Starting phenix.real_space_refine on Mon Aug 25 19:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibg_35343/08_2025/8ibg_35343_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibg_35343/08_2025/8ibg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibg_35343/08_2025/8ibg_35343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibg_35343/08_2025/8ibg_35343.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibg_35343/08_2025/8ibg_35343_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibg_35343/08_2025/8ibg_35343_neut.cif" } 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-2.0-5787/lib/python3.9/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: 60 Planarities with less than four sites: {'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1, 'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 47 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: 7.48, per 1000 atoms: 0.25 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: 3.03 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.09 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: 5.99 Time building geometry restraints manager: 3.91 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: 40667 3.21 - 6.43: 1315 6.43 - 9.64: 225 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 - 31.30: 18092 31.30 - 62.60: 314 62.60 - 93.90: 57 93.90 - 125.21: 2 125.21 - 156.51: 4 Dihedral angle restraints: 18469 sinusoidal: 7501 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=" C11 U10Ac 404 " pdb=" C12 U10Ac 404 " pdb=" C13 U10Ac 404 " pdb=" C14 U10Ac 404 " ideal model delta sinusoidal sigma weight residual 126.68 -76.81 -156.51 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 18466 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 " -0.096 2.00e-02 2.50e+03 8.37e-02 1.23e+02 pdb=" C1M U10Ac 404 " 0.100 2.00e-02 2.50e+03 pdb=" C2 U10Ac 404 " -0.103 2.00e-02 2.50e+03 pdb=" C3 U10Ac 404 " 0.050 2.00e-02 2.50e+03 pdb=" C4 U10Ac 404 " 0.092 2.00e-02 2.50e+03 pdb=" C5 U10Ac 404 " -0.082 2.00e-02 2.50e+03 pdb=" C6 U10Ac 404 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HECAd 401 " -0.020 2.00e-02 2.50e+03 5.84e-02 7.68e+01 pdb=" C2C HECAd 401 " 0.160 2.00e-02 2.50e+03 pdb=" C3C HECAd 401 " -0.023 2.00e-02 2.50e+03 pdb=" C4C HECAd 401 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HECAd 401 " -0.032 2.00e-02 2.50e+03 pdb=" CHC HECAd 401 " -0.030 2.00e-02 2.50e+03 pdb=" CHD HECAd 401 " 0.003 2.00e-02 2.50e+03 pdb=" CMC HECAd 401 " -0.047 2.00e-02 2.50e+03 pdb=" NC HECAd 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPAI 44 " 0.022 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C ASPAI 44 " -0.081 2.00e-02 2.50e+03 pdb=" O ASPAI 44 " 0.034 2.00e-02 2.50e+03 pdb=" N VALAI 45 " 0.025 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.100 Find NCS groups from input model: 0.600 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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= 0.674 Angle : 1.375 46.163 42266 Z= 0.900 Chirality : 0.061 0.596 4590 Planarity : 0.007 0.084 5364 Dihedral : 13.100 156.508 11388 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 aren 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 covalent geometry : bond 0.00994 (31137) covalent geometry : angle 1.35186 (42252) SS BOND : bond 0.07077 ( 7) SS BOND : angle 13.96925 ( 14) hydrogen bonds : bond 0.20000 ( 1735) hydrogen bonds : angle 7.90660 ( 4980) Misc. bond : bond 0.15350 ( 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 : 1.223 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: 0.7849 (m-10) cc_final: 0.7311 (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: 0.7376 (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: 0.6337 (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: 0.2243 time to fit residues: 452.5475 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 : 1.238 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN 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 = 0.3958 r_free = 0.3958 target = 0.133002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103856 restraints weight = 73324.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.105139 restraints weight = 40783.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107426 restraints weight = 28551.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107618 restraints weight = 22210.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.107681 restraints weight = 20185.328| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.574 31150 Z= 0.182 Angle : 0.748 13.512 42266 Z= 0.379 Chirality : 0.046 0.262 4590 Planarity : 0.006 0.105 5364 Dihedral : 10.700 135.692 4415 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.61 % Allowed : 15.63 % Favored : 80.76 % 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 aren not related in a simple way. whole: 0.05 (0.14), residues: 3721 helix: 0.68 (0.11), residues: 2001 sheet: -0.18 (0.28), residues: 362 loop : -0.75 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAF 34 TYR 0.026 0.002 TYRAD 255 PHE 0.036 0.002 PHEAC 95 TRP 0.028 0.002 TRPAC 165 HIS 0.012 0.002 HISAA 249 Details of bonding type rmsd covalent geometry : bond 0.00404 (31137) covalent geometry : angle 0.74568 (42252) SS BOND : bond 0.00796 ( 7) SS BOND : angle 3.59133 ( 14) hydrogen bonds : bond 0.05337 ( 1735) hydrogen bonds : angle 5.41356 ( 4980) Misc. bond : bond 0.37102 ( 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 979 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 864 time to evaluate : 0.868 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: AA 134 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8440 (mtpp) REVERT: AA 142 LYS cc_start: 0.9311 (tppt) cc_final: 0.8934 (tppt) REVERT: AA 172 MET cc_start: 0.9061 (mtm) cc_final: 0.8841 (mtm) REVERT: AA 190 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.9026 (t) REVERT: AA 229 MET cc_start: 0.8642 (mtp) cc_final: 0.8359 (mtp) REVERT: AA 341 PHE cc_start: 0.7829 (t80) cc_final: 0.7576 (t80) REVERT: AA 358 PHE cc_start: 0.8983 (p90) cc_final: 0.8529 (p90) REVERT: AA 376 TRP cc_start: 0.9194 (m-10) cc_final: 0.8910 (m-10) REVERT: AA 412 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (t0) REVERT: AA 440 MET cc_start: 0.8453 (ptp) cc_final: 0.8142 (ptp) REVERT: AA 463 GLU cc_start: 0.7269 (tt0) cc_final: 0.7040 (tt0) REVERT: AB 77 LEU cc_start: 0.9353 (mt) cc_final: 0.9104 (mp) REVERT: AB 172 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.7270 (ttm-80) REVERT: AB 235 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7979 (mt-10) REVERT: AB 271 ILE cc_start: 0.8435 (mt) cc_final: 0.8080 (pt) REVERT: AB 407 MET cc_start: 0.8075 (mpp) cc_final: 0.7818 (mpp) REVERT: AB 443 ASN cc_start: 0.8391 (t0) cc_final: 0.7821 (m-40) REVERT: AC 82 MET cc_start: 0.8295 (tpp) cc_final: 0.8015 (tpp) REVERT: AC 214 ASP cc_start: 0.8829 (m-30) cc_final: 0.8625 (m-30) REVERT: AC 216 ASP cc_start: 0.8575 (t0) cc_final: 0.8142 (t70) REVERT: AC 223 TYR cc_start: 0.8135 (m-80) cc_final: 0.7665 (m-80) REVERT: AC 252 ASP cc_start: 0.4838 (t0) cc_final: 0.4613 (t0) REVERT: AC 272 TRP cc_start: 0.7457 (p-90) cc_final: 0.7052 (p-90) REVERT: AC 376 MET cc_start: 0.8676 (mmm) cc_final: 0.8394 (tpp) REVERT: AD 134 HIS cc_start: 0.5978 (m90) cc_final: 0.5705 (m90) REVERT: AD 174 TYR cc_start: 0.7600 (m-80) cc_final: 0.7165 (m-80) REVERT: AD 244 MET cc_start: 0.7603 (tmm) cc_final: 0.7162 (tmm) REVERT: AD 288 MET cc_start: 0.8013 (mmm) cc_final: 0.7699 (mmm) REVERT: AD 292 MET cc_start: 0.7327 (mmp) cc_final: 0.7000 (mmp) REVERT: AE 87 ASP cc_start: 0.8350 (t0) cc_final: 0.8034 (t0) REVERT: AE 89 SER cc_start: 0.8384 (m) cc_final: 0.8118 (p) REVERT: AF 45 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9193 (mtpp) REVERT: AF 54 ASP cc_start: 0.8319 (m-30) cc_final: 0.8050 (m-30) REVERT: AF 57 ASN cc_start: 0.8197 (m110) cc_final: 0.7673 (p0) REVERT: AF 92 GLU cc_start: 0.8079 (tp30) cc_final: 0.7762 (tp30) REVERT: AF 103 LYS cc_start: 0.9302 (mtmm) cc_final: 0.8952 (mtmm) REVERT: AF 104 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8218 (mt-10) REVERT: AF 108 TRP cc_start: 0.8511 (t-100) cc_final: 0.8287 (t-100) REVERT: AF 110 LYS cc_start: 0.6696 (mtmt) cc_final: 0.6459 (mtmt) REVERT: AG 60 TYR cc_start: 0.7905 (t80) cc_final: 0.7630 (t80) REVERT: AG 64 ASN cc_start: 0.8611 (m-40) cc_final: 0.8051 (m-40) REVERT: AH 61 THR cc_start: 0.3856 (t) cc_final: 0.3216 (t) REVERT: AH 63 GLU cc_start: 0.3646 (mt-10) cc_final: 0.2981 (mt-10) REVERT: AH 86 LYS cc_start: 0.8848 (pttp) cc_final: 0.8203 (mtmm) REVERT: Aa 76 ASP cc_start: 0.7671 (t0) cc_final: 0.7451 (t0) REVERT: Aa 165 ARG cc_start: 0.9155 (ttm110) cc_final: 0.8738 (ttm110) REVERT: Aa 209 ARG cc_start: 0.8451 (mtm180) cc_final: 0.7556 (mtm180) REVERT: Aa 270 PHE cc_start: 0.7976 (t80) cc_final: 0.7640 (t80) REVERT: Aa 274 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: Aa 392 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8259 (mtmm) REVERT: Aa 449 PHE cc_start: 0.8581 (m-80) cc_final: 0.8162 (m-80) REVERT: Aa 450 TYR cc_start: 0.8251 (t80) cc_final: 0.7299 (t80) REVERT: Ab 135 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7435 (tp30) REVERT: Ab 161 ASP cc_start: 0.8797 (t0) cc_final: 0.8465 (t70) REVERT: Ab 384 MET cc_start: 0.7920 (mtm) cc_final: 0.7584 (mtm) REVERT: Ac 20 ASP cc_start: 0.8326 (m-30) cc_final: 0.8041 (m-30) REVERT: Ac 89 MET cc_start: 0.8453 (tpp) cc_final: 0.8160 (tpp) REVERT: Ac 129 MET cc_start: 0.6928 (ptp) cc_final: 0.6706 (ptp) REVERT: Ac 138 MET cc_start: 0.6479 (tpt) cc_final: 0.5473 (tpt) REVERT: Ac 200 LEU cc_start: 0.9239 (tp) cc_final: 0.8927 (tt) REVERT: Ac 212 ASN cc_start: 0.7757 (t0) cc_final: 0.7169 (t0) REVERT: Ac 240 MET cc_start: 0.8679 (mmp) cc_final: 0.8259 (mmp) REVERT: Ac 265 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8369 (Cg_exo) REVERT: Ac 369 SER cc_start: 0.8938 (p) cc_final: 0.8400 (t) REVERT: Ac 373 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7082 (mt-10) REVERT: Ac 376 MET cc_start: 0.8270 (mmm) cc_final: 0.7900 (mmm) REVERT: