Starting phenix.real_space_refine on Tue Aug 26 00:26:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ib7_35334/08_2025/8ib7_35334_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ib7_35334/08_2025/8ib7_35334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ib7_35334/08_2025/8ib7_35334_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ib7_35334/08_2025/8ib7_35334_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ib7_35334/08_2025/8ib7_35334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ib7_35334/08_2025/8ib7_35334.map" } resolution = 3.4 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= 0.068 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 15 5.49 5 S 152 5.16 5 C 20494 2.51 5 N 5375 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 31874 Number of models: 1 Model: "" Number of chains: 28 Chain: "AA" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3128 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 15, 'TRANS': 384} 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: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1896 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "AE" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "AF" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "AG" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "AH" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "AI" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 345 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain breaks: 3 Chain: "AJ" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 332 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "AK" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 281 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "Aa" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3225 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 16, 'TRANS': 395} Chain breaks: 1 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: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1895 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "Ae" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1432 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "Af" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "Ag" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "Ah" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "Aj" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "Ak" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "AC" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 228 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 104 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: "AF" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "Aa" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "Ac" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 252 Unusual residues: {'3PE': 2, 'CDL': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 134 Planarities with less than four sites: {'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: 35 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 56 Time building chain proxies: 7.44, per 1000 atoms: 0.23 Number of scatterers: 31874 At special positions: 0 Unit cell: (156.2, 146.3, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 152 16.00 P 15 15.00 O 5832 8.00 N 5375 7.00 C 20494 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=2.03 Simple disulfide: pdb=" SG CYSAa 338 " - pdb=" SG CYSAa 360 " distance=2.03 Simple disulfide: pdb=" SG CYSAe 222 " - pdb=" SG CYSAe 238 " distance=2.06 Simple disulfide: pdb=" SG CYSAh 35 " - pdb=" SG CYSAh 79 " distance=2.04 Simple disulfide: pdb=" SG CYSAh 51 " - pdb=" SG CYSAh 65 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7350 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 17 sheets defined 58.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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: 3.537A pdb=" N GLUAA 145 " --> pdb=" O PROAA 141 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEUAA 147 " --> pdb=" O VALAA 143 " (cutoff:3.500A) Processing helix chain 'AA' and resid 157 through 176 removed outlier: 3.716A 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 removed outlier: 3.544A 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: 3.870A pdb=" N ARGAB 172 " --> pdb=" O ASNAB 168 " (cutoff:3.500A) Processing helix chain 'AB' and resid 201 through 213 removed outlier: 3.500A pdb=" N LEUAB 205 " --> pdb=" O THRAB 201 " (cutoff:3.500A) Processing helix chain 'AB' and resid 214 through 216 No H-bonds generated for 'chain 'AB' and resid 214 through 216' Processing helix chain 'AB' and resid 226 through 237 removed outlier: 3.596A pdb=" N LEUAB 230 " --> pdb=" O SERAB 226 " (cutoff:3.500A) Processing helix chain 'AB' and resid 280 through 294 removed outlier: 3.828A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 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 9 through 18 removed outlier: 3.891A pdb=" N ILEAC 13 " --> pdb=" O PROAC 9 " (cutoff:3.500A) removed outlier: 3.520A 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: 3.579A 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: 3.553A pdb=" N ARGAC 177 " --> pdb=" O ALAAC 173 " (cutoff:3.500A) Proline residue: AC 186 - end of helix Processing helix chain 'AC' and resid 212 through 215 removed outlier: 4.576A pdb=" N ALAAC 215 " --> pdb=" O ASNAC 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 212 through 215' Processing helix chain 'AC' and resid 224 through 244 Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 284 removed outlier: 4.374A pdb=" N PHEAC 276 " --> pdb=" O TRPAC 272 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALAAC 277 " --> pdb=" O TYRAC 273 " (cutoff:3.500A) Processing helix chain 'AC' and resid 286 through 304 removed outlier: 3.507A pdb=" N ILEAC 298 " --> pdb=" O LEUAC 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAC 301 " --> pdb=" O SERAC 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 305 through 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 377 Processing helix chain 'AD' and resid 106 through 120 Processing helix chain 'AD' and resid 131 through 136 removed outlier: 3.877A pdb=" N LEUAD 135 " --> pdb=" O ALAAD 131 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VALAD 136 " --> pdb=" O TYRAD 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 131 through 136' Processing helix chain 'AD' and resid 141 through 152 removed outlier: 3.662A pdb=" N VALAD 152 " --> pdb=" O LEUAD 148 " (cutoff:3.500A) Processing helix chain 'AD' and resid 181 through 189 Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 206 through 216 Processing helix chain 'AD' and resid 237 through 241 removed outlier: 4.098A pdb=" N ALAAD 241 " --> pdb=" O PROAD 238 " (cutoff:3.500A) Processing helix chain 'AD' and resid 262 through 279 Processing helix chain 'AD' and resid 281 through 317 Proline residue: AD 301 - end of helix removed outlier: 3.865A pdb=" N VALAD 313 " --> pdb=" O HISAD 309 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEUAD 314 " --> pdb=" O LYSAD 310 " (cutoff:3.500A) Processing helix chain 'AE' and resid 107 