p) REVERT: Ak 23 MET cc_start: 0.7600 (mmp) cc_final: 0.6757 (mtm) outliers start: 137 outliers final: 87 residues processed: 765 average time/residue: 0.1847 time to fit residues: 227.9686 Evaluate side-chains 719 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 625 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 109 LEU Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 208 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 205 LEU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 75 ILE Chi-restraints excluded: chain Aa residue 133 ILE Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 253 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 261 GLN Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 102 LEU Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 252 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 174 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 229 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 295 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 119 HIS ** AA 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 261 GLN Ab 365 ASN Ac 16 HIS Ac 212 ASN Ac 267 HIS Ad 90 HIS Ad 284 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.128659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.098313 restraints weight = 74321.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099554 restraints weight = 42818.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101279 restraints weight = 31345.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.101781 restraints weight = 24311.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.101846 restraints weight = 22255.195| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.409 31150 Z= 0.147 Angle : 0.664 12.609 42266 Z= 0.324 Chirality : 0.042 0.297 4590 Planarity : 0.004 0.061 5364 Dihedral : 8.682 124.317 4431 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.30 % Allowed : 20.81 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 3721 helix: 1.09 (0.12), residues: 2008 sheet: -0.11 (0.27), residues: 374 loop : -0.22 (0.18), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAB 172 TYR 0.024 0.001 TYRAf 22 PHE 0.019 0.001 PHEAE 136 TRP 0.023 0.001 TRPAk 38 HIS 0.010 0.001 HISAA 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (31137) covalent geometry : angle 0.66375 / 0.32 (42252) SS BOND : bond 0.00461 / 0.20 ( 7) SS BOND : angle 1.35591 / 1.01 ( 14) hydrogen bonds : bond 0.03987 / 2.72 ( 1735) hydrogen bonds : angle 4.80891 / 3.47 ( 4980) Misc. bond : bond 0.26932 / 11.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 692 time to evaluate : 1.185 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: AA 91 TYR cc_start: 0.8704 (t80) cc_final: 0.8484 (t80) REVERT: AA 98 PHE cc_start: 0.8482 (m-80) cc_final: 0.8265 (m-80) REVERT: AA 172 MET cc_start: 0.8947 (mtm) cc_final: 0.8647 (mtm) REVERT: AA 363 MET cc_start: 0.8871 (mmt) cc_final: 0.8664 (mmt) REVERT: AA 387 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8929 (mp0) REVERT: AA 437 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.6802 (p0) REVERT: AB 77 LEU cc_start: 0.9395 (mt) cc_final: 0.9146 (mp) REVERT: AB 197 MET cc_start: 0.7084 (ttm) cc_final: 0.6379 (ttm) REVERT: AB 203 GLU cc_start: 0.8142 (pt0) cc_final: 0.7803 (tm-30) REVERT: AB 271 ILE cc_start: 0.8577 (mt) cc_final: 0.8246 (pt) REVERT: AB 415 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7977 (tm-30) REVERT: AB 443 ASN cc_start: 0.8338 (t0) cc_final: 0.7665 (m-40) REVERT: AC 31 TRP cc_start: 0.8212 (m-90) cc_final: 0.7321 (m-90) REVERT: AC 40 CYS cc_start: 0.8183 (t) cc_final: 0.7638 (t) REVERT: AC 90 PHE cc_start: 0.8409 (t80) cc_final: 0.8017 (t80) REVERT: AC 91 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7546 (t80) REVERT: AC 95 PHE cc_start: 0.7629 (m-80) cc_final: 0.6282 (m-80) REVERT: AC 181 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: AC 216 ASP cc_start: 0.8365 (t0) cc_final: 0.8150 (t70) REVERT: AC 282 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7242 (mmt-90) REVERT: AD 93 SER cc_start: 0.8297 (m) cc_final: 0.7892 (p) REVERT: AD 96 TRP cc_start: 0.7026 (m-90) cc_final: 0.6460 (m-90) REVERT: AD 174 TYR cc_start: 0.7536 (m-80) cc_final: 0.7245 (m-80) REVERT: AD 181 ASN cc_start: 0.7619 (t0) cc_final: 0.7161 (t0) REVERT: AD 244 MET cc_start: 0.7460 (tmm) cc_final: 0.7088 (tmm) REVERT: AE 92 ARG cc_start: 0.7271 (ttm110) cc_final: 0.6974 (ttm110) REVERT: AE 93 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6989 (ttm-80) REVERT: AF 71 MET cc_start: 0.8485 (tmm) cc_final: 0.8233 (tmm) REVERT: AF 79 ASP cc_start: 0.8648 (p0) cc_final: 0.8274 (p0) REVERT: AG 17 TYR cc_start: 0.8660 (m-80) cc_final: 0.8408 (m-80) REVERT: AG 60 TYR cc_start: 0.8382 (t80) cc_final: 0.8085 (t80) REVERT: AG 64 ASN cc_start: 0.8962 (m-40) cc_final: 0.8748 (m-40) REVERT: AG 65 GLN cc_start: 0.8135 (pp30) cc_final: 0.7930 (pp30) REVERT: Aa 79 SER cc_start: 0.9030 (m) cc_final: 0.8075 (t) REVERT: Aa 81 TYR cc_start: 0.8829 (m-80) cc_final: 0.8274 (m-80) REVERT: Aa 174 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7308 (tm-30) REVERT: Aa 274 GLU cc_start: 0.8391 (tt0) cc_final: 0.8136 (tt0) REVERT: Aa 468 TYR cc_start: 0.8372 (t80) cc_final: 0.8093 (t80) REVERT: Ab 159 LYS cc_start: 0.9012 (tmtt) cc_final: 0.8682 (tptt) REVERT: Ab 213 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: Ab 261 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7288 (mp-120) REVERT: Ab 311 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8423 (pp30) REVERT: Ab 407 MET cc_start: 0.8033 (mmp) cc_final: 0.7819 (tpp) REVERT: Ac 20 ASP cc_start: 0.8535 (m-30) cc_final: 0.8135 (m-30) REVERT: Ac 121 PHE cc_start: 0.7732 (m-80) cc_final: 0.7489 (m-80) REVERT: Ac 141 TRP cc_start: 0.8069 (m100) cc_final: 0.7456 (m100) REVERT: Ac 187 PHE cc_start: 0.7839 (m-80) cc_final: 0.7366 (m-80) REVERT: Ac 217 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8456 (mtmm) REVERT: Ac 282 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8411 (ptp90) REVERT: Ac 316 MET cc_start: 0.8665 (ttt) cc_final: 0.8251 (ttm) REVERT: Ac 373 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7299 (mt-10) REVERT: Ad 114 PHE cc_start: 0.9102 (t80) cc_final: 0.8898 (t80) REVERT: Ad 164 MET cc_start: 0.8808 (tpp) cc_final: 0.8571 (tpp) REVERT: Ad 273 PHE cc_start: 0.9004 (t80) cc_final: 0.8381 (t80) REVERT: Ad 288 MET cc_start: 0.8294 (mmt) cc_final: 0.7747 (mmt) REVERT: Ad 306 MET cc_start: 0.8796 (ttp) cc_final: 0.8462 (ttt) REVERT: Ae 131 ASN cc_start: 0.7021 (t0) cc_final: 0.6570 (t0) REVERT: Ae 156 LEU cc_start: 0.5251 (tp) cc_final: 0.4965 (tp) REVERT: Ae 244 ASP cc_start: 0.1373 (p0) cc_final: 0.0281 (t70) REVERT: Af 33 MET cc_start: 0.8397 (mmm) cc_final: 0.8009 (mtp) REVERT: Af 58 ASP cc_start: 0.8861 (t0) cc_final: 0.8425 (t0) REVERT: Af 60 MET cc_start: 0.9103 (tpp) cc_final: 0.8745 (tpp) REVERT: Af 83 LYS cc_start: 0.8594 (mptt) cc_final: 0.8314 (mptt) REVERT: Ag 60 TYR cc_start: 0.9128 (t80) cc_final: 0.8844 (t80) REVERT: Ag 77 MET cc_start: 0.7599 (ptp) cc_final: 0.7325 (ptp) REVERT: Ah 52 ASP cc_start: 0.8460 (t0) cc_final: 0.8150 (m-30) REVERT: Ai 67 THR cc_start: 0.8662 (m) cc_final: 0.8263 (p) REVERT: Ai 78 PHE cc_start: 0.6913 (m-80) cc_final: 0.6635 (m-10) REVERT: Ak 23 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6803 (mtm) outliers start: 137 outliers final: 88 residues processed: 774 average time/residue: 0.1811 time to fit residues: 227.1542 Evaluate side-chains 741 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 642 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 387 GLU Chi-restraints excluded: chain AA residue 399 LEU Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 437 ASP Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 220 LEU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 75 ILE Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 261 GLN Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 174 THR Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 21 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 310 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 240 GLN AD 282 HIS AD 309 HIS ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 103 ASN Ab 45 ASN Ab 167 GLN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 261 GLN Ab 365 ASN ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.095182 restraints weight = 74500.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097094 restraints weight = 40999.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.098812 restraints weight = 27627.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099151 restraints weight = 22267.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099233 restraints weight = 20446.655| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.531 31150 Z= 0.202 Angle : 0.713 14.807 42266 Z= 0.345 Chirality : 0.043 0.278 4590 Planarity : 0.005 0.059 5364 Dihedral : 8.570 123.381 4431 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.74 % Allowed : 20.72 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.69 (0.14), residues: 3721 helix: 1.10 (0.12), residues: 2000 sheet: -0.06 (0.27), residues: 374 loop : -0.22 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAA 378 TYR 0.027 0.002 TYRAc 104 PHE 0.027 0.002 PHEAa 449 TRP 0.017 0.001 TRPAa 376 HIS 0.008 0.001 HISAc 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (31137) covalent geometry : angle 0.71241 / 0.35 (42252) SS BOND : bond 0.00484 / 0.22 ( 7) SS BOND : angle 1.41030 / 1.04 ( 14) hydrogen bonds : bond 0.04114 / 2.82 ( 1735) hydrogen bonds : angle 4.86911 / 3.52 ( 4980) Misc. bond : bond 0.32077 / 13.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 662 time to evaluate : 1.189 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: AB 77 LEU cc_start: 0.9417 (mt) cc_final: 0.9157 (mp) REVERT: AB 197 MET cc_start: 0.7435 (ttm) cc_final: 0.6765 (ttm) REVERT: AB 203 GLU cc_start: 0.8184 (pt0) cc_final: 0.7833 (tm-30) REVERT: AB 271 ILE cc_start: 0.8634 (mt) cc_final: 0.8397 (pt) REVERT: AB 415 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7945 (tm-30) REVERT: AB 443 ASN cc_start: 0.8424 (t0) cc_final: 0.7715 (m-40) REVERT: AC 31 TRP cc_start: 0.8234 (m-90) cc_final: 0.7331 (m-90) REVERT: AC 40 CYS cc_start: 0.8187 (t) cc_final: 0.7706 (t) REVERT: AC 82 MET cc_start: 0.8619 (tpp) cc_final: 0.8112 (tpt) REVERT: AC 90 PHE cc_start: 0.8416 (t80) cc_final: 0.7921 (t80) REVERT: AC 91 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7553 (t80) REVERT: AC 95 PHE cc_start: 0.7871 (m-80) cc_final: 0.6463 (m-80) REVERT: AC 181 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: AC 216 ASP cc_start: 0.8380 (t0) cc_final: 0.8173 (t70) REVERT: AC 275 LEU cc_start: 0.8845 (tp) cc_final: 0.8625 (tp) REVERT: AC 313 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8113 (ttt180) REVERT: AD 96 TRP cc_start: 0.7001 (m-90) cc_final: 0.6487 (m-90) REVERT: AD 174 TYR cc_start: 0.7578 (m-80) cc_final: 0.7254 (m-80) REVERT: AD 181 ASN cc_start: 0.7606 (t0) cc_final: 0.7139 (t0) REVERT: AD 244 MET cc_start: 0.7349 (tmm) cc_final: 0.7027 (tmm) REVERT: AD 292 MET cc_start: 0.7515 (mmp) cc_final: 0.7308 (mmt) REVERT: AE 92 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6960 (ttm110) REVERT: AF 71 MET cc_start: 0.8488 (tmm) cc_final: 0.8217 (tmm) REVERT: AF 79 ASP cc_start: 0.8649 (p0) cc_final: 0.8244 (p0) REVERT: AG 64 ASN cc_start: 0.8985 (m-40) cc_final: 0.8728 (m-40) REVERT: Aa 79 SER cc_start: 0.9090 (m) cc_final: 0.8230 (t) REVERT: Aa 175 ASN cc_start: 0.8190 (t0) cc_final: 0.7718 (p0) REVERT: Aa 274 GLU cc_start: 0.8444 (tt0) cc_final: 0.8185 (tt0) REVERT: Ab 159 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8767 (tptt) REVERT: Ab 213 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: Ab 261 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7372 (mp-120) REVERT: Ac 20 ASP cc_start: 0.8579 (m-30) cc_final: 0.8173 (m-30) REVERT: Ac 121 PHE cc_start: 0.7824 (m-80) cc_final: 0.7530 (m-80) REVERT: Ac 138 MET cc_start: 0.7165 (tpt) cc_final: 0.6734 (tpp) REVERT: Ac 141 TRP cc_start: 0.8061 (m100) cc_final: 0.7394 (m100) REVERT: Ac 187 PHE cc_start: 0.7917 (m-80) cc_final: 0.7451 (m-80) REVERT: Ac 217 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8462 (mtmm) REVERT: Ac 223 TYR cc_start: 0.8521 (m-80) cc_final: 0.8253 (m-10) REVERT: Ac 282 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8235 (ptp90) REVERT: Ac 369 SER cc_start: 0.9120 (p) cc_final: 0.7949 (t) REVERT: Ac 373 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7271 (mt-10) REVERT: Ad 208 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: Ad 273 PHE cc_start: 0.8997 (t80) cc_final: 0.8407 (t80) REVERT: Ad 279 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8056 (mt-10) REVERT: Ad 288 MET cc_start: 0.8448 (mmt) cc_final: 0.7897 (mmt) REVERT: Ad 306 MET cc_start: 0.8852 (ttp) cc_final: 0.8472 (ttt) REVERT: Ae 131 ASN cc_start: 0.7131 (t0) cc_final: 0.6680 (t0) REVERT: Ae 140 MET cc_start: 0.8559 (mtm) cc_final: 0.8339 (ttp) REVERT: Ae 156 LEU cc_start: 0.5110 (tp) cc_final: 0.4813 (tp) REVERT: Ae 244 ASP cc_start: 0.1554 (p0) cc_final: 0.0508 (t70) REVERT: Ae 248 ARG cc_start: 0.3389 (OUTLIER) cc_final: 0.2038 (ptt180) REVERT: Af 33 MET cc_start: 0.8530 (mmm) cc_final: 0.8065 (mtp) REVERT: Af 58 ASP cc_start: 0.8938 (t0) cc_final: 0.8611 (t70) REVERT: Af 60 MET cc_start: 0.9245 (tpp) cc_final: 0.8934 (tpp) REVERT: Af 83 LYS cc_start: 0.8642 (mptt) cc_final: 0.8405 (mptt) REVERT: Af 89 PHE cc_start: 0.8226 (m-10) cc_final: 0.7995 (m-10) REVERT: Ag 60 TYR cc_start: 0.9203 (t80) cc_final: 0.8956 (t80) REVERT: Ag 77 MET cc_start: 0.7741 (ptp) cc_final: 0.7341 (ptp) REVERT: Ah 52 ASP cc_start: 0.8709 (t0) cc_final: 0.8150 (p0) REVERT: Ah 70 PHE cc_start: 0.8345 (m-80) cc_final: 0.8084 (m-80) REVERT: Ai 67 THR cc_start: 0.8673 (m) cc_final: 0.8307 (p) REVERT: Ai 78 PHE cc_start: 0.6713 (m-80) cc_final: 0.6304 (m-10) REVERT: Aj 13 LEU cc_start: 0.7497 (mm) cc_final: 0.7190 (mm) REVERT: Aj 16 ARG cc_start: 0.7024 (ptt-90) cc_final: 0.6780 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8145 (tt0) cc_final: 0.7694 (mm-40) REVERT: Ak 23 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6710 (mtm) outliers start: 151 outliers final: 112 residues processed: 748 average time/residue: 0.1739 time to fit residues: 211.5821 Evaluate side-chains 749 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 628 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 349 SER Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 437 ASP Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 220 LEU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 48 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 125 THR Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 261 GLN Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 208 GLU Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ad residue 311 TRP Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 248 ARG Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 296 optimal weight: 1.9990 chunk 318 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 239 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 319 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 249 HIS AB 36 GLN ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 148 ASN ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS AE 178 HIS ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 261 GLN Ab 365 ASN Ad 90 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 13 HIS Ah 34 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.125344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094817 restraints weight = 75156.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095575 restraints weight = 46735.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097492 restraints weight = 33127.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097590 restraints weight = 25697.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097755 restraints weight = 24710.373| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.621 31150 Z= 0.235 Angle : 0.757 17.784 42266 Z= 0.365 Chirality : 0.044 0.182 4590 Planarity : 0.005 0.093 5364 Dihedral : 8.542 122.664 4431 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.77 % Allowed : 22.25 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.52 (0.14), residues: 3721 helix: 0.99 (0.12), residues: 2006 sheet: -0.08 (0.28), residues: 364 loop : -0.37 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGAh 47 TYR 0.028 0.002 TYRAc 104 PHE 0.030 0.002 PHEAc 276 TRP 0.017 0.002 TRPAa 376 HIS 0.031 0.002 HISAD 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (31137) covalent geometry : angle 0.75653 / 0.36 (42252) SS BOND : bond 0.00435 / 0.17 ( 7) SS BOND : angle 1.29605 / 0.92 ( 14) hydrogen bonds : bond 0.04240 / 2.91 ( 1735) hydrogen bonds : angle 4.96165 / 3.59 ( 4980) Misc. bond : bond 0.35285 / 14.