Ad 102 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8961 (tt) REVERT: Ad 114 PHE cc_start: 0.8998 (t80) cc_final: 0.8754 (t80) REVERT: Ad 255 TYR cc_start: 0.7922 (m-80) cc_final: 0.7628 (m-80) REVERT: Ad 273 PHE cc_start: 0.9055 (t80) cc_final: 0.8548 (t80) REVERT: Ad 288 MET cc_start: 0.8203 (mmt) cc_final: 0.7671 (mmt) REVERT: Ae 156 LEU cc_start: 0.5812 (tp) cc_final: 0.5523 (tp) REVERT: Ae 244 ASP cc_start: 0.3024 (p0) cc_final: 0.1765 (t0) REVERT: Af 33 MET cc_start: 0.8378 (mmm) cc_final: 0.7858 (mmm) REVERT: Af 60 MET cc_start: 0.8827 (tpp) cc_final: 0.8095 (mpp) REVERT: Af 83 LYS cc_start: 0.8460 (mptt) cc_final: 0.8078 (mptt) REVERT: Af 89 PHE cc_start: 0.7579 (m-10) cc_final: 0.7327 (m-10) REVERT: Ah 70 PHE cc_start: 0.8323 (m-80) cc_final: 0.7809 (m-80) REVERT: Ai 78 PHE cc_start: 0.6443 (m-80) cc_final: 0.6218 (m-80) REVERT: Ak 23 MET cc_start: 0.7561 (mmp) cc_final: 0.6520 (mtm) outliers start: 115 outliers final: 58 residues processed: 926 average time/residue: 0.2088 time to fit residues: 303.7972 Evaluate side-chains 760 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 698 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 94 LEU 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 332 LEU Chi-restraints excluded: chain AD residue 205 HIS 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 85 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 57 SER 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 238 ILE 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 273 VAL 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 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: 0.3980 chunk 203 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 313 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 301 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 309 HIS ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 160 GLN Aa 175 ASN Aa 207 ASN Ab 45 ASN ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ac 68 HIS Ac 267 HIS Ac 308 HIS Ac 322 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.130728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100495 restraints weight = 73509.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102034 restraints weight = 43115.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103556 restraints weight = 30649.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104310 restraints weight = 24077.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.104426 restraints weight = 21777.037| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.491 31150 Z= 0.169 Angle : 0.694 14.492 42266 Z= 0.345 Chirality : 0.043 0.216 4590 Planarity : 0.005 0.070 5364 Dihedral : 9.956 130.503 4406 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.27 % Allowed : 18.17 % Favored : 77.56 % 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 aren not related in a simple way. whole: 0.54 (0.14), residues: 3721 helix: 1.01 (0.11), residues: 2004 sheet: -0.14 (0.27), residues: 379 loop : -0.35 (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 0.025 0.002 PHEAc 128 TRP 0.027 0.001 TRPAD 96 HIS 0.008 0.001 HISAA 249 Details of bonding type rmsd covalent geometry : bond 0.00392 (31137) covalent geometry : angle 0.69297 (42252) SS BOND : bond 0.00568 ( 7) SS BOND : angle 2.12566 ( 14) hydrogen bonds : bond 0.04460 ( 1735) hydrogen bonds : angle 5.05647 ( 4980) Misc. bond : bond 0.31374 ( 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 886 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 750 time to evaluate : 1.145 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: AA 91 TYR cc_start: 0.8640 (t80) cc_final: 0.8122 (t80) REVERT: AA 98 PHE cc_start: 0.8366 (m-10) cc_final: 0.8131 (m-80) REVERT: AA 134 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8321 (mtpp) REVERT: AA 149 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7099 (t0) REVERT: AA 229 MET cc_start: 0.8640 (mtp) cc_final: 0.8306 (mtp) REVERT: AA 440 MET cc_start: 0.8510 (ptp) cc_final: 0.8270 (ptp) REVERT: AB 77 LEU cc_start: 0.9420 (mt) cc_final: 0.9168 (mp) REVERT: AB 197 MET cc_start: 0.6713 (ttm) cc_final: 0.6494 (ttm) REVERT: AB 203 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: AB 235 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8037 (mt-10) REVERT: AB 271 ILE cc_start: 0.8387 (mt) cc_final: 0.8057 (pt) REVERT: AB 443 ASN cc_start: 0.8544 (t0) cc_final: 0.7849 (m-40) REVERT: AC 31 TRP cc_start: 0.8300 (m-90) cc_final: 0.7492 (m-90) REVERT: AC 82 MET cc_start: 0.8313 (tpp) cc_final: 0.8050 (tpp) REVERT: AC 89 MET cc_start: 0.8907 (mmm) cc_final: 0.8689 (mmm) REVERT: AC 214 ASP cc_start: 0.8841 (m-30) cc_final: 0.8595 (m-30) REVERT: AC 216 ASP cc_start: 0.8590 (t0) cc_final: 0.8329 (t0) REVERT: AC 282 ARG cc_start: 0.7752 (mmm-85) cc_final: 0.7547 (mmm-85) REVERT: AD 96 TRP cc_start: 0.6989 (m-90) cc_final: 0.6574 (m-90) REVERT: AD 146 LYS cc_start: 0.9419 (ptmt) cc_final: 0.9064 (ptmm) REVERT: AD 150 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8212 (mt-10) REVERT: AD 174 TYR cc_start: 0.7620 (m-80) cc_final: 0.7117 (m-80) REVERT: AD 181 ASN cc_start: 0.7636 (t0) cc_final: 0.7269 (t0) REVERT: AD 244 MET cc_start: 0.7648 (tmm) cc_final: 0.7342 (tmm) REVERT: AE 89 SER cc_start: 0.8628 (m) cc_final: 0.8315 (m) REVERT: AE 92 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6869 (ttm110) REVERT: AE 93 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6897 (ttm-80) REVERT: AF 45 LYS cc_start: 0.9377 (mtpp) cc_final: 0.8779 (mtmm) REVERT: AF 79 ASP cc_start: 0.8720 (p0) cc_final: 0.8422 (p0) REVERT: AF 101 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8813 (mt-10) REVERT: AF 110 LYS cc_start: 0.6876 (mtmt) cc_final: 0.6602 (mtmt) REVERT: AG 40 ARG cc_start: 0.8669 (tmm160) cc_final: 0.8128 (tmm160) REVERT: AG 60 TYR cc_start: 0.7888 (t80) cc_final: 0.7661 (t80) REVERT: AG 64 ASN cc_start: 0.8773 (m-40) cc_final: 0.8291 (m-40) REVERT: AG 65 GLN cc_start: 0.8329 (pp30) cc_final: 0.8109 (pp30) REVERT: AH 45 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7334 (mmt180) REVERT: AH 61 THR cc_start: 0.3753 (t) cc_final: 0.3533 (t) REVERT: AH 86 LYS cc_start: 0.8780 (pttp) cc_final: 0.8130 (mtmm) REVERT: Aa 79 SER cc_start: 0.9051 (m) cc_final: 0.7911 (t) REVERT: Aa 160 GLN cc_start: 0.5687 (OUTLIER) cc_final: 0.5119 (pm20) REVERT: Aa 164 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8438 (mm-30) REVERT: Aa 165 ARG cc_start: 0.9147 (ttm110) cc_final: 0.8853 (ttm110) REVERT: Aa 174 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7359 (tm-30) REVERT: Aa 209 ARG cc_start: 0.8504 (mtm180) cc_final: 0.7887 (mtm-85) REVERT: Aa 274 GLU cc_start: 0.8441 (tt0) cc_final: 0.8224 (tt0) REVERT: Aa 280 ASP cc_start: 0.8777 (m-30) cc_final: 0.8517 (m-30) REVERT: Aa 392 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8272 (mtmm) REVERT: Aa 450 TYR cc_start: 0.8276 (t80) cc_final: 0.7283 (t80) REVERT: Ab 135 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7500 (tp30) REVERT: Ab 161 ASP cc_start: 0.8951 (t0) cc_final: 0.8513 (t0) REVERT: Ab 261 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8290 (tp40) REVERT: Ab 384 MET cc_start: 0.8042 (mtm) cc_final: 0.7708 (mtm) REVERT: Ab 406 TYR cc_start: 0.7948 (t80) cc_final: 0.7490 (t80) REVERT: Ac 20 ASP cc_start: 0.8456 (m-30) cc_final: 0.8129 (m-30) REVERT: Ac 89 MET cc_start: 0.8364 (tpp) cc_final: 0.8153 (tpp) REVERT: Ac 91 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: Ac 138 MET cc_start: 0.7039 (tpt) cc_final: 0.5630 (tpt) REVERT: Ac 200 LEU cc_start: 0.9346 (tp) cc_final: 0.9080 (tt) REVERT: Ac 214 ASP cc_start: 0.8615 (m-30) cc_final: 0.8333 (p0) REVERT: Ac 369 SER cc_start: 0.9072 (p) cc_final: 0.8647 (t) REVERT: Ac 373 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7108 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8990 (tt) REVERT: Ad 114 PHE cc_start: 0.9074 (t80) cc_final: 0.8872 (t80) REVERT: Ad 255 TYR cc_start: 0.8044 (m-80) cc_final: 0.7677 (m-80) REVERT: Ad 273 PHE cc_start: 0.9008 (t80) cc_final: 0.8446 (t80) REVERT: Ad 288 MET cc_start: 0.8335 (mmt) cc_final: 0.7847 (mmt) REVERT: Ae 140 MET cc_start: 0.8047 (mtp) cc_final: 0.7647 (mtp) REVERT: Af 19 LYS cc_start: 0.8946 (tptm) cc_final: 0.8673 (tptp) REVERT: Af 58 ASP cc_start: 0.8889 (t0) cc_final: 0.8578 (t0) REVERT: Af 60 MET cc_start: 0.9012 (tpp) cc_final: 0.8634 (tpp) REVERT: Af 74 GLN cc_start: 0.8614 (mm110) cc_final: 0.8369 (mm110) REVERT: Af 83 LYS cc_start: 0.8381 (mptt) cc_final: 0.8016 (mptt) REVERT: Af 89 PHE cc_start: 0.7722 (m-10) cc_final: 0.7451 (m-10) REVERT: Ag 37 ASN cc_start: 0.8634 (m-40) cc_final: 0.8368 (t0) REVERT: Ah 70 PHE cc_start: 0.8299 (m-80) cc_final: 0.7997 (m-80) REVERT: Ai 67 THR cc_start: 0.8674 (m) cc_final: 0.8193 (p) REVERT: Ai 78 PHE cc_start: 0.6635 (m-80) cc_final: 0.6377 (m-80) REVERT: Ak 23 MET cc_start: 0.7443 (mmp) cc_final: 0.6545 (mtm) outliers start: 136 outliers final: 79 residues processed: 827 average time/residue: 0.2027 time to fit residues: 266.7830 Evaluate side-chains 727 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 640 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 133 ILE Chi-restraints excluded: chain AA residue 143 VAL Chi-restraints excluded: chain AA residue 149 ASP 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 417 LEU Chi-restraints excluded: chain AB residue 48 VAL 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 65 SER Chi-restraints excluded: chain AC residue 78 LEU 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 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 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 266 VAL Chi-restraints excluded: chain AD residue 290 LEU Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 92 ARG Chi-restraints excluded: chain AE residue 93 ARG 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 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 160 GLN 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 250 LEU Chi-restraints excluded: chain Aa residue 273 SER 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 258 ILE Chi-restraints excluded: chain Ab residue 261 GLN 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 91 PHE 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 205 SER Chi-restraints excluded: chain Ac residue 336 THR 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 Ad residue 303 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 Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Aj residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 240 optimal weight: 8.9990 chunk 148 optimal weight: 30.0000 chunk 254 optimal weight: 0.9980 chunk 357 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 338 optimal weight: 0.3980 chunk 322 optimal weight: 10.0000 chunk 237 optimal weight: 0.4980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 23 ASN ** AF 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 160 GLN Ab 167 GLN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 227 HIS Ab 365 ASN Ac 212 ASN Ad 134 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Ai 58 GLN Aj 48 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.129090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.099836 restraints weight = 73549.