through 141 Processing helix chain 'AE' and resid 143 through 148 Processing helix chain 'AE' and resid 157 through 159 No H-bonds generated for 'chain 'AE' and resid 157 through 159' Processing helix chain 'AE' and resid 168 through 172 Processing helix chain 'AE' and resid 180 through 190 Processing helix chain 'AE' and resid 200 through 205 Processing helix chain 'AF' and resid 15 through 26 removed outlier: 3.720A pdb=" N GLYAF 26 " --> pdb=" O TYRAF 22 " (cutoff:3.500A) Processing helix chain 'AF' and resid 34 through 38 removed outlier: 3.685A 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: 4.177A pdb=" N TYRAF 94 " --> pdb=" O TYRAF 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUAF 97 " --> pdb=" O PROAF 93 " (cutoff:3.500A) Processing helix chain 'AG' and resid 21 through 24 Processing helix chain 'AG' and resid 29 through 72 removed outlier: 3.850A pdb=" N ILEAG 35 " --> pdb=" O PHEAG 31 " (cutoff:3.500A) Proline residue: AG 36 - end of helix removed outlier: 5.324A pdb=" N LEUAG 47 " --> pdb=" O ARGAG 43 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGAG 48 " --> pdb=" O GLUAG 44 " (cutoff:3.500A) Proline residue: AG 51 - end of helix Processing helix chain 'AH' and resid 26 through 37 removed outlier: 3.627A pdb=" N THRAH 30 " --> pdb=" O ASPAH 26 " (cutoff:3.500A) Processing helix chain 'AH' and resid 38 through 58 Processing helix chain 'AH' and resid 65 through 84 removed outlier: 3.831A pdb=" N LYSAH 83 " --> pdb=" O CYSAH 79 " (cutoff:3.500A) Processing helix chain 'AH' and resid 85 through 88 Processing helix chain 'AI' and resid 8 through 16 Proline residue: AI 13 - end of helix removed outlier: 3.933A pdb=" N SERAI 16 " --> pdb=" O PROAI 13 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 9 through 15 Processing helix chain 'AJ' and resid 17 through 48 removed outlier: 4.295A pdb=" N ARGAJ 34 " --> pdb=" O LEUAJ 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 8 through 37 Proline residue: AK 19 - end of helix Processing helix chain 'Aa' and resid 78 through 82 Processing helix chain 'Aa' and resid 88 through 98 removed outlier: 4.369A pdb=" N PHEAa 98 " --> pdb=" O GLUAa 94 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 107 through 116 Processing helix chain 'Aa' and resid 139 through 152 Processing helix chain 'Aa' and resid 157 through 176 removed outlier: 3.752A pdb=" N ASPAa 176 " --> pdb=" O METAa 172 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 178 through 192 Processing helix chain 'Aa' and resid 204 through 210 Processing helix chain 'Aa' and resid 212 through 224 Processing helix chain 'Aa' and resid 225 through 227 No H-bonds generated for 'chain 'Aa' and resid 225 through 227' Processing helix chain 'Aa' and resid 238 through 251 Processing helix chain 'Aa' and resid 257 through 261 removed outlier: 4.022A pdb=" N ASPAa 260 " --> pdb=" O TYRAa 257 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 299 through 311 removed outlier: 4.195A pdb=" N THRAa 303 " --> pdb=" O PROAa 299 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 364 through 382 Processing helix chain 'Aa' and resid 384 through 396 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 removed outlier: 3.543A pdb=" N GLUAb 72 " --> pdb=" O SERAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 78 through 86 Processing helix chain 'Ab' and resid 95 through 106 removed outlier: 4.348A pdb=" N ILEAb 103 " --> pdb=" O ILEAb 99 " (cutoff:3.500A) removed outlier: 3.663A 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: 4.715A 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: 3.869A pdb=" N ARGAb 172 " --> pdb=" O ASNAb 168 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 201 through 213 Processing helix chain 'Ab' and resid 214 through 216 No H-bonds generated for 'chain 'Ab' and resid 214 through 216' Processing helix chain 'Ab' and resid 226 through 237 removed outlier: 3.591A pdb=" N LEUAb 230 " --> pdb=" O SERAb 226 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLUAb 235 " --> pdb=" O LYSAb 231 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLNAb 236 " --> pdb=" O GLNAb 232 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHEAb 237 " --> pdb=" O VALAb 233 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 280 through 293 removed outlier: 4.197A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALAAb 285 " --> pdb=" O ALAAb 281 " (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 9 through 19 removed outlier: 3.574A pdb=" N ILEAc 19 " --> pdb=" O ASNAc 15 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 28 through 31 Processing helix chain 'Ac' and resid 32 through 53 Processing helix chain 'Ac' and resid 61 through 72 Processing helix chain 'Ac' and resid 75 through 104 Processing helix chain 'Ac' and resid 105 through 108 removed outlier: 3.580A pdb=" N THRAc 108 " --> pdb=" O GLYAc 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 105 through 108' Processing helix chain 'Ac' and resid 109 through 133 Processing helix chain 'Ac' and resid 136 through 151 removed outlier: 3.857A pdb=" N LEUAc 150 " --> pdb=" O ILEAc 146 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 166 Processing helix chain 'Ac' and resid 171 through 202 removed outlier: 3.553A pdb=" N ARGAc 177 " --> pdb=" O ALAAc 173 " (cutoff:3.500A) Proline residue: Ac 186 - end of helix Processing helix chain 'Ac' and resid 212 through 215 removed outlier: 4.575A 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 241 Processing helix chain 'Ac' and resid 252 through 257 Processing helix chain 'Ac' and resid 271 through 273 No H-bonds generated for 'chain 'Ac' and resid 271 through 273' Processing helix chain 'Ac' and resid 274 through 284 Processing helix chain 'Ac' and resid 286 through 304 removed outlier: 3.506A pdb=" N ILEAc 298 " --> pdb=" O LEUAc 294 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 308 removed outlier: 3.963A pdb=" N HISAc 308 " --> pdb=" O PROAc 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 305 through 308' Processing helix chain 'Ac' and resid 318 through 341 removed outlier: 3.760A pdb=" N GLYAc 340 " --> pdb=" O THRAc 336 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 346 through 364 Processing helix chain 'Ac' and resid 364 through 377 Processing helix chain 'Ad' and resid 106 through 120 Processing helix chain 'Ad' and resid 121 through 124 removed outlier: 3.512A pdb=" N CYSAd 124 " --> pdb=" O CYSAd 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 121 through 124' Processing helix chain 'Ad' and resid 131 through 136 removed outlier: 3.866A pdb=" N LEUAd 135 " --> pdb=" O ALAAd 131 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VALAd 136 " --> pdb=" O TYRAd 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 131 through 136' Processing helix chain 'Ad' and resid 141 through 151 Processing helix chain 'Ad' and resid 181 through 189 removed outlier: 3.634A pdb=" N ALAAd 185 " --> pdb=" O ASNAd 181 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 199 through 204 Processing helix chain 'Ad' and resid 206 through 216 Processing helix chain 'Ad' and