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 657 time to evaluate : 1.048 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: AB 77 LEU cc_start: 0.9395 (mt) cc_final: 0.9127 (mp) REVERT: AB 197 MET cc_start: 0.7566 (ttm) cc_final: 0.6533 (ttm) REVERT: AB 203 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: AB 415 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7982 (tm-30) REVERT: AC 31 TRP cc_start: 0.8232 (m-90) cc_final: 0.7521 (m-90) REVERT: AC 37 LEU cc_start: 0.9214 (mt) cc_final: 0.8950 (mm) REVERT: AC 40 CYS cc_start: 0.8338 (t) cc_final: 0.7788 (t) REVERT: AC 82 MET cc_start: 0.8675 (tpp) cc_final: 0.8248 (tpp) REVERT: AC 90 PHE cc_start: 0.8441 (t80) cc_final: 0.7856 (t80) REVERT: AC 91 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7659 (t80) REVERT: AC 95 PHE cc_start: 0.7545 (m-80) cc_final: 0.6284 (m-80) REVERT: AC 181 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: AC 216 ASP cc_start: 0.8373 (t0) cc_final: 0.8154 (t70) REVERT: AC 275 LEU cc_start: 0.8794 (tp) cc_final: 0.8564 (tp) REVERT: AC 313 ARG cc_start: 0.8636 (ttt180) cc_final: 0.8186 (ttt180) REVERT: AD 96 TRP cc_start: 0.6981 (m-90) cc_final: 0.6465 (m-90) REVERT: AD 174 TYR cc_start: 0.7631 (m-80) cc_final: 0.7305 (m-80) REVERT: AD 181 ASN cc_start: 0.7682 (t0) cc_final: 0.7195 (t0) REVERT: AD 244 MET cc_start: 0.7224 (tmm) cc_final: 0.6877 (tmm) REVERT: AD 296 MET cc_start: 0.6978 (mmp) cc_final: 0.5722 (mtt) REVERT: AE 92 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6988 (ttm110) REVERT: AF 40 GLU cc_start: 0.8286 (mp0) cc_final: 0.8063 (mp0) REVERT: AF 45 LYS cc_start: 0.9418 (mtpp) cc_final: 0.8868 (mtmm) REVERT: AF 71 MET cc_start: 0.8406 (tmm) cc_final: 0.8155 (tmm) REVERT: AF 79 ASP cc_start: 0.8748 (p0) cc_final: 0.8296 (p0) REVERT: AF 92 GLU cc_start: 0.8500 (tp30) cc_final: 0.7938 (tp30) REVERT: AG 64 ASN cc_start: 0.8914 (m-40) cc_final: 0.8630 (m110) REVERT: Aa 79 SER cc_start: 0.9144 (m) cc_final: 0.8157 (t) REVERT: Aa 123 TYR cc_start: 0.8825 (p90) cc_final: 0.8328 (p90) REVERT: Aa 175 ASN cc_start: 0.8331 (t0) cc_final: 0.7957 (p0) REVERT: Aa 274 GLU cc_start: 0.8419 (tt0) cc_final: 0.8132 (tt0) REVERT: Aa 377 MET cc_start: 0.8574 (mmm) cc_final: 0.8221 (mmm) REVERT: Aa 468 TYR cc_start: 0.8500 (t80) cc_final: 0.8164 (t80) REVERT: Ab 213 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: Ab 261 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7992 (mp-120) REVERT: Ac 20 ASP cc_start: 0.8588 (m-30) cc_final: 0.8209 (m-30) REVERT: Ac 88 SER cc_start: 0.8958 (m) cc_final: 0.8693 (t) REVERT: Ac 141 TRP cc_start: 0.8049 (m100) cc_final: 0.7464 (m100) REVERT: Ac 187 PHE cc_start: 0.8060 (m-80) cc_final: 0.7448 (m-80) REVERT: Ac 214 ASP cc_start: 0.8406 (p0) cc_final: 0.8160 (p0) REVERT: Ac 217 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: Ac 304 MET cc_start: 0.9172 (tpp) cc_final: 0.8963 (tpt) REVERT: Ac 369 SER cc_start: 0.9150 (p) cc_final: 0.7992 (t) REVERT: Ac 373 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7186 (mt-10) REVERT: Ad 103 SER cc_start: 0.8910 (m) cc_final: 0.8399 (p) REVERT: Ad 164 MET cc_start: 0.8895 (tpp) cc_final: 0.8591 (tpp) REVERT: Ad 208 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: Ad 288 MET cc_start: 0.8476 (mmt) cc_final: 0.7948 (mmt) REVERT: Ae 131 ASN cc_start: 0.7191 (t0) cc_final: 0.6747 (t0) REVERT: Ae 244 ASP cc_start: 0.2015 (p0) cc_final: 0.0915 (t70) REVERT: Ae 248 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.2721 (ptt180) REVERT: Af 33 MET cc_start: 0.8580 (mmm) cc_final: 0.7919 (mmm) REVERT: Af 58 ASP cc_start: 0.8890 (t0) cc_final: 0.8565 (t70) REVERT: Af 60 MET cc_start: 0.9227 (tpp) cc_final: 0.8929 (tpp) REVERT: Af 83 LYS cc_start: 0.8670 (mptt) cc_final: 0.8452 (mptt) REVERT: Af 89 PHE cc_start: 0.8254 (m-10) cc_final: 0.7955 (m-10) REVERT: Ag 60 TYR cc_start: 0.9183 (t80) cc_final: 0.8796 (t80) REVERT: Ag 77 MET cc_start: 0.7770 (ptp) cc_final: 0.7318 (ptp) REVERT: Ah 52 ASP cc_start: 0.8765 (t0) cc_final: 0.8135 (p0) REVERT: Ai 67 THR cc_start: 0.8748 (m) cc_final: 0.8408 (p) REVERT: Ai 78 PHE cc_start: 0.6686 (m-80) cc_final: 0.6065 (m-10) REVERT: Aj 13 LEU cc_start: 0.7646 (mm) cc_final: 0.7328 (mm) REVERT: Aj 16 ARG cc_start: 0.7097 (ptt-90) cc_final: 0.6821 (ptt-90) REVERT: Ak 23 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6749 (mtm) outliers start: 152 outliers final: 120 residues processed: 746 average time/residue: 0.1816 time to fit residues: 219.9995 Evaluate side-chains 741 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 612 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 139 ASP Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 394 ILE Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 437 ASP Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 220 LEU Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AC residue 371 ILE Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 146 LYS Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 48 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 45 ARG Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 125 THR Chi-restraints excluded: chain Aa residue 133 ILE Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 253 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 353 LEU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 261 GLN Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 208 GLU Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 263 MET Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ad residue 293 LEU Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 248 ARG Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ai residue 45 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 112 optimal weight: 0.8980 chunk 263 optimal weight: 0.0370 chunk 262 optimal weight: 5.9990 chunk 217 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 341 GLN AC 345 HIS AD 282 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 95 HIS Ab 261 GLN Ab 365 ASN Ac 212 ASN Ad 90 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097415 restraints weight = 74311.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098536 restraints weight = 41429.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099834 restraints weight = 31204.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.100574 restraints weight = 24546.