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100262 restraints weight = 41999.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102172 restraints weight = 31885.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103251 restraints weight = 23095.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103130 restraints weight = 21560.915| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.429 31150 Z= 0.173 Angle : 0.684 15.239 42266 Z= 0.335 Chirality : 0.043 0.192 4590 Planarity : 0.004 0.063 5364 Dihedral : 9.640 134.250 4406 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.89 % Allowed : 19.99 % Favored : 76.11 % 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 aren not related in a simple way. whole: 0.63 (0.14), residues: 3721 helix: 1.07 (0.12), residues: 2004 sheet: -0.10 (0.27), residues: 384 loop : -0.27 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAF 34 TYR 0.020 0.002 TYRAf 22 PHE 0.023 0.002 PHEAE 136 TRP 0.022 0.001 TRPAk 38 HIS 0.006 0.001 HISAD 309 Details of bonding type rmsd covalent geometry : bond 0.00404 (31137) covalent geometry : angle 0.68354 (42252) SS BOND : bond 0.00456 ( 7) SS BOND : angle 1.26006 ( 14) hydrogen bonds : bond 0.04218 ( 1735) hydrogen bonds : angle 4.91910 ( 4980) Misc. bond : bond 0.29379 ( 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 813 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 689 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 91 TYR cc_start: 0.8709 (t80) cc_final: 0.8369 (t80) REVERT: AA 440 MET cc_start: 0.8513 (ptp) cc_final: 0.8277 (ptp) REVERT: AB 77 LEU cc_start: 0.9382 (mt) cc_final: 0.9146 (mp) REVERT: AB 197 MET cc_start: 0.6956 (ttm) cc_final: 0.6654 (ttm) REVERT: AB 203 GLU cc_start: 0.8137 (pt0) cc_final: 0.7753 (tm-30) REVERT: AB 235 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8106 (mt-10) REVERT: AB 271 ILE cc_start: 0.8557 (mt) cc_final: 0.8206 (pt) REVERT: AB 429 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8431 (ttmm) REVERT: AB 443 ASN cc_start: 0.8396 (t0) cc_final: 0.7806 (m-40) REVERT: AC 31 TRP cc_start: 0.8167 (m-90) cc_final: 0.7421 (m-90) REVERT: AC 69 ILE cc_start: 0.8580 (mm) cc_final: 0.8082 (mt) REVERT: AC 89 MET cc_start: 0.8806 (mmm) cc_final: 0.8543 (mmm) REVERT: AC 181 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: AC 212 ASN cc_start: 0.7819 (t0) cc_final: 0.7511 (m-40) REVERT: AC 216 ASP cc_start: 0.8472 (t0) cc_final: 0.8177 (t0) REVERT: AD 93 SER cc_start: 0.8545 (m) cc_final: 0.8046 (p) REVERT: AD 146 LYS cc_start: 0.9394 (ptmt) cc_final: 0.9051 (ptmm) REVERT: AD 150 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8035 (mt-10) REVERT: AD 174 TYR cc_start: 0.7634 (m-80) cc_final: 0.7406 (m-80) REVERT: AD 181 ASN cc_start: 0.7775 (t0) cc_final: 0.7378 (t0) REVERT: AD 244 MET cc_start: 0.7359 (tmm) cc_final: 0.7022 (tmm) REVERT: AD 291 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8239 (mmmm) REVERT: AE 92 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6884 (ttm110) REVERT: AF 42 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8011 (mm-30) REVERT: AF 45 LYS cc_start: 0.9389 (mtpp) cc_final: 0.8693 (mtmm) REVERT: AF 71 MET cc_start: 0.8459 (tmm) cc_final: 0.8225 (tmm) REVERT: AF 79 ASP cc_start: 0.8679 (p0) cc_final: 0.8340 (p0) REVERT: AF 85 GLU cc_start: 0.8458 (pm20) cc_final: 0.7643 (pm20) REVERT: AF 102 ARG cc_start: 0.9194 (tmm-80) cc_final: 0.8973 (tmm-80) REVERT: AF 110 LYS cc_start: 0.6926 (mtmt) cc_final: 0.6717 (mtmt) REVERT: AG 57 TYR cc_start: 0.8256 (t80) cc_final: 0.7928 (t80) REVERT: AH 45 ARG cc_start: 0.7442 (ttm110) cc_final: 0.7124 (mmt180) REVERT: Aa 79 SER cc_start: 0.9088 (m) cc_final: 0.8147 (t) REVERT: Aa 164 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8371 (mm-30) REVERT: Aa 165 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8912 (ttm110) REVERT: Aa 174 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7298 (tm-30) REVERT: Aa 280 ASP cc_start: 0.8830 (m-30) cc_final: 0.8594 (m-30) REVERT: Aa 449 PHE cc_start: 0.8706 (m-10) cc_final: 0.8409 (m-10) REVERT: Ab 261 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8267 (tp40) REVERT: Ab 311 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8483 (pp30) REVERT: Ab 384 MET cc_start: 0.8133 (mtm) cc_final: 0.7897 (mtm) REVERT: Ab 407 MET cc_start: 0.8161 (mmp) cc_final: 0.7852 (tpp) REVERT: Ac 20 ASP cc_start: 0.8458 (m-30) cc_final: 0.8045 (m-30) REVERT: Ac 141 TRP cc_start: 0.8018 (m100) cc_final: 0.7334 (m100) REVERT: Ac 200 LEU cc_start: 0.9391 (tp) cc_final: 0.9133 (tt) REVERT: Ac 214 ASP cc_start: 0.8765 (m-30) cc_final: 0.8476 (p0) REVERT: Ac 217 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8495 (mtmm) REVERT: Ac 373 GLU cc_start: 0.7861 (mt-10) cc_final: 0.6954 (mp0) REVERT: Ad 102 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9237 (tt) REVERT: Ad 103 SER cc_start: 0.8578 (m) cc_final: 0.8031 (p) REVERT: Ad 242 ILE cc_start: 0.8099 (tt) cc_final: 0.7880 (tt) REVERT: Ad 273 PHE cc_start: 0.9030 (t80) cc_final: 0.8398 (t80) REVERT: Ad 288 MET cc_start: 0.8473 (mmt) cc_final: 0.7915 (mmt) REVERT: Ae 140 MET cc_start: 0.8386 (mtp) cc_final: 0.7710 (mmm) REVERT: Ae 156 LEU cc_start: 0.5385 (tp) cc_final: 0.5130 (tp) REVERT: Ae 244 ASP cc_start: 0.1170 (p0) cc_final: 0.0459 (t70) REVERT: Ae 248 ARG cc_start: 0.4077 (mtm180) cc_final: 0.3583 (ptt180) REVERT: Af 19 LYS cc_start: 0.8866 (tptm) cc_final: 0.8640 (tptp) REVERT: Af 33 MET cc_start: 0.8197 (mmm) cc_final: 0.7964 (mtp) REVERT: Af 58 ASP cc_start: 0.8880 (t0) cc_final: 0.8481 (t0) REVERT: Af 60 MET cc_start: 0.9188 (tpp) cc_final: 0.8750 (tpp) REVERT: Af 74 GLN cc_start: 0.8632 (mm110) cc_final: 0.8292 (mm110) REVERT: Af 83 LYS cc_start: 0.8385 (mptt) cc_final: 0.8039 (mptt) REVERT: Af 89 PHE cc_start: 0.7863 (m-10) cc_final: 0.7600 (m-10) REVERT: Ag 37 ASN cc_start: 0.8531 (m-40) cc_final: 0.8170 (t0) REVERT: Ah 70 PHE cc_start: 0.8330 (m-80) cc_final: 0.7847 (m-10) REVERT: Ai 67 THR cc_start: 0.8710 (m) cc_final: 0.8229 (p) REVERT: Ai 78 PHE cc_start: 0.6966 (m-80) cc_final: 0.6573 (m-80) REVERT: Ak 23 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6689 (mtm) outliers start: 124 outliers final: 83 residues processed: 763 average time/residue: 0.1990 time to fit residues: 242.8178 Evaluate side-chains 719 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 628 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 142 THR 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 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 185 LEU 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 332 LEU Chi-restraints excluded: chain AC residue 366 MET 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 250 THR Chi-restraints excluded: chain AD residue 266 VAL 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 92 ARG 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 230 VAL Chi-restraints excluded: chain Aa residue 250 LEU 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 158 LEU Chi-restraints excluded: chain Ab residue 164 VAL 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 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 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 226 ILE Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ad residue 102 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 Chi-restraints excluded: chain Ad residue 266 VAL Chi-restraints excluded: chain Ad residue 272 THR 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 Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Ak residue 23 MET 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: 9.9990 chunk 49 optimal weight: 2.9990 chunk 210 optimal weight: 0.5980 chunk 232 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 276 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 295 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 303 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 249 HIS AB 211 ASN ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 309 HIS AF 57 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ac 212 ASN Ad 90 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 = 0.3963 r_free = 0.3963 target = 0.131466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.100260 restraints weight = 73153.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102407 restraints weight = 40357.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103846 restraints weight = 27295.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104411 restraints weight = 22392.