resid 237 through 241 removed outlier: 4.098A pdb=" N ALAAd 241 " --> pdb=" O PROAd 238 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 262 through 279 Processing helix chain 'Ad' and resid 281 through 317 Proline residue: Ad 301 - end of helix removed outlier: 3.864A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEUAd 314 " --> pdb=" O LYSAd 310 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 106 through 140 removed outlier: 3.724A pdb=" N METAe 140 " --> pdb=" O PHEAe 136 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 143 through 148 Processing helix chain 'Ae' and resid 155 through 159 Processing helix chain 'Ae' and resid 168 through 172 Processing helix chain 'Ae' and resid 180 through 190 Processing helix chain 'Ae' and resid 200 through 205 Processing helix chain 'Af' and resid 15 through 26 removed outlier: 3.720A pdb=" N GLYAf 26 " --> pdb=" O TYRAf 22 " (cutoff:3.500A) Processing helix chain 'Af' and resid 34 through 38 removed outlier: 3.687A 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: 3.606A 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: 3.849A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 5.045A pdb=" N LEUAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARGAg 48 " --> pdb=" O GLUAg 44 " (cutoff:3.500A) Proline residue: Ag 51 - end of helix Processing helix chain 'Ah' and resid 26 through 38 removed outlier: 3.778A pdb=" N THRAh 30 " --> pdb=" O ASPAh 26 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEUAh 38 " --> pdb=" O HISAh 34 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 38 through 58 Processing helix chain 'Ah' and resid 65 through 83 Processing helix chain 'Aj' and resid 8 through 14 Processing helix chain 'Aj' and resid 17 through 48 removed outlier: 3.527A pdb=" N ILEAj 25 " --> pdb=" O PHEAj 21 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARGAj 34 " --> pdb=" O LEUAj 30 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 8 through 37 removed outlier: 3.616A pdb=" N GLUAk 12 " --> pdb=" O PROAk 8 " (cutoff:3.500A) Proline residue: Ak 19 - end of helix Processing helix chain 'Ak' and resid 38 through 43 removed outlier: 3.798A pdb=" N LEUAk 42 " --> pdb=" O TRPAk 38 " (cutoff:3.500A) 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: 6.417A 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: 6.652A 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: 6.036A 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 Processing sheet with id=AA3, first strand: chain 'AB' and resid 41 through 42 removed outlier: 6.157A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.670A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.329A 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: 3.639A pdb=" N GLYAB 334 " --> pdb=" O SERAB 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AC' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'AD' and resid 153 through 154 Processing sheet with id=AA7, first strand: chain 'AE' and resid 154 through 155 Processing sheet with id=AA8, first strand: chain 'AE' and resid 163 through 165 Processing sheet with id=AA9, first strand: chain 'AE' and resid 225 through 226 removed outlier: 6.659A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AI' and resid 75 through 76 removed outlier: 6.529A pdb=" N VALAb 48 " --> pdb=" O LEUAb 220 " (cutoff:3.500A) removed outlier: 8.010A 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) Processing sheet with id=AB2, first strand: chain 'Aa' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Aa' and resid 341 through 348 removed outlier: 3.664A pdb=" N GLNAa 342 " --> pdb=" O HISAa 357 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHEAa 344 " --> pdb=" O GLYAa 355 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THRAa 351 " --> pdb=" O TYRAa 348 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SERAa 273 " --> pdb=" O VALAa 456 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLYAa 458 " --> pdb=" O SERAa 273 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILEAa 275 " --> pdb=" O GLYAa 458 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLYAa 460 " --> pdb=" O ILEAa 275 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HISAa 277 " --> pdb=" O GLYAa 460 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SERAg 16 " --> pdb=" O ARGAa 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ab' and resid 256 through 260 removed outlier: 3.535A pdb=" N GLYAb 256 " --> pdb=" O LYSAb 436 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Ac' and resid 23 through 24 Processing sheet with id=AB6, first strand: chain 'Ad' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'Ae' and resid 163 through 165 Processing sheet with id=AB8, first strand: chain 'Ae' and resid 225 through 226 removed outlier: 6.660A pdb=" N HISAe 242 " --> pdb=" O ARGAe 250 " (cutoff:3.500A) 1787 hydrogen bonds defined for protein. 5124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 10214 1.35 - 1.54: 21979 1.54 - 1.73: 177 1.73 - 1.93: 258 1.93 - 2.12: 20 Bond restraints: 32648 Sorted by residual: bond pdb=" CB7 CDLAC 406 " pdb=" OB8 CDLAC 406 " ideal model delta sigma weight residual 1.334 1.456 -0.122 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CB7 CDLAg 101 " pdb=" OB8 CDLAg 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDLAc 407 " pdb=" OA8 CDLAc 407 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CB7 CDLAc 407 " pdb=" OB8 CDLAc 407 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDLAC 406 " pdb=" OA8 CDLAC 406 " ideal model delta sigma weight residual 1.334 1.448 -0.114 1.10e-02 8.26e+03 1.08e+02 ... (remaining 32643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 42909 3.27 - 6.53: 1173 6.53 - 9.80: 174 9.80 - 13.06: 20 13.06 - 16.33: 6 Bond angle restraints: 44282 Sorted by residual: angle pdb=" N ALAAI 60 " pdb=" CA ALAAI 60 " pdb=" C ALAAI 60 " ideal model delta sigma weight residual 109.18 125.51 -16.33 1.42e+00 4.96e-01 1.32e+02 angle pdb=" N ARGAj 16 " pdb=" CA ARGAj 16 " pdb=" C ARGAj 16 " ideal model delta sigma weight residual 111.02 123.71 -12.69 1.22e+00 6.72e-01 1.08e+02 angle pdb=" N ALAAa 261 " pdb=" CA ALAAa 261 " pdb=" C ALAAa 261 " ideal model delta sigma weight residual 109.71 95.21 14.50 1.41e+00 5.03e-01 1.06e+02 angle pdb=" N THRAB 306 " pdb=" CA THRAB 306 " pdb=" C THRAB 306 " ideal model delta sigma weight residual 111.33 123.35 -12.02 1.21e+00 6.83e-01 9.87e+01 angle pdb=" N ASNAB 303 " pdb=" CA ASNAB 303 " pdb=" C ASNAB 303 " ideal model delta sigma weight residual 112.88 100.16 12.72 1.29e+00 6.01e-01 9.72e+01 ... (remaining 44277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 19124 35.95 - 71.89: 289 71.89 - 107.84: 33 107.84 - 143.79: 6 143.79 - 179.73: 1 Dihedral angle restraints: 19453 sinusoidal: 8034 harmonic: 11419 Sorted by residual: dihedral pdb=" C11 U10AC 404 " pdb=" C8 U10AC 404 " pdb=" C9 U10AC 404 " pdb=" C7 U10AC 404 " ideal model delta sinusoidal sigma weight residual 180.05 0.32 179.73 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2B HEMAc 403 " pdb=" C3B HEMAc 403 " pdb=" CAB HEMAc 403 " pdb=" CBB HEMAc 403 " ideal model delta sinusoidal sigma weight residual -0.00 -72.53 72.53 2 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" C2B HEMAC 402 " pdb=" C3B HEMAC 402 " pdb=" CAB HEMAC 402 " pdb=" CBB HEMAC 402 " ideal model delta sinusoidal sigma weight residual -0.00 -72.29 72.29 2 1.00e+01 1.00e-02 4.36e+01 ... (remaining 19450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4133 0.082 - 0.165: 579 0.165 - 0.247: 60 0.247 - 0.329: 11 0.329 - 0.411: 2 Chirality restraints: 4785 Sorted by residual: chirality pdb=" CA ARGAj 16 " pdb=" N ARGAj 16 " pdb=" C ARGAj 16 " pdb=" CB ARGAj 16 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA VALAe 272 " pdb=" N VALAe 272 " pdb=" C VALAe 272 " pdb=" CB VALAe 272 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA PHEAj 15 " pdb=" N PHEAj 15 " pdb=" C PHEAj 15 " pdb=" CB PHEAj 15 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 4782 not shown) Planarity restraints: 5608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYRAd 179 " -0.062 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PROAd 180 " 0.177 5.00e-02 4.00e+02 pdb=" CA PROAd 180 " -0.054 5.00e-02 4.00e+02 pdb=" CD PROAd 180 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHEAe 113 " -0.047 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHEAe 113 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHEAe 113 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHEAe 113 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHEAe 113 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHEAe 113 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHEAe 113 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAE 113 " 0.046 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHEAE 113 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHEAE 113 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHEAE 113 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHEAE 113 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHEAE 113 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHEAE 113 " 0.029 2.00e-02 2.50e+03 ... (remaining 5605 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 852 2.65 - 3.21: 32794 3.21 - 3.77: 54085 3.77 - 4.34: 75493 4.34 - 4.90: 117964 Nonbonded interactions: 281188 Sorted by model distance: nonbonded pdb=" NE2 HISAc 83 " pdb="FE HEMAc 402 " model vdw 2.083 3.080 nonbonded pdb=" NE2 HISAD 125 " pdb="FE HECAD 401 " model vdw 2.089 3.080 nonbonded pdb=" NE2 HISAC 182 " pdb="FE HEMAC 401 " model vdw 2.142 3.080 nonbonded pdb=" CD LYSAd 170 " pdb=" CD LYSAe 151 " model vdw 2.199 3.840 nonbonded pdb=" CZ PHEAI 78 " pdb=" ND2 ASNAb 168 " model vdw 2.205 3.420 ... (remaining 281183 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 311 or resid 338 through 479)) selection = (chain 'Aa' and (resid 45 through 256 or resid 267 through 311 or resid 338 thro \ ugh 479)) } ncs_group { reference = chain 'AB' selection = chain 'Ab' } ncs_group { reference = (chain 'AC' and (resid 8 through 380 or resid 402)) selection = (chain 'Ac' and (resid 8 through 380 or resid 402)) } ncs_group { reference = (chain 'AD' and (resid 88 through 324 or resid 401 through 402)) selection = (chain 'Ad' and resid 88 through 402) } ncs_group { reference = (chain 'AE' and resid 79 through 273) selection = (chain 'Ae' and (resid 79 through 94 or resid 106 through 273)) } ncs_group { reference = (chain 'AF' and resid 14 through 111) selection = chain 'Af' } ncs_group { reference = chain 'AG' selection = (chain 'Ag' and resid 4 through 79) } ncs_group { reference = chain 'AH' selection = (chain 'Ah' and resid 24 through 88) } ncs_group { reference = chain 'AJ' selection = (chain 'Aj' and resid 8 through 48) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 29.200 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.011 0.385 32661 Z= 0.636 Angle : 1.262 16.326 44296 Z= 0.798 Chirality : 0.058 0.411 4785 Planarity : 0.007 0.102 5608 Dihedral : 13.729 179.733 12082 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 29.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.18 % Allowed : 2.41 % Favored : 97.41 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.06 % 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: -1.71 (0.12), residues: 3880 helix: -0.91 (0.10), residues: 2027 sheet: -0.58 (0.27), residues: 361 loop : -1.40 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAE 250 TYR 0.049 0.002 TYRAe 235 PHE 0.049 0.002 PHEAC 183 TRP 0.025 0.002 TRPAC 141 HIS 0.009 0.001 HISAC 196 Details of bonding type rmsd covalent geometry : bond 0.01020 (32648) covalent geometry : angle 1.26119 (44282) SS BOND : bond 0.01529 ( 7) SS BOND : angle 2.83120 ( 14) hydrogen bonds : bond 0.18930 ( 1787) hydrogen bonds : angle 7.73515 ( 5124) Misc. bond : bond 0.23108 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1213 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 478 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7227 (mp) REVERT: AC 299 LEU cc_start: 0.8593 (mt) cc_final: 0.7795 (tt) REVERT: AC 375 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7514 (ttmt) REVERT: AD 165 PHE cc_start: 0.6825 (p90) cc_final: 0.6046 (p90) REVERT: AD 170 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7623 (mtmm) REVERT: AD 255 TYR cc_start: 0.5740 (m-80) cc_final: 0.5221 (m-10) REVERT: AG 74 ASN cc_start: 0.7960 (t0) cc_final: 0.7600 (t0) REVERT: AH 49 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7220 (mm-30) REVERT: AI 18 THR cc_start: 0.8702 (m) cc_final: 0.8363 (p) REVERT: AI 20 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7196 (mtm-85) REVERT: Aa 364 SER cc_start: 0.8740 (m) cc_final: 0.8369 (t) REVERT: Ab 82 LEU cc_start: 0.8554 (tp) cc_final: 0.8316 (tp) REVERT: Ab 179 ASP cc_start: 0.8430 (t70) cc_final: 0.8082 (t0) REVERT: Ab 202 SER cc_start: 0.8086 (m) cc_final: 0.7805 (t) REVERT: Ab 321 PHE cc_start: 0.7827 (p90) cc_final: 0.7530 (p90) REVERT: Ab 322 ASP cc_start: 0.7802 (t70) cc_final: 0.7429 (m-30) REVERT: Ab 437 SER cc_start: 0.8729 (m) cc_final: 0.8330 (p) REVERT: Ac 203 THR cc_start: 0.8492 (t) cc_final: 0.8218 (p) REVERT: Ac 269 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8700 (mtmm) REVERT: Ac 313 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8397 (ttt180) REVERT: Ad 118 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8208 (tttm) REVERT: Ad 141 THR cc_start: 0.7390 (p) cc_final: 0.7099 (p) REVERT: Ad 166 MET cc_start: 0.8331 (mtt) cc_final: 0.7590 (mmt) REVERT: Ag 60 TYR cc_start: 0.8961 (t80) cc_final: 0.8664 (t80) REVERT: Ag 66 GLU cc_start: 0.8616 (tp30) cc_final: 0.8316 (tp30) REVERT: Ak 38 TRP cc_start: 0.6510 (t60) cc_final: 0.6272 (t60) outliers start: 6 outliers final: 2 residues processed: 1215 average time/residue: 0.2033 time to fit residues: 383.0256 Evaluate side-chains 707 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 704 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 478 LEU Chi-restraints excluded: chain AC residue 294 LEU Chi-restraints excluded: chain AI residue 14 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 397 ASN AA 402 HIS AA 452 GLN ** AA 