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100755 restraints weight = 22862.212| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.471 31150 Z= 0.155 Angle : 0.728 16.841 42266 Z= 0.346 Chirality : 0.043 0.289 4590 Planarity : 0.004 0.057 5364 Dihedral : 8.351 123.290 4431 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.11 % Allowed : 23.32 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.64 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 2001 sheet: -0.23 (0.27), residues: 384 loop : -0.29 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAA 278 TYR 0.023 0.002 TYRAf 22 PHE 0.033 0.002 PHEAh 70 TRP 0.015 0.001 TRPAa 376 HIS 0.006 0.001 HISAE 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (31137) covalent geometry : angle 0.72765 / 0.35 (42252) SS BOND : bond 0.00340 / 0.13 ( 7) SS BOND : angle 1.10037 / 0.83 ( 14) hydrogen bonds : bond 0.03972 / 2.72 ( 1735) hydrogen bonds : angle 4.83385 / 3.50 ( 4980) Misc. bond : bond 0.28248 / 11.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 675 time to evaluate : 1.216 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 92 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: AA 271 THR cc_start: 0.8891 (m) cc_final: 0.8544 (p) REVERT: AB 77 LEU cc_start: 0.9392 (mt) cc_final: 0.9110 (mp) REVERT: AB 172 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7662 (ttm-80) REVERT: AB 197 MET cc_start: 0.7275 (ttm) cc_final: 0.6236 (ttm) REVERT: AB 203 GLU cc_start: 0.8115 (pt0) cc_final: 0.7822 (tm-30) REVERT: AB 220 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8431 (tt) REVERT: AB 415 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7980 (tm-30) REVERT: AC 82 MET cc_start: 0.8520 (tpp) cc_final: 0.8232 (tpp) REVERT: AC 90 PHE cc_start: 0.8392 (t80) cc_final: 0.8108 (t80) REVERT: AC 91 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7614 (t80) REVERT: AC 95 PHE cc_start: 0.7539 (m-80) cc_final: 0.6204 (m-80) REVERT: AC 216 ASP cc_start: 0.8368 (t0) cc_final: 0.8146 (t70) REVERT: AC 226 ILE cc_start: 0.8581 (tp) cc_final: 0.8203 (tt) REVERT: AC 313 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8320 (ttt180) REVERT: AD 96 TRP cc_start: 0.7035 (m-90) cc_final: 0.6492 (m-90) REVERT: AD 174 TYR cc_start: 0.7639 (m-80) cc_final: 0.7340 (m-80) REVERT: AD 181 ASN cc_start: 0.7646 (t0) cc_final: 0.7155 (t0) REVERT: AD 244 MET cc_start: 0.7359 (tmm) cc_final: 0.7004 (tmm) REVERT: AD 296 MET cc_start: 0.7104 (mmp) cc_final: 0.6020 (mtt) REVERT: AE 92 ARG cc_start: 0.7378 (ttm110) cc_final: 0.7011 (ttm110) REVERT: AF 40 GLU cc_start: 0.8288 (mp0) cc_final: 0.8003 (mp0) REVERT: AF 71 MET cc_start: 0.8383 (tmm) cc_final: 0.8122 (tmm) REVERT: AF 79 ASP cc_start: 0.8687 (p0) cc_final: 0.8195 (p0) REVERT: AF 92 GLU cc_start: 0.8538 (tp30) cc_final: 0.8034 (tp30) REVERT: AF 103 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8868 (pttp) REVERT: AG 57 TYR cc_start: 0.8338 (t80) cc_final: 0.7954 (t80) REVERT: AG 60 TYR cc_start: 0.8241 (t80) cc_final: 0.7942 (t80) REVERT: AG 64 ASN cc_start: 0.8882 (m-40) cc_final: 0.8657 (m-40) REVERT: AH 82 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8007 (t-170) REVERT: Aa 79 SER cc_start: 0.9012 (m) cc_final: 0.8134 (t) REVERT: Aa 91 TYR cc_start: 0.7807 (t80) cc_final: 0.7605 (t80) REVERT: Aa 123 TYR cc_start: 0.8755 (p90) cc_final: 0.8272 (p90) REVERT: Aa 209 ARG cc_start: 0.8458 (mtm180) cc_final: 0.8139 (mtm-85) REVERT: Aa 274 GLU cc_start: 0.8402 (tt0) cc_final: 0.8173 (tt0) REVERT: Aa 449 PHE cc_start: 0.8461 (m-10) cc_final: 0.8260 (m-10) REVERT: Ab 159 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8571 (tptt) REVERT: Ab 213 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: Ab 349 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: Ab 407 MET cc_start: 0.8082 (mmp) cc_final: 0.7848 (mmt) REVERT: Ac 20 ASP cc_start: 0.8557 (m-30) cc_final: 0.8205 (m-30) REVERT: Ac 88 SER cc_start: 0.8886 (m) cc_final: 0.8607 (t) REVERT: Ac 121 PHE cc_start: 0.7904 (m-80) cc_final: 0.7429 (m-80) REVERT: Ac 138 MET cc_start: 0.5998 (tpp) cc_final: 0.4761 (tpp) REVERT: Ac 141 TRP cc_start: 0.8030 (m100) cc_final: 0.7474 (m100) REVERT: Ac 187 PHE cc_start: 0.7915 (m-80) cc_final: 0.7383 (m-80) REVERT: Ac 217 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8596 (mtmm) REVERT: Ac 233 LEU cc_start: 0.9004 (mm) cc_final: 0.8355 (tt) REVERT: Ac 282 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8305 (ptp90) REVERT: Ac 304 MET cc_start: 0.9148 (tpp) cc_final: 0.8922 (tpt) REVERT: Ac 369 SER cc_start: 0.9140 (p) cc_final: 0.7896 (t) REVERT: Ac 373 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7151 (mt-10) REVERT: Ad 103 SER cc_start: 0.8824 (m) cc_final: 0.8385 (p) REVERT: Ad 164 MET cc_start: 0.8933 (tpp) cc_final: 0.8674 (tpp) REVERT: Ad 174 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6959 (t80) REVERT: Ad 249 TYR cc_start: 0.7048 (p90) cc_final: 0.6821 (p90) REVERT: Ad 273 PHE cc_start: 0.8937 (t80) cc_final: 0.8266 (t80) REVERT: Ad 288 MET cc_start: 0.8496 (mmt) cc_final: 0.8126 (mmt) REVERT: Ae 131 ASN cc_start: 0.7050 (t0) cc_final: 0.6646 (t0) REVERT: Ae 156 LEU cc_start: 0.4696 (tp) cc_final: 0.4364 (tp) REVERT: Ae 244 ASP cc_start: 0.1980 (p0) cc_final: 0.0711 (t0) REVERT: Ae 248 ARG cc_start: 0.4416 (OUTLIER) cc_final: 0.2709 (ptt180) REVERT: Af 33 MET cc_start: 0.8461 (mmm) cc_final: 0.8042 (mtp) REVERT: Af 53 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8207 (tm-30) REVERT: Af 58 ASP cc_start: 0.8869 (t0) cc_final: 0.8538 (t70) REVERT: Af 60 MET cc_start: 0.9168 (tpp) cc_final: 0.8888 (tpp) REVERT: Af 89 PHE cc_start: 0.8217 (m-10) cc_final: 0.7934 (m-10) REVERT: Ag 40 ARG cc_start: 0.8843 (tmm-80) cc_final: 0.8630 (tmm-80) REVERT: Ag 77 MET cc_start: 0.7847 (ptp) cc_final: 0.7514 (ptp) REVERT: Ah 39 GLU cc_start: 0.8508 (pm20) cc_final: 0.8298 (pm20) REVERT: Ah 43 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8436 (ptpt) REVERT: Ah 47 ARG cc_start: 0.8593 (mmm160) cc_final: 0.8372 (mmm160) REVERT: Ai 67 THR cc_start: 0.8666 (m) cc_final: 0.8337 (p) REVERT: Aj 13 LEU cc_start: 0.7623 (mm) cc_final: 0.7313 (mm) REVERT: Aj 16 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6872 (ptt-90) REVERT: Ak 23 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6868 (mtm) outliers start: 131 outliers final: 104 residues processed: 750 average time/residue: 0.1881 