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104574 restraints weight = 20375.333| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.373 31150 Z= 0.152 Angle : 0.668 14.595 42266 Z= 0.326 Chirality : 0.042 0.242 4590 Planarity : 0.004 0.058 5364 Dihedral : 9.418 125.165 4406 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.24 % Allowed : 20.21 % Favored : 75.55 % 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 aren not related in a simple way. whole: 0.74 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 2007 sheet: 0.05 (0.28), residues: 368 loop : -0.21 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGAA 378 TYR 0.023 0.002 TYRAf 22 PHE 0.030 0.002 PHEAD 237 TRP 0.022 0.001 TRPAk 38 HIS 0.005 0.001 HISAd 134 Details of bonding type rmsd covalent geometry : bond 0.00359 (31137) covalent geometry : angle 0.66796 (42252) SS BOND : bond 0.00451 ( 7) SS BOND : angle 1.04975 ( 14) hydrogen bonds : bond 0.04017 ( 1735) hydrogen bonds : angle 4.81930 ( 4980) Misc. bond : bond 0.25254 ( 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 827 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 692 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 91 TYR cc_start: 0.8721 (t80) cc_final: 0.8501 (t80) REVERT: AA 149 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7300 (t0) REVERT: AA 440 MET cc_start: 0.8553 (ptp) cc_final: 0.8322 (ptp) REVERT: AB 77 LEU cc_start: 0.9354 (mt) cc_final: 0.9121 (mp) REVERT: AB 197 MET cc_start: 0.6860 (ttm) cc_final: 0.6316 (ttm) REVERT: AB 203 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: AB 235 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8047 (mt-10) REVERT: AB 271 ILE cc_start: 0.8455 (mt) cc_final: 0.8207 (pt) REVERT: AB 429 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8428 (ttmm) REVERT: AB 443 ASN cc_start: 0.8337 (t0) cc_final: 0.7688 (m-40) REVERT: AC 31 TRP cc_start: 0.8113 (m-90) cc_final: 0.7225 (m-90) REVERT: AC 82 MET cc_start: 0.8531 (tpp) cc_final: 0.8066 (tpt) REVERT: AC 181 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: AC 212 ASN cc_start: 0.7587 (t0) cc_final: 0.7124 (m-40) REVERT: AC 216 ASP cc_start: 0.8493 (t0) cc_final: 0.8237 (t70) REVERT: AD 93 SER cc_start: 0.8281 (m) cc_final: 0.7872 (p) REVERT: AD 96 TRP cc_start: 0.7149 (m-90) cc_final: 0.6529 (m-90) REVERT: AD 114 PHE cc_start: 0.7411 (t80) cc_final: 0.7158 (t80) REVERT: AD 146 LYS cc_start: 0.9402 (ptmt) cc_final: 0.9081 (ptmm) REVERT: AD 150 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8027 (mt-10) REVERT: AD 174 TYR cc_start: 0.7700 (m-80) cc_final: 0.7428 (m-80) REVERT: AD 181 ASN cc_start: 0.7591 (t0) cc_final: 0.7098 (t0) REVERT: AD 244 MET cc_start: 0.7379 (tmm) cc_final: 0.7019 (tmm) REVERT: AE 92 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6805 (ttm110) REVERT: AF 40 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7727 (mt-10) REVERT: AF 42 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7959 (mm-30) REVERT: AF 45 LYS cc_start: 0.9404 (mtpp) cc_final: 0.8798 (mtmm) REVERT: AF 71 MET cc_start: 0.8458 (tmm) cc_final: 0.8195 (tmm) REVERT: AF 79 ASP cc_start: 0.8655 (p0) cc_final: 0.8329 (p0) REVERT: AF 85 GLU cc_start: 0.8172 (pm20) cc_final: 0.7767 (pm20) REVERT: AG 57 TYR cc_start: 0.8310 (t80) cc_final: 0.8006 (t80) REVERT: AG 60 TYR cc_start: 0.8461 (t80) cc_final: 0.8067 (t80) REVERT: AH 86 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7623 (ptpp) REVERT: Aa 79 SER cc_start: 0.8993 (m) cc_final: 0.7974 (t) REVERT: Aa 165 ARG cc_start: 0.9106 (ttm110) cc_final: 0.8852 (ttm110) REVERT: Aa 174 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7282 (tm-30) REVERT: Aa 280 ASP cc_start: 0.8841 (m-30) cc_final: 0.8601 (m-30) REVERT: Aa 468 TYR cc_start: 0.8516 (t80) cc_final: 0.7995 (t80) REVERT: Ab 159 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8688 (tptt) REVERT: Ab 261 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8270 (tp40) REVERT: Ab 407 MET cc_start: 0.8059 (mmp) cc_final: 0.7795 (mmt) REVERT: Ac 20 ASP cc_start: 0.8478 (m-30) cc_final: 0.8092 (m-30) REVERT: Ac 53 MET cc_start: 0.5282 (ttt) cc_final: 0.4996 (ttt) REVERT: Ac 141 TRP cc_start: 0.8002 (m100) cc_final: 0.7403 (m100) REVERT: Ac 214 ASP cc_start: 0.8711 (m-30) cc_final: 0.8486 (p0) REVERT: Ac 217 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8487 (mtmm) REVERT: Ac 282 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8344 (ptp90) REVERT: Ac 373 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7138 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9263 (tt) REVERT: Ad 103 SER cc_start: 0.8739 (m) cc_final: 0.8030 (p) REVERT: Ad 244 MET cc_start: 0.8849 (ttp) cc_final: 0.8467 (ttp) REVERT: Ad 273 PHE cc_start: 0.9002 (t80) cc_final: 0.8384 (t80) REVERT: Ad 288 MET cc_start: 0.8312 (mmt) cc_final: 0.7779 (mmt) REVERT: Ae 131 ASN cc_start: 0.7096 (t0) cc_final: 0.6636 (t0) REVERT: Ae 140 MET cc_start: 0.8658 (mtp) cc_final: 0.7975 (mmm) REVERT: Ae 156 LEU cc_start: 0.5178 (tp) cc_final: 0.4892 (tp) REVERT: Ae 244 ASP cc_start: 0.1069 (p0) cc_final: -0.0066 (t0) REVERT: Ae 248 ARG cc_start: 0.4125 (mtm180) cc_final: 0.3610 (ptt180) REVERT: Af 33 MET cc_start: 0.8208 (mmm) cc_final: 0.7989 (mtp) REVERT: Af 58 ASP cc_start: 0.8840 (t0) cc_final: 0.8372 (t0) REVERT: Af 60 MET cc_start: 0.9191 (tpp) cc_final: 0.8756 (tpp) REVERT: Af 83 LYS cc_start: 0.8331 (mptt) cc_final: 0.8120 (mptt) REVERT: Ag 37 ASN cc_start: 0.8501 (m-40) cc_final: 0.8247 (t0) REVERT: Ag 60 TYR cc_start: 0.9059 (t80) cc_final: 0.8770 (t80) REVERT: Ah 52 ASP cc_start: 0.8583 (t0) cc_final: 0.8262 (p0) REVERT: Ai 67 THR cc_start: 0.8708 (m) cc_final: 0.8315 (p) REVERT: Ai 78 PHE cc_start: 0.6926 (m-80) cc_final: 0.6465 (m-80) REVERT: Ak 23 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.6761 (mtm) outliers start: 135 outliers final: 92 residues processed: 765 average time/residue: 0.2041 time to fit residues: 249.5436 Evaluate side-chains 736 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 633 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain AA residue 149 ASP Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 250 LEU 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 445 CYS Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 58 LEU 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 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 42 MET 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 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 185 LEU 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 332 LEU Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 154 VAL 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 250 THR 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 92 ARG Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 63 ILE 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 AH residue 86 LYS Chi-restraints excluded: chain Aa residue 52 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 250 LEU 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 Aa residue 399 LEU Chi-restraints excluded: chain Aa residue 462 ILE Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 209 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 43 VAL Chi-restraints excluded: chain Ac residue 57 SER 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 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 226 ILE 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 Ad residue 102 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 Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 132 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 Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 48 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 21 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 198 optimal weight: 0.0040 chunk 310 optimal weight: 0.0980 overall best weight: 2.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 119 HIS ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Aa 249 HIS Ab 45 ASN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ac 16 HIS Ac 212 ASN Af 23 ASN ** Ag 37 ASN ** 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 = 0.3898 r_free = 0.3898 target = 0.127503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096431 restraints weight = 73627.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097620 restraints weight = 45134.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.098298 restraints weight = 30252.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.098951 restraints weight = 29484.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.099466 restraints weight = 24452.137| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.556 31150 Z= 0.223 Angle : 0.738 18.034 42266 Z= 0.357 Chirality : 0.045 0.301 4590 Planarity : 0.005 0.073 5364 Dihedral : 9.426 128.289 4406 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.08 % Allowed : 20.31 % Favored : 74.61 % 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 aren not related in a simple way. whole: 0.60 (0.14), residues: 3721 helix: 0.99 (0.12), residues: 2016 sheet: 0.07 (0.28), residues: 359 loop : -0.27 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGAh 47 TYR 0.022 0.002 TYRAg 17 PHE 0.025 0.002 PHEAa 449 TRP 0.017 0.002 TRPAF 108 HIS 0.010 0.001 HISAc 196 Details of bonding type rmsd covalent geometry : bond 0.00518 (31137) covalent geometry : angle 0.73728 (42252) SS BOND : bond 0.00505 ( 7) SS BOND : angle 1.33126 ( 14) hydrogen bonds : bond 0.04286 ( 1735) hydrogen bonds : angle 4.94243 ( 4980) Misc. bond : bond 0.33553 ( 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 826 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 664 time to evaluate : 1.206 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: AA 437 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7575 (p0) REVERT: AB 77 LEU cc_start: 0.9382 (mt) cc_final: 0.9121 (mp) REVERT: AB 172 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7540 (ttm-80) REVERT: AB 197 MET cc_start: 0.7379 (ttm) cc_final: 0.6718 (ttm) REVERT: AB 203 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: AB 271 ILE cc_start: 0.8627 (mt) cc_final: 0.8347 (pt) REVERT: AB 415 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7942 (tm-30) REVERT: AB 429 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8493 (ttmm) REVERT: AC 31 TRP cc_start: 0.8170 (m-90) cc_final: 