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 139 ASN AB 304 ASN AD 159 ASN AD 189 ASN ** AD 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 219 HIS ** AE 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 80 GLN ** AH 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 46 HIS AK 16 ASN Aa 55 ASN Aa 87 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 103 ASN ** Aa 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 173 GLN Aa 181 ASN Aa 207 ASN Ab 118 ASN Ab 236 GLN Ab 284 ASN Ab 290 GLN ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 312 GLN Ad 190 ASN Ad 284 HIS Ae 242 HIS Af 74 GLN Ag 37 ASN Ah 60 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.115475 restraints weight = 56262.962| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.95 r_work: 0.3480 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.508 32661 Z= 0.185 Angle : 0.748 20.832 44296 Z= 0.365 Chirality : 0.045 0.240 4785 Planarity : 0.005 0.049 5608 Dihedral : 11.713 164.091 4800 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.16 % Allowed : 12.56 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.27 (0.13), residues: 3880 helix: 0.79 (0.11), residues: 2064 sheet: -0.20 (0.28), residues: 364 loop : -0.45 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAf 100 TYR 0.034 0.002 TYRAD 236 PHE 0.027 0.002 PHEAD 273 TRP 0.024 0.002 TRPAC 165 HIS 0.009 0.001 HISAa 119 Details of bonding type rmsd covalent geometry : bond 0.00419 (32648) covalent geometry : angle 0.74300 (44282) SS BOND : bond 0.00224 ( 7) SS BOND : angle 4.88262 ( 14) hydrogen bonds : bond 0.05097 ( 1787) hydrogen bonds : angle 5.24505 ( 5124) Misc. bond : bond 0.36895 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 817 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 247 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8007 (tm-30) REVERT: AA 469 ASN cc_start: 0.8598 (m-40) cc_final: 0.8188 (m110) REVERT: AB 37 ASP cc_start: 0.8379 (t0) cc_final: 0.8047 (p0) REVERT: AB 241 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6033 (ttp-110) REVERT: AC 94 LEU cc_start: 0.8333 (tp) cc_final: 0.8075 (mp) REVERT: AC 129 MET cc_start: 0.7396 (ptp) cc_final: 0.6983 (ptp) REVERT: AC 138 MET cc_start: 0.8374 (mmt) cc_final: 0.7986 (mmm) REVERT: AC 226 ILE cc_start: 0.8761 (tp) cc_final: 0.8555 (tt) REVERT: AC 240 MET cc_start: 0.9402 (mmm) cc_final: 0.9191 (mmm) REVERT: AC 249 MET cc_start: 0.5847 (tpp) cc_final: 0.5535 (tpp) REVERT: AC 269 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8252 (ttmm) REVERT: AC 322 GLN cc_start: 0.7784 (mt0) cc_final: 0.7557 (mt0) REVERT: AC 375 LYS cc_start: 0.7614 (tmtt) cc_final: 0.7181 (ttmt) REVERT: AD 118 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8071 (mmtt) REVERT: AD 249 TYR cc_start: 0.7138 (p90) cc_final: 0.6808 (p90) REVERT: AD 279 GLU cc_start: 0.8089 (tt0) cc_final: 0.7388 (tm-30) REVERT: AD 288 MET cc_start: 0.8870 (mtt) cc_final: 0.8517 (mtp) REVERT: AD 318 LYS cc_start: 0.8141 (mptt) cc_final: 0.7588 (mttt) REVERT: AE 146 VAL cc_start: 0.6652 (OUTLIER) cc_final: 0.6243 (p) REVERT: AE 165 MET cc_start: 0.4521 (tpt) cc_final: 0.4244 (ptm) REVERT: AF 22 TYR cc_start: 0.8973 (t80) cc_final: 0.8618 (t80) REVERT: AF 29 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8472 (ttmm) REVERT: AF 33 MET cc_start: 0.8409 (mmt) cc_final: 0.8189 (mmt) REVERT: AF 45 LYS cc_start: 0.8515 (mttt) cc_final: 0.8297 (mttp) REVERT: AF 46 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7563 (mm-30) REVERT: AF 60 MET cc_start: 0.7807 (mmm) cc_final: 0.6792 (mpp) REVERT: AF 99 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8634 (pt) REVERT: AG 8 LEU cc_start: 0.8763 (mt) cc_final: 0.8338 (mt) REVERT: AG 47 LEU cc_start: 0.8989 (mm) cc_final: 0.8296 (tp) REVERT: AG 65 GLN cc_start: 0.8256 (pp30) cc_final: 0.7963 (pp30) REVERT: AG 72 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7413 (mmm160) REVERT: AG 79 GLU cc_start: 0.4715 (tp30) cc_final: 0.4263 (mp0) REVERT: AH 33 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8344 (pp20) REVERT: AI 20 ARG cc_start: 0.7462 (mtm180) cc_final: 0.6616 (mtm-85) REVERT: AJ 32 PHE cc_start: 0.8035 (t80) cc_final: 0.7730 (t80) REVERT: AK 34 TRP cc_start: 0.6209 (t60) cc_final: 0.5932 (t60) REVERT: Aa 87 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8503 (t0) REVERT: Aa 99 LYS cc_start: 0.8228 (mmtp) cc_final: 0.7978 (mttp) REVERT: Aa 131 TYR cc_start: 0.8996 (m-80) cc_final: 0.8636 (m-80) REVERT: Aa 179 MET cc_start: 0.6272 (mtm) cc_final: 0.5910 (mtm) REVERT: Aa 363 MET cc_start: 0.8930 (mmm) cc_final: 0.8590 (mmm) REVERT: Aa 364 SER cc_start: 0.9038 (m) cc_final: 0.8190 (t) REVERT: Aa 368 MET cc_start: 0.9058 (tpt) cc_final: 0.8586 (tpt) REVERT: Ab 82 LEU cc_start: 0.8951 (tp) cc_final: 0.8646 (tp) REVERT: Ab 124 GLU cc_start: 0.8897 (pp20) cc_final: 0.8240 (pp20) REVERT: Ab 148 ARG cc_start: 0.7129 (ptm-80) cc_final: 0.6811 (ptt90) REVERT: Ab 179 ASP cc_start: 0.8997 (t70) cc_final: 0.8734 (t0) REVERT: Ab 238 LEU cc_start: 0.8660 (mt) cc_final: 0.8447 (mp) REVERT: Ab 260 GLU cc_start: 0.8240 (pt0) cc_final: 0.7987 (pt0) REVERT: Ab 309 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7920 (mm) REVERT: Ac 49 LEU cc_start: 0.8382 (tp) cc_final: 0.8168 (tp) REVERT: Ac 162 GLU cc_start: 0.6667 (mp0) cc_final: 0.6321 (pm20) REVERT: Ac 221 HIS cc_start: 0.8346 (t70) cc_final: 0.7768 (t70) REVERT: Ac 269 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8784 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9139 (mt) cc_final: 0.8573 (tt) REVERT: Ac 356 ILE cc_start: 0.8817 (mm) cc_final: 0.8598 (tp) REVERT: Ac 375 LYS cc_start: 0.7408 (tmtt) cc_final: 0.7119 (mttt) REVERT: Ad 127 MET cc_start: 0.7634 (mmm) cc_final: 0.7429 (mmm) REVERT: Ad 166 MET cc_start: 0.7941 (mtt) cc_final: 0.7116 (mmt) REVERT: Ad 223 THR cc_start: 0.8551 (t) cc_final: 0.8349 (p) REVERT: Ad 284 HIS cc_start: 0.7724 (t70) cc_final: 0.7520 (t-90) REVERT: Ae 197 ASP cc_start: 0.5722 (t0) cc_final: 0.5520 (t0) REVERT: Af 33 MET cc_start: 0.8269 (mmt) cc_final: 0.8031 (mmm) REVERT: Af 80 GLN cc_start: 0.8583 (mt0) cc_final: 0.8307 (mt0) REVERT: Af 84 TYR cc_start: 0.7859 (t80) cc_final: 0.7484 (t80) REVERT: Af 92 GLU cc_start: 0.8646 (tt0) cc_final: 0.8329 (tm-30) REVERT: Af 97 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7895 (mt-10) REVERT: Af 103 LYS cc_start: 0.8660 (mmmt) cc_final: 0.7983 (mmtm) REVERT: Ag 22 PHE cc_start: 0.8556 (m-80) cc_final: 0.8188 (m-80) REVERT: Ag 47 LEU cc_start: 0.9147 (tp) cc_final: 0.8930 (tp) REVERT: Ag 60 TYR cc_start: 0.8996 (t80) cc_final: 0.8563 (t80) REVERT: Ag 77 MET cc_start: 0.8353 (ttm) cc_final: 0.7782 (mtt) REVERT: Ah 45 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8462 (tpp80) REVERT: Ah 73 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (mm) REVERT: Ah 89 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7545 (pttt) REVERT: Aj 15 PHE cc_start: 0.7495 (m-10) cc_final: 0.7207 (m-80) REVERT: Ak 38 TRP cc_start: 0.6196 (t60) cc_final: 0.5873 (t60) outliers start: 105 outliers final: 54 residues processed: 877 average time/residue: 0.1917 time to fit