time to fit residues: 228.4707 Evaluate side-chains 754 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 639 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 349 SER Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 220 LEU Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 146 LYS Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 48 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 45 ARG Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 125 THR Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 353 LEU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 261 GLN Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 349 GLU Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 174 THR Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ad residue 174 TYR Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 248 ARG Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 45 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 329 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 333 optimal weight: 0.7980 chunk 263 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 327 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AF 57 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ad 90 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096973 restraints weight = 74193.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098140 restraints weight = 43133.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100431 restraints weight = 31945.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100433 restraints weight = 22988.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100663 restraints weight = 23586.968| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.483 31150 Z= 0.162 Angle : 0.743 15.858 42266 Z= 0.352 Chirality : 0.043 0.270 4590 Planarity : 0.005 0.095 5364 Dihedral : 8.315 124.025 4431 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.99 % Allowed : 23.85 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 3721 helix: 1.18 (0.12), residues: 1990 sheet: -0.25 (0.27), residues: 387 loop : -0.33 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAh 47 TYR 0.036 0.002 TYRAa 450 PHE 0.032 0.002 PHEAc 276 TRP 0.017 0.001 TRPAC 163 HIS 0.008 0.001 HISAa 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (31137) covalent geometry : angle 0.74311 / 0.35 (42252) SS BOND : bond 0.00317 / 0.12 ( 7) SS BOND : angle 1.10965 / 0.81 ( 14) hydrogen bonds : bond 0.03977 / 2.73 ( 1735) hydrogen bonds : angle 4.80523 / 3.47 ( 4980) Misc. bond : bond 0.28334 / 11.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 671 time to evaluate : 1.184 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 92 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8598 (m-80) REVERT: AA 158 ASP cc_start: 0.8804 (m-30) cc_final: 0.8573 (m-30) REVERT: AA 271 THR cc_start: 0.8895 (m) cc_final: 0.8675 (t) REVERT: AB 77 LEU cc_start: 0.9381 (mt) cc_final: 0.9109 (mp) REVERT: AB 172 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7501 (ttm-80) REVERT: AB 197 MET cc_start: 0.7320 (ttm) cc_final: 0.6228 (ttm) REVERT: AB 203 GLU cc_start: 0.8109 (pt0) cc_final: 0.7907 (tm-30) REVERT: AB 415 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7989 (tm-30) REVERT: AC 31 TRP cc_start: 0.8203 (m-90) cc_final: 0.7588 (m-90) REVERT: AC 82 MET cc_start: 0.8481 (tpp) cc_final: 0.8056 (tpt) REVERT: AC 90 PHE cc_start: 0.8445 (t80) cc_final: 0.8241 (t80) REVERT: AC 91 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7690 (t80) REVERT: AC 95 PHE cc_start: 0.7558 (m-80) cc_final: 0.6214 (m-80) REVERT: AC 313 ARG cc_start: 0.8533 (ttt180) cc_final: 0.8064 (ttt180) REVERT: AC 322 GLN cc_start: 0.8443 (mt0) cc_final: 0.8045 (mt0) REVERT: AD 96 TRP cc_start: 0.7064 (m-90) cc_final: 0.6530 (m-90) REVERT: AD 174 TYR cc_start: 0.7850 (m-80) cc_final: 0.7535 (m-80) REVERT: AD 181 ASN cc_start: 0.7598 (t0) cc_final: 0.7097 (t0) REVERT: AD 244 MET cc_start: 0.7308 (tmm) cc_final: 0.6970 (tmm) REVERT: AD 296 MET cc_start: 0.7216 (mmp) cc_final: 0.6091 (mtt) REVERT: AE 92 ARG cc_start: 0.7463 (ttm110) cc_final: 0.7091 (ttm110) REVERT: AF 40 GLU cc_start: 0.8302 (mp0) cc_final: 0.7999 (mp0) REVERT: AF 70 THR cc_start: 0.9248 (m) cc_final: 0.8947 (p) REVERT: AF 79 ASP cc_start: 0.8681 (p0) cc_final: 0.8194 (p0) REVERT: AF 92 GLU cc_start: 0.8528 (tp30) cc_final: 0.8025 (tp30) REVERT: AF 106 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8610 (mp0) REVERT: AG 57 TYR cc_start: 0.8355 (t80) cc_final: 0.8015 (t80) REVERT: AG 73 LYS cc_start: 0.7312 (pttp) cc_final: 0.6903 (pptt) REVERT: AH 72 PHE cc_start: 0.5279 (t80) cc_final: 0.4576 (t80) REVERT: AH 82 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8094 (t-170) REVERT: Aa 79 SER cc_start: 0.9089 (m) cc_final: 0.8083 (t) REVERT: Aa 123 TYR cc_start: 0.8725 (p90) cc_final: 0.8249 (p90) REVERT: Aa 175 ASN cc_start: 0.8299 (t0) cc_final: 0.7946 (p0) REVERT: Aa 199 GLN cc_start: 0.8087 (pt0) cc_final: 0.7690 (pt0) REVERT: Aa 274 GLU cc_start: 0.8390 (tt0) cc_final: 0.8175 (tt0) REVERT: Aa 377 MET cc_start: 0.8260 (mmm) cc_final: 0.7725 (mmm) REVERT: Aa 450 TYR cc_start: 0.7997 (t80) cc_final: 0.7524 (t80) REVERT: Aa 468 TYR cc_start: 0.8190 (t80) cc_final: 0.7917 (t80) REVERT: Ab 159 LYS cc_start: 0.8868 (tmtt) cc_final: 0.8576 (tptt) REVERT: Ab 213 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: Ab 349 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: Ab 407 MET cc_start: 0.8104 (mmp) cc_final: 0.7862 (tpp) REVERT: Ac 20 ASP cc_start: 0.8571 (m-30) cc_final: 0.8237 (m-30) REVERT: Ac 88 SER cc_start: 0.8895 (m) cc_final: 0.8600 (t) REVERT: Ac 121 PHE cc_start: 0.7874 (m-80) cc_final: 0.7419 (m-80) REVERT: Ac 138 MET cc_start: 0.6030 (tpp) cc_final: 0.4795 (tpp) REVERT: Ac 141 TRP cc_start: 0.8000 (m100) cc_final: 0.7485 (m100) REVERT: Ac 187 PHE cc_start: 0.7834 (m-80) cc_final: 0.7349 (m-80) REVERT: Ac 217 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8526 (mtmm) REVERT: Ac 233 LEU cc_start: 0.8987 (mm) cc_final: 0.8338 (tt) REVERT: Ac 282 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8303 (ptp90) REVERT: Ac 304 MET cc_start: 0.9157 (tpp) cc_final: 0.8952 (tpt) REVERT: Ac 369 SER cc_start: 0.9103 (p) cc_final: 0.7856 (t) REVERT: Ac 373 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7232 (mt-10) REVERT: Ad 103 SER cc_start: 0.8852 (m) cc_final: 0.8437 (p) REVERT: Ad 127 MET cc_start: 0.7584 (tpp) cc_final: 0.7239 (tpp) REVERT: Ad 164 MET cc_start: 0.8978 (tpp) cc_final: 0.8753 (tpp) REVERT: Ad 249 TYR cc_start: 0.7048 (p90) cc_final: 0.6811 (p90) REVERT: Ad 253 LEU cc_start: 0.7830 (tp) cc_final: 0.7495 (pt) REVERT: Ad 288 MET cc_start: 0.8506 (mmt) cc_final: 0.8125 (mmt) REVERT: Ae 131 ASN cc_start: 0.6987 (t0) cc_final: 0.6611 (t0) REVERT: Ae 156 LEU cc_start: 0.4347 (tp) cc_final: 0.4123 (tp) REVERT: Ae 244 ASP cc_start: 0.2061 (p0) cc_final: 0.0779 (t0) REVERT: Ae 248 ARG cc_start: 0.4374 (OUTLIER) cc_final: 0.2687 (ptt180) REVERT: Af 33 MET cc_start: 0.8469 (mmm) cc_final: 0.8020 (mtp) REVERT: Af 58 ASP cc_start: 0.8846 (t0) cc_final: 0.8512 (t70) REVERT: Af 60 MET cc_start: 0.9174 (tpp) cc_final: 0.8906 (tpp) REVERT: Ag 72 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7218 (mmp80) REVERT: Ag 77 MET cc_start: 0.7871 (ptp) cc_final: 0.7538 (ptp) REVERT: Ah 39 GLU cc_start: 0.8465 (pm20) cc_final: 0.8258 (pm20) REVERT: Ah 43 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8388 (ptpt) REVERT: Ai 67 THR cc_start: 0.8685 (m) cc_final: 0.8326 (p) REVERT: Aj 13 LEU cc_start: 0.7665 (mm) cc_final: 0.7354 (mm) REVERT: Aj 16 ARG cc_start: 0.7347 (ptt-90) cc_final: 0.6681 (ptt-90) REVERT: Ak 23 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6716 (mtm) outliers start: 127 outliers final: 100 residues processed: 741 average time/residue: 0.1858 time to fit residues: 222.7747 Evaluate side-chains 744 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 635 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 40 PHE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 99 ILE Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 239 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 146 LYS Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 48 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 45 ARG Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 125 THR Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 353 LEU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 349 GLU Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 248 ARG Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 45 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AF 57 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 304 ASN Ab 365 ASN Ad 90 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.128056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.097343 restraints weight = 73929.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099049 restraints weight = 42827.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100946 restraints weight = 29655.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101055 restraints weight = 23591.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101166 restraints weight = 22299.014| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.427 31150 Z= 0.158 Angle : 0.758 15.697 42266 Z= 0.362 Chirality : 0.044 0.256 4590 Planarity : 0.005 0.078 5364 Dihedral : 8.251 124.567 4431 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.55 % Allowed : 24.73 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.65 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 1996 sheet: -0.15 (0.27), residues: 381 loop : -0.31 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGAh 47 TYR 0.029 0.001 TYRAa 450 PHE 0.045 0.002 PHEAa 449 TRP 0.016 0.001 TRPAC 163 HIS 0.007 0.001 HISAa 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (31137) covalent geometry : angle 0.75819 / 0.36 (42252) SS BOND : bond 0.00329 / 0.13 ( 7) SS BOND : angle 0.97165 / 0.75 ( 14) hydrogen bonds : bond 0.03998 / 2.73 ( 1735) hydrogen bonds : angle 4.84517 / 3.50 ( 4980) Misc. bond : bond 0.26147 / 10.98 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 671 time to evaluate : 0.908 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 92 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: AA 158 ASP cc_start: 0.8820 (m-30) cc_final: 0.8612 (m-30) REVERT: AA 271 THR cc_start: 0.8926 (m) cc_final: 0.8635 (p) REVERT: AA 354 LEU cc_start: 0.9164 (tp) cc_final: 0.8719 (tp) REVERT: AB 77 LEU cc_start: 0.9371 (mt) cc_final: 0.9101 (mp) REVERT: AB 172 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7511 (ttm-80) REVERT: AB 203 GLU cc_start: 0.8096 (pt0) cc_final: 0.7886 (tm-30) REVERT: AB 257 GLU cc_start: 0.6744 (tt0) cc_final: 0.6359 (mt-10) REVERT: AB 415 GLN cc_start: 0.8265 (tm-30) cc_final: 0.8004 (tm-30) REVERT: AC 31 TRP cc_start: 0.8213 (m-90) cc_final: 0.7508 (m-90) REVERT: AC 82 MET cc_start: 0.8478 (tpp) cc_final: 0.8101 (tpp) REVERT: AC 91 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7657 (t80) REVERT: AC 95 PHE cc_start: 0.7636 (m-80) cc_final: 0.6259 (m-80) REVERT: AC 322 GLN cc_start: 0.8452 (mt0) cc_final: 0.8057 (mt0) REVERT: AC 343 VAL cc_start: 0.8971 (m) cc_final: 0.8722 (m) REVERT: AD 96 TRP cc_start: 0.7136 (m-90) cc_final: 0.6584 (m-90) REVERT: AD 174 TYR cc_start: 0.7905 (m-80) cc_final: 0.7613 (m-80) REVERT: AD 244 MET cc_start: 0.7132 (tmm) cc_final: 0.6778 (tmm) REVERT: AD 296 MET cc_start: 0.7303 (mmp) cc_final: 0.6179 (mtt) REVERT: AD 306 MET cc_start: 0.8861 (tpp) cc_final: 0.8649 (tpp) REVERT: AE 92 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7050 (ttm110) REVERT: AF 40 GLU cc_start: 0.8312 (mp0) cc_final: 0.8058 (mp0) REVERT: AF 79 ASP cc_start: 0.8736 (p0) cc_final: 0.8291 (p0) REVERT: AF 92 GLU cc_start: 0.8546 (tp30) cc_final: 0.8035 (tp30) REVERT: AG 17 TYR cc_start: 