0.7427 (m-90) REVERT: AC 82 MET cc_start: 0.8664 (tpp) cc_final: 0.8233 (tpt) REVERT: AC 89 MET cc_start: 0.8770 (mmm) cc_final: 0.8497 (mmm) REVERT: AC 91 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7827 (t80) REVERT: AC 212 ASN cc_start: 0.7931 (t0) cc_final: 0.7607 (m-40) REVERT: AC 216 ASP cc_start: 0.8371 (t0) cc_final: 0.8060 (t70) REVERT: AC 313 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8081 (ttt180) REVERT: AD 96 TRP cc_start: 0.7052 (m-90) cc_final: 0.6529 (m-90) REVERT: AD 174 TYR cc_start: 0.7588 (m-80) cc_final: 0.7275 (m-80) REVERT: AD 181 ASN cc_start: 0.7666 (t0) cc_final: 0.7168 (t0) REVERT: AD 244 MET cc_start: 0.7230 (tmm) cc_final: 0.6901 (tmm) REVERT: AD 292 MET cc_start: 0.7586 (mmp) cc_final: 0.7346 (mmt) REVERT: AE 92 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6985 (ttm110) REVERT: AF 40 GLU cc_start: 0.8789 (mt-10) cc_final: 0.7821 (mt-10) REVERT: AF 45 LYS cc_start: 0.9456 (mtpp) cc_final: 0.8963 (mtmm) REVERT: AF 71 MET cc_start: 0.8375 (tmm) cc_final: 0.8129 (tmm) REVERT: AF 79 ASP cc_start: 0.8726 (p0) cc_final: 0.8354 (p0) REVERT: AF 85 GLU cc_start: 0.8356 (pm20) cc_final: 0.7958 (pm20) REVERT: AF 86 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7542 (mm-30) REVERT: AK 23 MET cc_start: 0.3020 (tmm) cc_final: 0.2780 (tmm) REVERT: Aa 79 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8096 (t) REVERT: Aa 175 ASN cc_start: 0.8337 (t0) cc_final: 0.7956 (p0) REVERT: Aa 209 ARG cc_start: 0.8610 (mtm180) cc_final: 0.8240 (mtm180) REVERT: Aa 468 TYR cc_start: 0.8536 (t80) cc_final: 0.8097 (t80) REVERT: Ab 213 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: Ac 20 ASP cc_start: 0.8578 (m-30) cc_final: 0.8157 (m-30) REVERT: Ac 53 MET cc_start: 0.5641 (ttt) cc_final: 0.5292 (ttt) REVERT: Ac 141 TRP cc_start: 0.8006 (m100) cc_final: 0.7316 (m100) REVERT: Ac 187 PHE cc_start: 0.7914 (m-80) cc_final: 0.7373 (m-80) REVERT: Ac 214 ASP cc_start: 0.8916 (m-30) cc_final: 0.8638 (p0) REVERT: Ac 217 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8448 (mtmm) REVERT: Ac 369 SER cc_start: 0.9084 (p) cc_final: 0.8678 (t) REVERT: Ac 373 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7361 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9357 (tt) REVERT: Ad 103 SER cc_start: 0.8938 (m) cc_final: 0.8411 (p) REVERT: Ad 164 MET cc_start: 0.8701 (tpp) cc_final: 0.8467 (tpp) REVERT: Ad 288 MET cc_start: 0.8508 (mmt) cc_final: 0.7971 (mmt) REVERT: Ae 131 ASN cc_start: 0.7223 (t0) cc_final: 0.6791 (t0) REVERT: Ae 140 MET cc_start: 0.8787 (mtp) cc_final: 0.8022 (mmm) REVERT: Ae 156 LEU cc_start: 0.5185 (tp) cc_final: 0.4876 (tp) REVERT: Ae 244 ASP cc_start: 0.1380 (p0) cc_final: 0.0278 (t0) REVERT: Ae 248 ARG cc_start: 0.4206 (mtm180) cc_final: 0.3534 (ptt180) REVERT: Af 33 MET cc_start: 0.8613 (mmm) cc_final: 0.8158 (mtp) REVERT: Af 58 ASP cc_start: 0.8883 (t0) cc_final: 0.8430 (t0) REVERT: Af 60 MET cc_start: 0.9269 (tpp) cc_final: 0.8874 (tpp) REVERT: Af 75 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9038 (mp) REVERT: Af 83 LYS cc_start: 0.8518 (mptt) cc_final: 0.8249 (mptt) REVERT: Ah 47 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7812 (mmm160) REVERT: Ah 50 LEU cc_start: 0.8408 (mm) cc_final: 0.8145 (mm) REVERT: Ah 52 ASP cc_start: 0.8731 (t0) cc_final: 0.8274 (p0) REVERT: Ai 67 THR cc_start: 0.8733 (m) cc_final: 0.8350 (p) REVERT: Ai 78 PHE cc_start: 0.7065 (m-80) cc_final: 0.6639 (m-80) REVERT: Aj 38 GLN cc_start: 0.8192 (tt0) cc_final: 0.7724 (mm-40) REVERT: Ak 23 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6844 (mtm) outliers start: 162 outliers final: 113 residues processed: 758 average time/residue: 0.2011 time to fit residues: 245.4443 Evaluate side-chains 736 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 613 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 143 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 437 ASP Chi-restraints excluded: chain AA residue 445 CYS 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 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 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 189 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 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 AC residue 366 MET Chi-restraints excluded: chain AD residue 196 ASP Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 250 THR 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 79 SER 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 184 PHE 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 250 LEU Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 275 ILE Chi-restraints excluded: chain Aa residue 310 ILE 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 156 SER Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 192 CYS 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 419 VAL Chi-restraints excluded: chain Ab residue 447 THR 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 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 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL 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 226 ILE Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 294 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 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 Ad residue 300 LEU Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Af residue 23 ASN Chi-restraints excluded: chain Af residue 71 MET Chi-restraints excluded: chain Af residue 75 ILE 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 Ag residue 74 ASN 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: 4.9990 chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 338 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Aa 95 HIS Ab 45 ASN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ac 212 ASN Ad 90 HIS Af 23 ASN Ag 7 ASN Ah 34 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.095695 restraints weight = 74143.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097503 restraints weight = 43539.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097790 restraints weight = 30014.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098149 restraints weight = 28025.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.098565 restraints weight = 25150.733| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.553 31150 Z= 0.218 Angle : 0.738 17.757 42266 Z= 0.356 Chirality : 0.045 0.268 4590 Planarity : 0.005 0.055 5364 Dihedral : 9.308 123.324 4406 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.83 % Allowed : 21.78 % Favored : 73.38 % 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 aren not related in a simple way. whole: 0.54 (0.14), residues: 3721 helix: 0.99 (0.12), residues: 2002 sheet: -0.07 (0.28), residues: 363 loop : -0.33 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGAh 47 TYR 0.028 0.002 TYRAc 104 PHE 0.034 0.002 PHEAh 70 TRP 0.015 0.001 TRPAF 108 HIS 0.027 0.001 HISAD 309 Details of bonding type rmsd covalent geometry : bond 0.00506 (31137) covalent geometry : angle 0.73811 (42252) SS BOND : bond 0.00433 ( 7) SS BOND : angle 1.25009 ( 14) hydrogen bonds : bond 0.04222 ( 1735) hydrogen bonds : angle 4.94799 ( 4980) Misc. bond : bond 0.32875 ( 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 801 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 647 time to evaluate : 1.277 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: AA 437 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7343 (p0) REVERT: AB 77 LEU cc_start: 0.9401 (mt) cc_final: 0.9118 (mp) REVERT: AB 172 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7543 (ttm-80) REVERT: AB 197 MET cc_start: 0.7575 (ttm) cc_final: 0.6624 (ttm) REVERT: AB 203 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: AB 257 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6634 (mt-10) REVERT: AB 271 ILE cc_start: 0.8673 (mt) cc_final: 0.8421 (pt) REVERT: AB 415 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7959 (tm-30) REVERT: AB 429 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: AC 31 TRP cc_start: 0.8184 (m-90) cc_final: 0.7460 (m-90) REVERT: AC 82 MET cc_start: 0.8693 (tpp) cc_final: 0.8247 (tpt) REVERT: AC 91 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7808 (t80) REVERT: AC 212 ASN cc_start: 0.8092 (t0) cc_final: 0.7846 (m-40) REVERT: AC 216 ASP cc_start: 0.8340 (t0) cc_final: 0.7988 (t70) REVERT: AC 226 ILE cc_start: 0.8586 (tp) cc_final: 0.8251 (tt) REVERT: AC 313 ARG cc_start: 0.8560 (ttt180) cc_final: 0.8062 (ttt180) REVERT: AD 96 TRP cc_start: 0.7065 (m-90) cc_final: 0.6533 (m-90) REVERT: AD 174 TYR cc_start: 0.7639 (m-80) cc_final: 0.7322 (m-80) REVERT: AD 181 ASN cc_start: 0.7709 (t0) cc_final: 0.7213 (t0) REVERT: AD 244 MET cc_start: 0.7219 (tmm) cc_final: 0.6903 (tmm) REVERT: AD 296 MET cc_start: 0.6976 (mmp) cc_final: 0.5677 (mtt) REVERT: AE 92 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7117 (ttm110) REVERT: AF 40 GLU cc_start: 0.8810 (mt-10) cc_final: 0.7906 (mt-10) REVERT: AF 45 LYS cc_start: 0.9445 (mtpp) cc_final: 0.8979 (mtmm) REVERT: AF 76 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8984 (mm) REVERT: AF 79 ASP cc_start: 0.8746 (p0) cc_final: 0.8328 (p0) REVERT: AF 85 GLU cc_start: 0.8338 (pm20) cc_final: 0.8000 (pm20) REVERT: AF 92 GLU cc_start: 0.8496 (tp30) cc_final: 0.7866 (tp30) REVERT: Aa 79 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8078 (t) REVERT: Aa 123 TYR cc_start: 0.8731 (p90) cc_final: 0.8235 (p90) REVERT: Aa 175 ASN cc_start: 0.8382 (t0) cc_final: 0.7981 (p0) REVERT: Aa 468 TYR cc_start: 0.8440 (t80) cc_final: 0.8043 (t80) REVERT: Ab 213 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8329 (m-80) REVERT: Ab 407 MET cc_start: 0.8157 (mmp) cc_final: 0.7942 (tpp) REVERT: Ac 20 ASP cc_start: 0.8585 (m-30) cc_final: 0.8160 (m-30) REVERT: Ac 138 MET cc_start: 0.5952 (tpp) cc_final: 0.4909 (tpp) REVERT: Ac 141 TRP cc_start: 0.8002 (m100) cc_final: 0.7386 (m100) REVERT: Ac 187 PHE cc_start: 0.7992 (m-80) cc_final: 0.7467 (m-80) REVERT: Ac 217 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8449 (mtmm) REVERT: Ac 282 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8281 (ptp90) REVERT: Ac 373 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7397 (mt-10) REVERT: Ad 103 SER cc_start: 0.8880 (m) cc_final: 0.8405 (p) REVERT: Ad 288 MET cc_start: 0.8498 (mmt) cc_final: 0.7955 (mmt) REVERT: Ae 131 ASN cc_start: 0.7284 (t0) cc_final: 0.6818 (t0) REVERT: Ae 140 MET cc_start: 0.8679 (mtp) cc_final: 0.8364 (mmm) REVERT: Ae 244 ASP cc_start: 0.1390 (p0) cc_final: 0.0381 (t0) REVERT: Ae 248 ARG cc_start: 0.4292 (mtm180) cc_final: 0.3602 (ptt180) REVERT: Af 33 MET cc_start: 0.8563 (mmm) cc_final: 0.8087 (mtp) REVERT: Af 58 ASP cc_start: 0.8879 (t0) cc_final: 0.8425 (t0) REVERT: Af 60 MET cc_start: 0.9277 (tpp) cc_final: 0.8914 (tpp) REVERT: Af 75 ILE cc_start: 0.9221 (pt) cc_final: 0.8994 (mp) REVERT: Af 83 LYS cc_start: 0.8502 (mptt) cc_final: 0.8253 (mptt) REVERT: Ah 52 ASP cc_start: 0.8770 (t0) cc_final: 0.8198 (p0) REVERT: Ai 67 THR cc_start: 0.8718 (m) cc_final: 0.8336 (p) REVERT: Ai 78 PHE cc_start: 0.6980 (m-80) cc_final: 0.6510 (m-80) REVERT: Aj 13 LEU cc_start: 0.7548 (mm) cc_final: 0.7230 (mm) REVERT: Aj 16 ARG cc_start: 0.6914 (ptt-90) cc_final: 0.6675 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8170 (tt0) cc_final: 0.7698 (mm-40) REVERT: Ak 23 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6819 (mtm) outliers start: 154 outliers final: 116 residues processed: 732 average time/residue: 0.2015 time to fit residues: 237.6249 Evaluate side-chains 734 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 607 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 143 VAL 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 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 257 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 42 MET 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 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 189 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 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 AC residue 366 MET Chi-restraints excluded: chain AD residue 146 LYS 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 76 LEU Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AF residue 99 ILE 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 79 SER 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 250 LEU 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 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 192 CYS 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 43 VAL Chi-restraints excluded: chain Ac residue 57 SER 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 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 226 ILE 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 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 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 Af residue 23 ASN 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 Ag residue 74 ASN 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 42 VAL Chi-restraints excluded: chain Ai residue 45 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 112 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 207 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 36 GLN ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 365 ASN Ac 212 ASN Ad 90 HIS Af 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.129350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098107 restraints weight = 73821.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.100487 restraints weight = 41367.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101275 restraints weight = 26933.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101991 restraints weight = 24275.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.102155 restraints weight = 21268.466| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.423 31150 Z= 0.155 Angle : 0.711 16.111 42266 Z= 0.343 Chirality : 0.043 0.229 4590 Planarity : 0.004 0.063 5364 Dihedral : 9.183 131.942 4406 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.11 % Allowed : 22.82 % Favored : 73.07 % 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 aren not related in a simple way. whole: 0.66 (0.14), residues: 3721 helix: 1.08 (0.12), residues: 2004 sheet: -0.13 (0.27), residues: 384 loop : -0.24 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAD 111 TYR 0.030 0.001 TYRAf 21 PHE 0.034 0.002 PHEAc 276 TRP 0.015 0.001 TRPAa 376 HIS 0.007 0.001 HISAa 95 Details of bonding type rmsd covalent geometry : bond 0.00366 (31137) covalent geometry : angle 0.71107 (42252) SS BOND : bond 0.00361 ( 7) SS BOND : angle 1.19751 ( 14) hydrogen bonds : bond 0.03990 ( 1735) hydrogen bonds : angle 4.83936 ( 4980) Misc. bond : bond 0.26567 ( 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 803 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 672 time to evaluate : 1.457 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: AA 172 MET cc_start: 0.8804 (mtm) cc_final: 0.8516 (mtm) REVERT: AB 77 LEU cc_start: 0.9398 (mt) cc_final: 0.9117 (mp) REVERT: AB 197 MET cc_start: 0.7352 (ttm) cc_final: 0.6350 (ttm) REVERT: AB 271 ILE cc_start: 0.8628 (mt) cc_final: 0.8386 (pt) REVERT: AB 415 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7962 (tm-30) REVERT: AC 31 TRP cc_start: 0.8176 (m-90) cc_final: 0.7455 (m-90) REVERT: AC 79 ILE cc_start: 0.8241 (mm) cc_final: 0.8022 (tt) REVERT: AC 82 MET cc_start: 0.8500 (tpp) cc_final: 0.8073 (tpt) REVERT: AC 91 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7719 (t80) REVERT: AC 95 PHE cc_start: 0.7889 (m-80) cc_final: 0.7618 (m-80) REVERT: AC 212 ASN cc_start: 0.8113 (t0) cc_final: 0.7903 (m-40) REVERT: AC 216 ASP cc_start: 0.8317 (t0) cc_final: 0.7927 (t70) REVERT: AD 96 TRP cc_start: 0.7062 (m-90) cc_final: 0.6502 (m-90) REVERT: AD 174 TYR cc_start: 0.7808 (m-80) cc_final: 0.7524 (m-80) REVERT: AD 181 ASN cc_start: 0.7669 (t0) cc_final: 0.7170 (t0) REVERT: AD 244 MET cc_start: 0.7226 (tmm) cc_final: 0.6880 (tmm) REVERT: AD 296 MET cc_start: 0.7046 (mmp) cc_final: 0.5796 (mtt) REVERT: AD 306 MET cc_start: 0.8875 (tpp) cc_final: 0.8617 (tpp) REVERT: AE 92 ARG cc_start: 0.7439 (ttm110) cc_final: 0.7134 (ttm110) REVERT: AF 40 GLU cc_start: 0.8782 (mt-10) cc_final: 0.7961 (mt-10) REVERT: AF 45 LYS cc_start: 0.9423 (mtpp) cc_final: 0.8946 (mtmm) REVERT: AF 76 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8982 (mm) REVERT: AF 79 ASP cc_start: 0.8708 (p0) cc_final: 0.8226 (p0) REVERT: AF 85 GLU cc_start: 0.8210 (pm20) cc_final: 0.7884 (pm20) REVERT: AF 86 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7436 (mm-30) REVERT: AF 92 GLU cc_start: 0.8497 (tp30) cc_final: 0.7982 (tp30) REVERT: AG 17 TYR cc_start: 0.8602 (m-80) cc_final: 0.8384 (m-80) REVERT: AG 57 TYR cc_start: 0.8338 (t80) cc_final: 0.7969 (t80) REVERT: AG 73 LYS cc_start: 0.7496 (pttp) cc_final: 0.7154 (pptt) REVERT: AH 72 PHE cc_start: 0.5293 (t80) cc_final: 0.4558 (t80) REVERT: AH 82 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7973 (t-170) REVERT: Aa 63 GLN cc_start: 0.8680 (tt0) cc_final: 0.8459 (tp40) REVERT: Aa 79 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8063 (t) REVERT: Aa 209 ARG cc_start: 0.8429 (mtm180) cc_final: 0.8083 (mtm180) REVERT: Aa 212 SER cc_start: 0.8738 (p) cc_final: 0.8538 (p) REVERT: Ab 159 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8635 (tptt) REVERT: Ab 213 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: Ab 349 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: Ab 407 MET cc_start: 0.8082 (mmp) cc_final: 0.7864 (tpp) REVERT: Ac 20 ASP cc_start: 0.8529 (m-30) cc_final: 0.8139 (m-30) REVERT: Ac 138 MET cc_start: 0.5992 (tpp) cc_final: 0.4678 (tpp) REVERT: Ac 141 TRP cc_start: 0.8007 (m100) cc_final: 0.7397 (m100) REVERT: Ac 187 PHE cc_start: 0.7895 (m-80) cc_final: 0.7442 (m-80) REVERT: Ac 217 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: Ac 223 TYR cc_start: 0.8612 (m-80) cc_final: 0.8387 (m-80) REVERT: Ac 233 LEU cc_start: 0.9030 (mm) cc_final: 0.8300 (tt) REVERT: Ac 282 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8442 (ptp90) REVERT: Ac 373 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7406 (mt-10) REVERT: Ad 164 MET cc_start: 0.8775 (tpp) cc_final: 0.8378 (tpp) REVERT: Ad 253 LEU cc_start: 0.7806 (tp) cc_final: 0.7517 (pt) REVERT: Ad 279 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7867 (mt-10) REVERT: Ad 288 MET cc_start: 0.8489 (mmt) cc_final: 0.7939 (mmt) REVERT: Ae 131 ASN cc_start: 0.7137 (t0) cc_final: 0.6746 (t0) REVERT: Ae 156 LEU cc_start: 0.4673 (tp) cc_final: 0.4347 (tp) REVERT: Ae 244 ASP cc_start: 0.1341 (p0) cc_final: 0.0256 (t0) REVERT: Ae 248 ARG cc_start: 0.4067 (mtm180) cc_final: 0.3409 (ptt180) REVERT: Af 33 MET cc_start: 0.8298 (mmm) cc_final: 0.7967 (mtp) REVERT: Af 53 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8042 (tm-30) REVERT: Af 58 ASP cc_start: 0.8879 (t0) cc_final: 0.8451 (t0) REVERT: Af 60 MET cc_start: 0.9243 (tpp) cc_final: 0.8899 (tpp) REVERT: Af 75 ILE cc_start: 0.9161 (pt) cc_final: 0.8948 (mp) REVERT: Ai 67 THR cc_start: 0.8737 (m) cc_final: 0.8375 (p) REVERT: Ai 78 PHE cc_start: 0.6689 (m-80) cc_final: 0.6321 (m-10) REVERT: Aj 13 LEU cc_start: 0.7635 (mm) cc_final: 0.7352 (mm) REVERT: Aj 16 ARG cc_start: 0.7038 (ptt-90) cc_final: 0.6800 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8179 (tt0) cc_final: 0.7724 (mm-40) REVERT: Ak 23 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6962 (mtm) outliers start: 131 outliers final: 99 residues processed: 741 average time/residue: 0.2030 time to fit residues: 241.7011 Evaluate side-chains 737 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 629 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 133 ILE 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 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 94 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 162 GLU 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 332 LEU Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 146 LYS 