residues: 268.1369 Evaluate side-chains 716 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 655 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 142 LYS Chi-restraints excluded: chain AA residue 164 GLU Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 402 HIS Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 52 LEU Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 139 ASN Chi-restraints excluded: chain AB residue 241 ARG Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 293 LEU Chi-restraints excluded: chain AC residue 102 LEU Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 344 GLU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AE residue 117 VAL Chi-restraints excluded: chain AE residue 146 VAL Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 40 GLU Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 87 ASN Chi-restraints excluded: chain Aa residue 114 GLU Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 216 LEU Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 111 GLU Chi-restraints excluded: chain Ac residue 249 MET Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 344 GLU Chi-restraints excluded: chain Ad residue 128 ASP Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 328 optimal weight: 0.2980 chunk 208 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 160 GLN ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 75 ASN AB 139 ASN ** AD 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 219 HIS AE 242 HIS AJ 46 HIS ** AK 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 87 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 280 ASN Ab 291 HIS Ab 298 HIS Ad 284 HIS Aj 48 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.149208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.112103 restraints weight = 56282.334| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.96 r_work: 0.3441 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.462 32661 Z= 0.172 Angle : 0.663 17.207 44296 Z= 0.322 Chirality : 0.043 0.214 4785 Planarity : 0.004 0.042 5608 Dihedral : 11.238 150.272 4796 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.62 % Allowed : 15.58 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.77 (0.14), residues: 3880 helix: 1.21 (0.11), residues: 2068 sheet: -0.13 (0.28), residues: 365 loop : -0.22 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAe 110 TYR 0.035 0.002 TYRAg 78 PHE 0.028 0.002 PHEAD 273 TRP 0.019 0.001 TRPAj 53 HIS 0.007 0.001 HISAA 402 Details of bonding type rmsd covalent geometry : bond 0.00394 (32648) covalent geometry : angle 0.66276 (44282) SS BOND : bond 0.01141 ( 7) SS BOND : angle 0.83590 ( 14) hydrogen bonds : bond 0.04586 ( 1787) hydrogen bonds : angle 4.94449 ( 5124) Misc. bond : bond 0.34194 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 695 time to evaluate : 1.284 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: AA 247 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8045 (tm-30) REVERT: AA 363 MET cc_start: 0.8929 (mmm) cc_final: 0.8726 (mmm) REVERT: AA 411 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6900 (tm-30) REVERT: AA 463 GLU cc_start: 0.7956 (tt0) cc_final: 0.7725 (tt0) REVERT: AA 469 ASN cc_start: 0.8592 (m-40) cc_final: 0.8192 (m110) REVERT: AB 37 ASP cc_start: 0.8464 (t0) cc_final: 0.7978 (p0) REVERT: AB 75 ASN cc_start: 0.8975 (t0) cc_final: 0.8503 (p0) REVERT: AB 318 HIS cc_start: 0.7419 (t-90) cc_final: 0.7200 (t-90) REVERT: AC 89 MET cc_start: 0.8543 (tpp) cc_final: 0.8222 (tpp) REVERT: AC 94 LEU cc_start: 0.8254 (tp) cc_final: 0.8026 (mp) REVERT: AC 129 MET cc_start: 0.7222 (ptp) cc_final: 0.6838 (ptp) REVERT: AC 138 MET cc_start: 0.8495 (mmt) cc_final: 0.7849 (mmm) REVERT: AC 235 MET cc_start: 0.9051 (tmm) cc_final: 0.8832 (tmm) REVERT: AC 240 MET cc_start: 0.9407 (mmm) cc_final: 0.9102 (mmm) REVERT: AC 249 MET cc_start: 0.6321 (tpp) cc_final: 0.5914 (tpp) REVERT: AC 257 MET cc_start: 0.7694 (ptp) cc_final: 0.7124 (ptp) REVERT: AC 269 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8226 (ttmm) REVERT: AC 375 LYS cc_start: 0.7487 (tmtt) cc_final: 0.6983 (ttmt) REVERT: AD 166 MET cc_start: 0.6840 (mpp) cc_final: 0.6552 (mmm) REVERT: AD 196 ASP cc_start: 0.8031 (p0) cc_final: 0.7663 (p0) REVERT: AD 279 GLU cc_start: 0.8255 (tt0) cc_final: 0.7600 (tt0) REVERT: AF 29 LYS cc_start: 0.8959 (mttt) cc_final: 0.8563 (ttmm) REVERT: AF 46 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7609 (mm-30) REVERT: AF 60 MET cc_start: 0.7812 (mmm) cc_final: 0.6661 (mpp) REVERT: AF 86 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8285 (mt-10) REVERT: AF 99 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8637 (pt) REVERT: AG 8 LEU cc_start: 0.8882 (mt) cc_final: 0.8654 (mt) REVERT: AG 25 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7929 (mtm180) REVERT: AG 47 LEU cc_start: 0.9048 (mm) cc_final: 0.8413 (tp) REVERT: AG 69 GLN cc_start: 0.7649 (tm-30) cc_final: 0.7360 (tm-30) REVERT: AH 33 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8361 (pp20) REVERT: AI 20 ARG cc_start: 0.7423 (mtm180) cc_final: 0.6524 (mtm-85) REVERT: AI 77 ARG cc_start: 0.7600 (tmt170) cc_final: 0.7336 (tmt170) REVERT: AJ 32 PHE cc_start: 0.8052 (t80) cc_final: 0.7753 (t80) REVERT: AK 34 TRP cc_start: 0.6227 (t60) cc_final: 0.5942 (t60) REVERT: Aa 68 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8848 (t) REVERT: Aa 87 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8420 (t0) REVERT: Aa 174 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: Aa 215 ASP cc_start: 0.8490 (t0) cc_final: 0.8258 (t0) REVERT: Aa 364 SER cc_start: 0.9020 (m) cc_final: 0.8207 (t) REVERT: Aa 368 MET cc_start: 0.9034 (tpt) cc_final: 0.8621 (tpt) REVERT: Ab 82 LEU cc_start: 0.8930 (tp) cc_final: 0.8677 (tp) REVERT: Ab 148 ARG cc_start: 0.7060 (ptm-80) cc_final: 0.6749 (ptt90) REVERT: Ab 179 ASP cc_start: 0.9036 (t70) cc_final: 0.8812 (t0) REVERT: Ab 204 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7629 (mm-30) REVERT: Ab 309 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7795 (mm) REVERT: Ac 49 LEU cc_start: 0.8471 (tp) cc_final: 0.8208 (tp) REVERT: Ac 89 MET cc_start: 0.8725 (mmm) cc_final: 0.8525 (mmm) REVERT: Ac 171 ASP cc_start: 0.7444 (p0) cc_final: 0.7199 (t70) REVERT: Ac 221 HIS cc_start: 0.8467 (t70) cc_final: 0.7772 (t70) REVERT: Ac 224 TYR cc_start: 0.8246 (m-80) cc_final: 0.8015 (m-80) REVERT: Ac 269 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8747 (mtmm) REVERT: Ac 281 LEU cc_start: 0.8936 (tp) cc_final: 0.8711 (tt) REVERT: Ac 299 LEU cc_start: 0.9175 (mt) cc_final: 0.8541 (tt) REVERT: Ac 356 ILE cc_start: 0.8782 (mm) cc_final: 0.8559 (tp) REVERT: Ac 375 LYS cc_start: 0.7365 (tmtt) cc_final: 0.6941 (mttt) REVERT: Ad 164 MET cc_start: 0.6752 (ptm) cc_final: 0.6047 (ppp) REVERT: Ad 166 MET cc_start: 0.8088 (mtt) cc_final: 0.7190 (mmt) REVERT: Ad 284 HIS cc_start: 0.7699 (t-90) cc_final: 0.7419 (t-90) REVERT: Ad 310 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7717 (mmtm) REVERT: Ae 110 ARG cc_start: 0.8372 (mtm110) cc_final: 0.8163 (mtm110) REVERT: Ae 130 LYS cc_start: 0.7523 (ttpt) cc_final: 0.7239 (ptmt) REVERT: Ae 163 LYS cc_start: 0.3219 (tptp) cc_final: 0.2698 (mmtt) REVERT: Ae 197 ASP cc_start: 0.6122 (t0) cc_final: 0.5898 (t0) REVERT: Af 33 MET cc_start: 0.8344 (mmt) cc_final: 0.8101 (mmm) REVERT: Af 46 GLU cc_start: 0.8277 (tp30) cc_final: 0.8042 (tp30) REVERT: Af 80 GLN cc_start: 0.8587 (mt0) cc_final: 0.8279 (mt0) REVERT: Af 84 TYR cc_start: 0.8084 (t80) cc_final: 0.7758 (t80) REVERT: Af 92 GLU cc_start: 0.8667 (tt0) cc_final: 0.8334 (tm-30) REVERT: Af 97 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7903 (mt-10) REVERT: Ag 47 LEU cc_start: 0.9172 (tp) cc_final: 0.8911 (tp) REVERT: Ag 60 TYR cc_start: 0.9003 (t80) cc_final: 0.8642 (t80) REVERT: Ag 73 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7880 (ttpt) REVERT: Ag 77 MET cc_start: 0.8616 (ttm) cc_final: 0.8004 (mtt) REVERT: Ag 78 TYR cc_start: 0.6540 (m-80) cc_final: 0.6171 (m-80) REVERT: Ah 45 ARG cc_start: 0.8704 (tpp80) cc_final: 0.8316 (mmm160) REVERT: Ah 89 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7467 (pttm) REVERT: Aj 15 PHE cc_start: 0.7584 (m-10) cc_final: 0.7122 (m-80) outliers start: 120 outliers final: 72 residues processed: 765 average time/residue: 0.2017 time to fit residues: 251.1409 Evaluate side-chains 710 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 632 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 93 LEU Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 151 VAL Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 402 HIS Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 233 VAL Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AC residue 102 LEU Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 241 THR Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 20 THR Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 87 ASN Chi-restraints excluded: chain Aa residue 114 GLU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 433 ILE Chi-restraints excluded: chain Aa residue 462 ILE Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 60 MET Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 249 MET Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 344 GLU Chi-restraints excluded: chain Ad residue 128 ASP Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Aj residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 38 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 281 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 190 optimal weight: 8.9990 chunk 355 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 308 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 64 ASN AH 87 ASN AJ 46 HIS AK 16 ASN Aa 87 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 290 GLN Ac 44 GLN Ad 90 HIS Ad 282 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.148761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111413 restraints weight = 56047.559| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.97 r_work: 0.3431 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.452 32661 Z= 0.157 Angle : 0.632 14.729 44296 Z= 0.307 Chirality : 0.042 0.249 4785 Planarity : 0.004 0.040 5608 Dihedral : 10.920 142.225 4796 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.89 % Allowed : 16.15 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.98 (0.14), residues: 3880 helix: 1.44 (0.11), residues: 2055 sheet: -0.28 (0.27), residues: 369 loop : -0.13 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAh 47 TYR 0.029 0.001 TYRAD 236 PHE 0.023 0.001 PHEAD 273 TRP 0.014 0.001 TRPAj 53 HIS 0.006 0.001 HISAd 205 Details of bonding type rmsd covalent geometry : bond 0.00360 (32648) covalent geometry : angle 0.63171 (44282) SS BOND : bond 0.00275 ( 7) SS BOND : angle 0.84468 ( 14) hydrogen bonds : bond 0.04247 ( 1787) hydrogen bonds : angle 4.77579 ( 5124) Misc. bond : bond 0.33673 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 675 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 96 LEU cc_start: 0.8923 (mm) cc_final: 0.8677 (mm) REVERT: AA 247 GLN cc_start: 0.8464 (tm-30) cc_final: 0.8017 (tm-30) REVERT: AA 363 MET cc_start: 0.8854 (mmm) cc_final: 0.8617 (mmm) REVERT: AA 411 GLU cc_start: 0.7263 (tm-30) cc_final: 0.7034 (tm-30) REVERT: AA 469 ASN cc_start: 0.8613 (m-40) cc_final: 0.8244 (m110) REVERT: AB 37 ASP cc_start: 0.8303 (t0) cc_final: 0.7818 (p0) REVERT: AB 75 ASN cc_start: 0.8958 (t0) cc_final: 0.8507 (p0) REVERT: AB 126 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8421 (pt) REVERT: AB 155 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7983 (mtt90) REVERT: AC 89 MET cc_start: 0.8504 (tpp) cc_final: 0.7850 (tpp) REVERT: AC 113 TRP cc_start: 0.8548 (t-100) cc_final: 0.8197 (t-100) REVERT: AC 129 MET cc_start: 0.7034 (ptp) cc_final: 0.6684 (ptp) REVERT: AC 138 MET cc_start: 0.8455 (mmt) cc_final: 0.7924 (mmm) REVERT: AC 235 MET cc_start: 0.9051 (tmm) cc_final: 0.8785 (tmm) REVERT: AC 240 MET cc_start: 0.9374 (mmm) cc_final: 0.9068 (mmm) REVERT: AC 249 MET cc_start: 0.6673 (tpp) cc_final: 0.6261 (tpp) REVERT: AC 257 MET cc_start: 0.7543 (ptp) cc_final: 0.7066 (ptp) REVERT: AC 269 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8322 (ttmm) REVERT: AC 375 LYS cc_start: 0.7503 (tmtt) cc_final: 0.6990 (ttmt) REVERT: AD 103 SER cc_start: 0.8269 (m) cc_final: 0.7853 (p) REVERT: AD 166 MET cc_start: 0.6821 (mpp) cc_final: 0.6458 (mmm) REVERT: AD 170 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8377 (mtmm) REVERT: AD 279 GLU cc_start: 0.8231 (tt0) cc_final: 0.7615 (tt0) REVERT: AD 306 MET cc_start: 0.8897 (mtp) cc_final: 0.8597 (mtm) REVERT: AF 29 LYS cc_start: 0.9043 (mttt) cc_final: 0.8829 (ttmm) REVERT: AF 46 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7596 (mm-30) REVERT: AF 60 MET cc_start: 0.7817 (mmm) cc_final: 0.6642 (mpp) REVERT: AF 86 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8286 (mt-10) REVERT: AF 99 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8607 (pt) REVERT: AF 106 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8474 (mm-30) REVERT: AG 8 LEU cc_start: 0.8950 (mt) cc_final: 0.8697 (mt) REVERT: AG 33 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8183 (tptt) REVERT: AG 47 LEU cc_start: 0.9055 (mm) cc_final: 0.8458 (tp) REVERT: AG 65 GLN cc_start: 0.8315 (pp30) cc_final: 0.8022 (pp30) REVERT: AH 33 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8327 (pp20) REVERT: AH 67 GLU cc_start: 0.7333 (tp30) cc_final: 0.7069 (tp30) REVERT: AI 20 ARG cc_start: 0.7385 (mtm180) cc_final: 0.6353 (mtm-85) REVERT: AJ 32 PHE cc_start: 0.8114 (t80) cc_final: 0.7851 (t80) REVERT: Aa 153 ASN cc_start: 0.7733 (m-40) cc_final: 0.6997 (t0) REVERT: Aa 166 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: Aa 170 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.7844 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: Aa 364 SER cc_start: 0.9002 (m) cc_final: 0.8263 (t) REVERT: Aa 368 MET cc_start: 0.9006 (tpt) cc_final: 0.8699 (tpt) REVERT: Ab 82 LEU cc_start: 0.8905 (tp) cc_final: 0.8698 (tp) REVERT: Ab 179 ASP cc_start: 0.8998 (t70) cc_final: 0.8793 (t0) REVERT: Ab 204 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7609 (mm-30) REVERT: Ac 47 THR