0.8518 (m-80) cc_final: 0.8243 (m-80) REVERT: AG 57 TYR cc_start: 0.8356 (t80) cc_final: 0.8022 (t80) REVERT: AG 73 LYS cc_start: 0.7145 (pttp) cc_final: 0.6867 (pptt) REVERT: AH 72 PHE cc_start: 0.5333 (t80) cc_final: 0.4429 (t80) REVERT: AH 82 HIS cc_start: 0.8505 (t-170) cc_final: 0.8146 (t-170) REVERT: Aa 79 SER cc_start: 0.9054 (m) cc_final: 0.8098 (t) REVERT: Aa 123 TYR cc_start: 0.8727 (p90) cc_final: 0.8263 (p90) REVERT: Aa 209 ARG cc_start: 0.8462 (mtm180) cc_final: 0.8109 (mtm180) REVERT: Aa 274 GLU cc_start: 0.8384 (tt0) cc_final: 0.8153 (tt0) REVERT: Aa 377 MET cc_start: 0.8299 (mmm) cc_final: 0.7892 (mmm) REVERT: Ab 159 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8604 (tptt) REVERT: Ab 213 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8470 (m-80) REVERT: Ab 407 MET cc_start: 0.8104 (mmp) cc_final: 0.7878 (tpp) REVERT: Ac 20 ASP cc_start: 0.8630 (m-30) cc_final: 0.8318 (m-30) REVERT: Ac 129 MET cc_start: 0.7201 (ptt) cc_final: 0.6887 (ppp) REVERT: Ac 138 MET cc_start: 0.5993 (tpp) cc_final: 0.4789 (tpp) REVERT: Ac 141 TRP cc_start: 0.7929 (m100) cc_final: 0.7494 (m100) REVERT: Ac 187 PHE cc_start: 0.7734 (m-80) cc_final: 0.7296 (m-80) REVERT: Ac 217 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8520 (mtmm) REVERT: Ac 233 LEU cc_start: 0.8990 (mm) cc_final: 0.8341 (tt) REVERT: Ac 282 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8488 (ptp90) REVERT: Ac 369 SER cc_start: 0.9117 (p) cc_final: 0.7844 (t) REVERT: Ac 373 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7262 (mt-10) REVERT: Ad 103 SER cc_start: 0.8861 (m) cc_final: 0.8494 (p) REVERT: Ad 209 ASP cc_start: 0.8524 (m-30) cc_final: 0.8307 (m-30) REVERT: Ad 253 LEU cc_start: 0.7950 (tp) cc_final: 0.7567 (pt) REVERT: Ad 288 MET cc_start: 0.8509 (mmt) cc_final: 0.8124 (mmt) REVERT: Ae 113 PHE cc_start: 0.7661 (t80) cc_final: 0.7302 (m-80) REVERT: Ae 140 MET cc_start: 0.7663 (ttp) cc_final: 0.7461 (mmm) REVERT: Ae 156 LEU cc_start: 0.4372 (tp) cc_final: 0.4113 (tp) REVERT: Ae 165 MET cc_start: 0.7398 (ttm) cc_final: 0.7172 (ptm) REVERT: Ae 244 ASP cc_start: 0.2225 (p0) cc_final: 0.0915 (t0) REVERT: Ae 248 ARG cc_start: 0.4413 (OUTLIER) cc_final: 0.2736 (ptt180) REVERT: Af 33 MET cc_start: 0.8486 (mmm) cc_final: 0.8073 (mtp) REVERT: Af 53 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8091 (tm-30) REVERT: Af 58 ASP cc_start: 0.8845 (t0) cc_final: 0.8540 (t70) REVERT: Af 60 MET cc_start: 0.9169 (tpp) cc_final: 0.8922 (tpp) REVERT: Ag 72 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7231 (mmp80) REVERT: Ag 77 MET cc_start: 0.7912 (ptp) cc_final: 0.7653 (ptp) REVERT: Ah 47 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8125 (mmm160) REVERT: Ah 50 LEU cc_start: 0.8683 (pp) cc_final: 0.8462 (pt) REVERT: Ah 52 ASP cc_start: 0.8851 (t0) cc_final: 0.8381 (p0) REVERT: Ai 67 THR cc_start: 0.8608 (m) cc_final: 0.8271 (p) REVERT: Ai 77 ARG cc_start: 0.7436 (tmm160) cc_final: 0.7160 (tmm160) REVERT: Aj 13 LEU cc_start: 0.7698 (mm) cc_final: 0.7376 (mm) REVERT: Aj 16 ARG cc_start: 0.7340 (ptt-90) cc_final: 0.7019 (ptt-90) REVERT: Ak 23 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6811 (mtm) outliers start: 113 outliers final: 94 residues processed: 731 average time/residue: 0.1805 time to fit residues: 212.9300 Evaluate side-chains 743 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 642 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 36 GLN Chi-restraints excluded: chain AB residue 40 PHE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 239 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 146 LYS Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 48 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 125 THR Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 353 LEU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 59 THR Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ad residue 150 GLU Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 248 ARG Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 45 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 161 optimal weight: 5.9990 chunk 183 optimal weight: 0.0070 chunk 278 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 323 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 95 HIS AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AF 57 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ac 267 HIS Ad 90 HIS Ae 200 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Ak 16 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.099152 restraints weight = 74210.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100319 restraints weight = 44167.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102394 restraints weight = 30702.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102931 restraints weight = 23183.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.103019 restraints weight = 22340.409| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 31150 Z= 0.141 Angle : 0.744 15.931 42266 Z= 0.356 Chirality : 0.043 0.219 4590 Planarity : 0.005 0.077 5364 Dihedral : 8.133 124.992 4431 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.26 % Allowed : 25.27 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.70 (0.14), residues: 3721 helix: 1.18 (0.12), residues: 1973 sheet: -0.10 (0.28), residues: 377 loop : -0.31 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAh 47 TYR 0.023 0.001 TYRAG 78 PHE 0.033 0.001 PHEAc 276 TRP 0.030 0.001 TRPAk 38 HIS 0.007 0.001 HISAa 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (31137) covalent geometry : angle 0.74422 / 0.36 (42252) SS BOND : bond 0.00263 / 0.11 ( 7) SS BOND : angle 0.93869 / 0.67 ( 14) hydrogen bonds : bond 0.03896 / 2.66 ( 1735) hydrogen bonds : angle 4.76756 / 3.44 ( 4980) Misc. bond : bond 0.22859 / 9.78 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6010.88 seconds wall clock time: 104 minutes 40.60 seconds (6280.60 seconds total)