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 75 ILE Chi-restraints excluded: chain AF residue 76 LEU Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AF residue 99 ILE 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 Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER 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 273 SER Chi-restraints excluded: chain Aa residue 369 VAL 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 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 349 GLU Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 57 SER 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 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 203 THR Chi-restraints excluded: chain Ac residue 217 LYS 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 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 Ad residue 252 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Af residue 23 ASN 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 79 CYS Chi-restraints excluded: chain Ai residue 45 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 329 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 302 optimal weight: 6.9990 chunk 333 optimal weight: 30.0000 chunk 263 optimal weight: 4.9990 chunk 61 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 247 optimal weight: 0.0070 chunk 327 optimal weight: 0.0980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN ** AC 32 ASN ** 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** Aa 160 GLN Ab 365 ASN Ac 54 HIS Ac 212 ASN Ad 90 HIS ** Af 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 16 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099912 restraints weight = 73454.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101920 restraints weight = 41262.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.103746 restraints weight = 29422.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104271 restraints weight = 22551.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104415 restraints weight = 19529.301| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.317 31150 Z= 0.136 Angle : 0.716 16.517 42266 Z= 0.344 Chirality : 0.043 0.211 4590 Planarity : 0.004 0.055 5364 Dihedral : 9.011 124.416 4406 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.42 % Allowed : 23.98 % Favored : 72.60 % 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 aren not related in a simple way. whole: 0.73 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 1997 sheet: 0.07 (0.28), residues: 366 loop : -0.20 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAg 10 TYR 0.029 0.001 TYRAf 22 PHE 0.034 0.002 PHEAc 276 TRP 0.016 0.001 TRPAk 38 HIS 0.009 0.001 HISAa 95 Details of bonding type rmsd covalent geometry : bond 0.00319 (31137) covalent geometry : angle 0.71595 (42252) SS BOND : bond 0.00389 ( 7) SS BOND : angle 1.31867 ( 14) hydrogen bonds : bond 0.03896 ( 1735) hydrogen bonds : angle 4.79021 ( 4980) Misc. bond : bond 0.21704 ( 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 790 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 681 time to evaluate : 1.249 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: AA 92 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8535 (m-80) REVERT: AA 172 MET cc_start: 0.8800 (mtm) cc_final: 0.8495 (mtm) REVERT: AB 77 LEU cc_start: 0.9360 (mt) cc_final: 0.9079 (mp) REVERT: AB 197 MET cc_start: 0.7216 (ttm) cc_final: 0.6192 (ttm) REVERT: AB 415 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7998 (tm-30) REVERT: AC 31 TRP cc_start: 0.8231 (m-90) cc_final: 0.7370 (m-90) REVERT: AC 82 MET cc_start: 0.8364 (tpp) cc_final: 0.7908 (tpt) REVERT: AC 89 MET cc_start: 0.8712 (mmm) cc_final: 0.8348 (mmm) REVERT: AC 91 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7799 (t80) REVERT: AC 95 PHE cc_start: 0.7864 (m-80) cc_final: 0.7662 (m-80) REVERT: AC 212 ASN cc_start: 0.8127 (t0) cc_final: 0.7842 (m-40) REVERT: AC 216 ASP cc_start: 0.8293 (t0) cc_final: 0.7922 (t70) REVERT: AC 225 THR cc_start: 0.8681 (m) cc_final: 0.8365 (m) REVERT: AC 344 GLU cc_start: 0.8228 (pm20) cc_final: 0.8012 (pm20) REVERT: AD 96 TRP cc_start: 0.7141 (m-90) cc_final: 0.6583 (m-90) REVERT: AD 174 TYR cc_start: 0.7880 (m-80) cc_final: 0.7593 (m-80) REVERT: AD 244 MET cc_start: 0.7311 (tmm) cc_final: 0.7000 (tmm) REVERT: AD 296 MET cc_start: 0.7066 (mmp) cc_final: 0.5700 (mtt) REVERT: AD 306 MET cc_start: 0.8784 (tpp) cc_final: 0.8547 (tpp) REVERT: AE 92 ARG cc_start: 0.7417 (ttm110) cc_final: 0.7074 (ttm110) REVERT: AF 40 GLU cc_start: 0.8756 (mt-10) cc_final: 0.7838 (mt-10) REVERT: AF 76 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8975 (mm) REVERT: AF 79 ASP cc_start: 0.8649 (p0) cc_final: 0.8119 (p0) REVERT: AF 85 GLU cc_start: 0.8132 (pm20) cc_final: 0.7877 (pm20) REVERT: AF 92 GLU cc_start: 0.8507 (tp30) cc_final: 0.7990 (tp30) REVERT: AF 103 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8879 (pttp) REVERT: AG 57 TYR cc_start: 0.8324 (t80) cc_final: 0.8032 (t80) REVERT: AH 72 PHE cc_start: 0.5249 (t80) cc_final: 0.4590 (t80) REVERT: AH 82 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8079 (t-170) REVERT: Aa 79 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8010 (t) REVERT: Aa 209 ARG cc_start: 0.8400 (mtm180) cc_final: 0.8037 (mtm180) REVERT: Aa 380 CYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8291 (t) REVERT: Aa 445 CYS cc_start: 0.8356 (m) cc_final: 0.7248 (t) REVERT: Aa 449 PHE cc_start: 0.8458 (m-10) cc_final: 0.8197 (m-10) REVERT: Ab 159 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8581 (tptt) REVERT: Ab 213 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: Ab 349 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: Ab 407 MET cc_start: 0.8060 (mmp) cc_final: 0.7830 (tpp) REVERT: Ac 20 ASP cc_start: 0.8533 (m-30) cc_final: 0.8151 (m-30) REVERT: Ac 51 LEU cc_start: 0.8719 (mt) cc_final: 0.8353 (tt) REVERT: Ac 135 TRP cc_start: 0.8601 (t-100) cc_final: 0.8134 (t-100) REVERT: Ac 138 MET cc_start: 0.5626 (tpp) cc_final: 0.4835 (tpp) REVERT: Ac 141 TRP cc_start: 0.7979 (m100) cc_final: 0.7431 (m100) REVERT: Ac 187 PHE cc_start: 0.7722 (m-80) cc_final: 0.7311 (m-80) REVERT: Ac 214 ASP cc_start: 0.8749 (m-30) cc_final: 0.8497 (p0) REVERT: Ac 217 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8452 (mtmm) REVERT: Ac 223 TYR cc_start: 0.8595 (m-80) cc_final: 0.8300 (m-80) REVERT: Ac 233 LEU cc_start: 0.8993 (mm) cc_final: 0.8252 (tt) REVERT: Ac 282 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8439 (ptp90) REVERT: Ac 369 SER cc_start: 0.9114 (p) cc_final: 0.8110 (t) REVERT: Ac 373 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7446 (mt-10) REVERT: Ad 103 SER cc_start: 0.8759 (m) cc_final: 0.8344 (p) REVERT: Ad 164 MET cc_start: 0.8929 (tpp) cc_final: 0.8661 (tpp) REVERT: Ad 202 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7587 (mtt180) REVERT: Ad 244 MET cc_start: 0.9113 (ttp) cc_final: 0.8844 (ttp) REVERT: Ad 253 LEU cc_start: 0.7936 (tp) cc_final: 0.7524 (pt) REVERT: Ad 288 MET cc_start: 0.8499 (mmt) cc_final: 0.7826 (mmt) REVERT: Ad 314 LEU cc_start: 0.9212 (mp) cc_final: 0.8933 (mp) REVERT: Ae 113 PHE cc_start: 0.7675 (t80) cc_final: 0.7156 (t80) REVERT: Ae 156 LEU cc_start: 0.4207 (tp) cc_final: 0.3986 (tp) REVERT: Ae 170 ARG cc_start: 0.7031 (tpt170) cc_final: 0.6466 (mtp85) REVERT: Ae 195 LEU cc_start: 0.5428 (tp) cc_final: 0.4886 (tt) REVERT: Af 33 MET cc_start: 0.8185 (mmm) cc_final: 0.7922 (mtp) REVERT: Af 53 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7958 (tm-30) REVERT: Af 58 ASP cc_start: 0.8859 (t0) cc_final: 0.8461 (t0) REVERT: Af 60 MET cc_start: 0.9216 (tpp) cc_final: 0.8904 (tpp) REVERT: Af 75 ILE cc_start: 0.9072 (pt) cc_final: 0.8630 (mt) REVERT: Af 106 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7725 (tm-30) REVERT: Ag 72 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7308 (mmp80) REVERT: Ah 45 ARG cc_start: 0.8056 (tpp-160) cc_final: 0.7704 (tpp-160) REVERT: Ah 67 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7490 (tm-30) REVERT: Ai 67 THR cc_start: 0.8723 (m) cc_final: 0.8374 (p) REVERT: Ai 78 PHE cc_start: 0.6599 (m-80) cc_final: 0.6307 (m-10) REVERT: Aj 13 LEU cc_start: 0.7642 (mm) cc_final: 0.7322 (mm) REVERT: Aj 16 ARG cc_start: 0.7038 (ptt-90) cc_final: 0.6797 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8190 (tt0) cc_final: 0.7740 (mm-40) REVERT: Ak 23 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.6900 (mtm) outliers start: 109 outliers final: 82 residues processed: 741 average time/residue: 0.2053 time to fit residues: 243.8144 Evaluate side-chains 724 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 632 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 109 LEU Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 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 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 113 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 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 162 GLU 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 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 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 93 ARG Chi-restraints excluded: chain AF residue 76 LEU Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AF residue 99 ILE 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 Aa residue 68 THR 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 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 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 156 SER Chi-restraints excluded: chain Ab residue 158 LEU 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 384 MET Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 57 SER 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 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 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 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 Ad residue 252 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 Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 274 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 54 optimal weight: 0.0050 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 95 HIS AB 36 GLN AB 167 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 131 ASN Af 23 ASN Ag 13 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099884 restraints weight = 73320.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101448 restraints weight = 41462.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.104434 restraints weight = 29740.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.104534 restraints weight = 20840.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.104537 restraints weight = 19379.534| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.372 31150 Z= 0.141 Angle : 0.729 16.213 42266 Z= 0.351 Chirality : 0.043 0.228 4590 Planarity : 0.005 0.117 5364 Dihedral : 8.993 132.254 4406 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.04 % Allowed : 24.17 % Favored : 72.79 % 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 aren not related in a simple way. whole: 0.73 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 2001 sheet: -0.01 (0.28), residues: 375 loop : -0.19 (0.18), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAc 71 TYR 0.026 0.001 TYRAd 174 PHE 0.034 0.002 PHEAc 276 TRP 0.032 0.001 TRPAk 38 HIS 0.008 0.001 HISAa 95 Details of bonding type rmsd covalent geometry : bond 0.00334 (31137) covalent geometry : angle 0.72925 (42252) SS BOND : bond 0.00381 ( 7) SS BOND : angle 1.25202 ( 14) hydrogen bonds : bond 0.03861 ( 1735) hydrogen bonds : angle 4.78992 ( 4980) Misc. bond : bond 0.23420 ( 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 750 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 653 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 92 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: AA 158 ASP cc_start: 0.8816 (m-30) cc_final: 0.8612 (m-30) REVERT: AA 172 MET cc_start: 0.8767 (mtm) cc_final: 0.8470 (mtm) REVERT: AB 77 LEU cc_start: 0.9351 (mt) cc_final: 0.9084 (mp) REVERT: AB 197 MET cc_start: 0.7062 (ttm) cc_final: 0.6073 (ttm) REVERT: AB 415 GLN cc_start: 0.8235 (tm-30) cc_final: 0.8004 (tm-30) REVERT: AC 31 TRP cc_start: 0.8251 (m-90) cc_final: 0.7367 (m-90) REVERT: AC 82 MET cc_start: 0.8339 (tpp) cc_final: 0.7852 (tpt) REVERT: AC 89 MET cc_start: 0.8582 (mmm) cc_final: 0.8286 (mtp) REVERT: AC 91 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7766 (t80) REVERT: AC 212 ASN cc_start: 0.8150 (t0) cc_final: 0.7885 (m-40) REVERT: AC 216 ASP cc_start: 0.8314 (t0) cc_final: 0.7891 (t70) REVERT: AC 225 THR cc_start: 0.8680 (m) cc_final: 0.8370 (m) REVERT: AC 344 GLU cc_start: 0.8246 (pm20) cc_final: 0.7986 (pm20) REVERT: AD 96 TRP cc_start: 0.7161 (m-90) cc_final: 0.6593 (m-90) REVERT: AD 174 TYR cc_start: 0.7910 (m-80) cc_final: 0.7650 (m-80) REVERT: AD 244 MET cc_start: 0.7210 (tmm) cc_final: 0.6888 (tmm) REVERT: AD 296 MET cc_start: 0.7084 (mmp) cc_final: 0.5803 (mtt) REVERT: AD 306 MET cc_start: 0.8809 (tpp) cc_final: 0.8565 (tpp) REVERT: AE 92 ARG cc_start: 0.7425 (ttm110) cc_final: 0.7082 (ttm110) REVERT: AF 40 GLU cc_start: 0.8700 (mt-10) cc_final: 0.7986 (mt-10) REVERT: AF 45 LYS cc_start: 0.9312 (mtpp) cc_final: 0.8876 (mtmm) REVERT: AF 79 ASP cc_start: 0.8606 (p0) cc_final: 0.8090 (p0) REVERT: AF 85 GLU cc_start: 0.8115 (pm20) cc_final: 0.7866 (pm20) REVERT: AF 92 GLU cc_start: 0.8496 (tp30) cc_final: 0.7997 (tp30) REVERT: AF 103 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8883 (pttp) REVERT: AG 46 ILE cc_start: 0.8141 (tp) cc_final: 0.7865 (pt) REVERT: AG 57 TYR cc_start: 0.8313 (t80) cc_final: 0.8031 (t80) REVERT: AH 72 PHE cc_start: 0.5155 (t80) cc_final: 0.4601 (t80) REVERT: AH 82 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8112 (t-170) REVERT: Aa 79 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.7974 (t) REVERT: Aa 209 ARG cc_start: 0.8372 (mtm180) cc_final: 0.7912 (mtm180) REVERT: Aa 450 TYR cc_start: 0.7870 (t80) cc_final: 0.7599 (t80) REVERT: Ab 159 LYS cc_start: 0.8960 (tmtt) cc_final: 0.8600 (tptt) REVERT: Ab 213 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: Ab 266 LEU cc_start: 0.9174 (mm) cc_final: 0.8573 (mt) REVERT: Ab 311 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8634 (pp30) REVERT: Ab 349 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: Ab 407 MET cc_start: 0.8025 (mmp) cc_final: 0.7775 (tpp) REVERT: Ac 20 ASP cc_start: 0.8531 (m-30) cc_final: 0.8139 (m-30) REVERT: Ac 135 TRP cc_start: 0.8563 (t-100) cc_final: 0.8108 (t-100) REVERT: Ac 138 MET cc_start: 0.5650 (tpp) cc_final: 0.4817 (tpp) REVERT: Ac 141 TRP cc_start: 0.7994 (m100) cc_final: 0.7430 (m100) REVERT: Ac 187 PHE cc_start: 0.7569 (m-80) cc_final: 0.7155 (m-80) REVERT: Ac 217 LYS cc_start: 0.8805 (ttmm) cc_final: 0.8479 (mtmm) REVERT: Ac 223 TYR cc_start: 0.8611 (m-80) cc_final: 0.8307 (m-80) REVERT: Ac 233 LEU cc_start: 0.8992 (mm) cc_final: 0.8234 (tt) REVERT: Ac 282 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8433 (ptp90) REVERT: Ac 369 SER cc_start: 0.9107 (p) cc_final: 0.8115 (t) REVERT: Ac 373 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7524 (mt-10) REVERT: Ad 103 SER cc_start: 0.8890 (m) cc_final: 0.8495 (p) REVERT: Ad 164 MET cc_start: 0.8899 (tpp) cc_final: 0.8618 (tpp) REVERT: Ad 253 LEU cc_start: 0.7968 (tp) cc_final: 0.7541 (pt) REVERT: Ad 288 MET cc_start: 0.8585 (mmt) cc_final: 0.8067 (mmt) REVERT: Ad 314 LEU cc_start: 0.9187 (mp) cc_final: 0.8901 (mp) REVERT: Ae 113 PHE cc_start: 0.7550 (t80) cc_final: 0.7078 (t80) REVERT: Ae 156 LEU cc_start: 0.4199 (tp) cc_final: 0.3941 (tp) REVERT: Ae 170 ARG cc_start: 0.6964 (tpt170) cc_final: 0.6602 (mtp85) REVERT: Af 33 MET cc_start: 0.8201 (mmm) cc_final: 0.7921 (mtp) REVERT: Af 53 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7935 (tm-30) REVERT: Af 58 ASP cc_start: 0.8848 (t0) cc_final: 0.8452 (t0) REVERT: Af 60 MET cc_start: 0.9235 (tpp) cc_final: 0.8922 (tpp) REVERT: Af 75 ILE cc_start: 0.9011 (pt) cc_final: 0.8557 (mt) REVERT: Af 106 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7820 (tm-30) REVERT: Ag 72 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7229 (mmp80) REVERT: Ai 67 THR cc_start: 0.8720 (m) cc_final: 0.8384 (p) REVERT: Ai 78 PHE cc_start: 0.6574 (m-80) cc_final: 0.6313 (m-10) REVERT: Aj 16 ARG cc_start: 0.7283 (ptt-90) cc_final: 0.6901 (ptt-90) REVERT: Aj 33 GLU cc_start: 0.8613 (tm-30) cc_final: 0.7959 (tp30) REVERT: Aj 38 GLN cc_start: 0.8195 (tt0) cc_final: 0.7754 (mm-40) REVERT: Ak 23 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6842 (mtm) REVERT: Ak 24 TRP cc_start: 0.7438 (OUTLIER) cc_final: 0.7058 (m100) outliers start: 97 outliers final: 78 residues processed: 703 average time/residue: 0.2033 time to fit residues: 229.8775 Evaluate side-chains 711 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 623 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 109 LEU Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 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 58 LEU 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 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 162 GLU 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 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 366 MET 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 AD residue 293 LEU Chi-restraints excluded: chain AE residue 80 HIS 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 AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 125 THR 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 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 156 SER Chi-restraints excluded: chain Ab residue 158 LEU 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 311 GLN Chi-restraints excluded: chain Ab residue 349 GLU Chi-restraints excluded: chain Ab residue 432 VAL 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 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 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 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 Ad residue 252 VAL Chi-restraints excluded: chain Af residue 23 ASN 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 Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL 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 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: 8.9990 chunk 183 optimal weight: 0.0000 chunk 278 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 153 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 304 ASN Ab 365 ASN Ad 90 HIS Af 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.131177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099966 restraints weight = 73839.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.102048 restraints weight = 40690.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104310 restraints weight = 30559.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.104817 restraints weight = 21774.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.105104 restraints weight = 19405.150| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.431 31150 Z= 0.144 Angle : 0.741 16.370 42266 Z= 0.354 Chirality : 0.043 0.200 4590 Planarity : 0.005 0.086 5364 Dihedral : 8.953 130.831 4406 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.98 % Allowed : 24.36 % Favored : 72.66 % 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 aren not related in a simple way. whole: 0.74 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 1993 sheet: -0.06 (0.27), residues: 376 loop : -0.16 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAB 172 TYR 0.028 0.001 TYRAf 22 PHE 0.037 0.002 PHEAa 449 TRP 0.030 0.001 TRPAk 38 HIS 0.008 0.001 HISAa 95 Details of bonding type rmsd covalent geometry : bond 0.00338 (31137) covalent geometry : angle 0.74076 (42252) SS BOND : bond 0.00344 ( 7) SS BOND : angle 1.29214 ( 14) hydrogen bonds : bond 0.03842 ( 1735) hydrogen bonds : angle 4.78866 ( 4980) Misc. bond : bond 0.25490 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6767.70 seconds wall clock time: 117 minutes 48.78 seconds (7068.78 seconds total)