cc_start: 0.8325 (p) cc_final: 0.8097 (p) REVERT: Ac 49 LEU cc_start: 0.8565 (tp) cc_final: 0.8335 (tp) REVERT: Ac 221 HIS cc_start: 0.8531 (t70) cc_final: 0.7743 (t70) REVERT: Ac 269 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8765 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9203 (mt) cc_final: 0.8481 (tt) REVERT: Ac 375 LYS cc_start: 0.7514 (tmtt) cc_final: 0.6976 (mtpt) REVERT: Ad 166 MET cc_start: 0.8174 (mtt) cc_final: 0.7400 (mmt) REVERT: Ad 310 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7931 (mmtm) REVERT: Ae 122 THR cc_start: 0.8505 (m) cc_final: 0.8264 (p) REVERT: Ae 163 LYS cc_start: 0.4019 (tptp) cc_final: 0.3319 (mmtt) REVERT: Ae 165 MET cc_start: 0.6983 (mtm) cc_final: 0.6683 (mtm) REVERT: Ae 197 ASP cc_start: 0.6302 (t0) cc_final: 0.6055 (t0) REVERT: Ae 220 LEU cc_start: 0.5399 (OUTLIER) cc_final: 0.5106 (mm) REVERT: Ae 230 ASP cc_start: 0.5996 (OUTLIER) cc_final: 0.5730 (p0) REVERT: Af 33 MET cc_start: 0.8320 (mmt) cc_final: 0.8067 (mmm) REVERT: Af 40 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8733 (mt-10) REVERT: Af 46 GLU cc_start: 0.8246 (tp30) cc_final: 0.8022 (tp30) REVERT: Af 84 TYR cc_start: 0.8302 (t80) cc_final: 0.8028 (t80) REVERT: Af 92 GLU cc_start: 0.8640 (tt0) cc_final: 0.8314 (tm-30) REVERT: Af 97 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7864 (mt-10) REVERT: Ag 47 LEU cc_start: 0.9197 (tp) cc_final: 0.8913 (tp) REVERT: Ag 60 TYR cc_start: 0.8979 (t80) cc_final: 0.8572 (t80) REVERT: Ag 77 MET cc_start: 0.8491 (ttm) cc_final: 0.8226 (mtt) REVERT: Ag 78 TYR cc_start: 0.6733 (m-80) cc_final: 0.6355 (m-80) REVERT: Ah 45 ARG cc_start: 0.8602 (tpp80) cc_final: 0.8395 (mmm160) REVERT: Ah 89 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7577 (pttm) REVERT: Aj 15 PHE cc_start: 0.7523 (m-10) cc_final: 0.6985 (m-10) REVERT: Aj 44 TYR cc_start: 0.8678 (t80) cc_final: 0.8389 (t80) REVERT: Aj 53 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.6195 (m100) outliers start: 129 outliers final: 80 residues processed: 748 average time/residue: 0.1895 time to fit residues: 230.3936 Evaluate side-chains 707 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 619 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 402 HIS Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 258 ILE Chi-restraints excluded: chain AC residue 102 LEU Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 233 LEU Chi-restraints excluded: chain AC residue 241 THR Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 189 ASN Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 32 LEU Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 42 GLU Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 64 ASN Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 43 LEU Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain AK residue 32 LEU Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 462 ILE Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 240 MET Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 60 MET Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 249 MET Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 22 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 334 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AA 452 GLN ** AA 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 119 GLN AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.160360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.126087 restraints weight = 57486.056| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.66 r_work: 0.3484 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.540 32661 Z= 0.208 Angle : 0.668 16.709 44296 Z= 0.321 Chirality : 0.044 0.214 4785 Planarity : 0.004 0.040 5608 Dihedral : 10.840 136.841 4796 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.53 % Allowed : 18.11 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.00 (0.14), residues: 3880 helix: 1.45 (0.11), residues: 2055 sheet: -0.37 (0.27), residues: 372 loop : -0.07 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAe 110 TYR 0.023 0.002 TYRAD 236 PHE 0.021 0.002 PHEAD 273 TRP 0.014 0.001 TRPAj 53 HIS 0.015 0.001 HISAA 402 Details of bonding type rmsd covalent geometry : bond 0.00486 (32648) covalent geometry : angle 0.66774 (44282) SS BOND : bond 0.00149 ( 7) SS BOND : angle 0.65945 ( 14) hydrogen bonds : bond 0.04325 ( 1787) hydrogen bonds : angle 4.79350 ( 5124) Misc. bond : bond 0.31737 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 662 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 76 ASP cc_start: 0.8308 (t0) cc_final: 0.8057 (t0) REVERT: AA 247 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7942 (tm-30) REVERT: AA 341 PHE cc_start: 0.8683 (t80) cc_final: 0.8465 (t80) REVERT: AA 463 GLU cc_start: 0.8059 (tt0) cc_final: 0.7845 (tt0) REVERT: AA 469 ASN cc_start: 0.8622 (m-40) cc_final: 0.8145 (m110) REVERT: AB 37 ASP cc_start: 0.8358 (t0) cc_final: 0.7639 (p0) REVERT: AB 75 ASN cc_start: 0.8947 (t0) cc_final: 0.8554 (p0) REVERT: AB 126 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8485 (pt) REVERT: AB 155 ARG cc_start: 0.8339 (mtm180) cc_final: 0.8103 (mtt90) REVERT: AB 355 TYR cc_start: 0.8054 (t80) cc_final: 0.7825 (t80) REVERT: AC 89 MET cc_start: 0.8451 (tpp) cc_final: 0.8154 (tpp) REVERT: AC 94 LEU cc_start: 0.8290 (tp) cc_final: 0.8051 (mp) REVERT: AC 129 MET cc_start: 0.7400 (ptp) cc_final: 0.7009 (ptp) REVERT: AC 138 MET cc_start: 0.8457 (mmt) cc_final: 0.7953 (mmm) REVERT: AC 223 TYR cc_start: 0.9042 (m-80) cc_final: 0.8754 (m-80) REVERT: AC 235 MET cc_start: 0.8993 (tmm) cc_final: 0.8715 (tmm) REVERT: AC 240 MET cc_start: 0.9343 (mmm) cc_final: 0.9049 (mmm) REVERT: AC 249 MET cc_start: 0.6859 (tpp) cc_final: 0.6425 (tpp) REVERT: AC 257 MET cc_start: 0.7802 (ptp) cc_final: 0.7307 (ptp) REVERT: AC 269 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8256 (ttmm) REVERT: AC 344 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7946 (mm-30) REVERT: AC 375 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7124 (ttmt) REVERT: AD 103 SER cc_start: 0.8404 (m) cc_final: 0.8024 (p) REVERT: AD 110 ILE cc_start: 0.8632 (mt) cc_final: 0.8306 (mm) REVERT: AD 272 THR cc_start: 0.8744 (m) cc_final: 0.8368 (p) REVERT: AD 279 GLU cc_start: 0.8224 (tt0) cc_final: 0.7659 (tt0) REVERT: AD 288 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8385 (mmm) REVERT: AE 115 TYR cc_start: 0.7312 (m-10) cc_final: 0.6750 (m-10) REVERT: AF 46 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7688 (mm-30) REVERT: AF 86 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8327 (mt-10) REVERT: AF 99 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8667 (pt) REVERT: AF 110 LYS cc_start: 0.7681 (mttt) cc_final: 0.7471 (tmmt) REVERT: AG 33 LYS cc_start: 0.8430 (ttpp) cc_final: 0.8041 (tptt) REVERT: AG 47 LEU cc_start: 0.9032 (mm) cc_final: 0.8509 (tp) REVERT: AH 33 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8274 (pp20) REVERT: AI 20 ARG cc_start: 0.7630 (mtm180) cc_final: 0.6556 (mtm-85) REVERT: AI 77 ARG cc_start: 0.7350 (tmt170) cc_final: 0.6966 (tmt170) REVERT: AJ 32 PHE cc_start: 0.8176 (t80) cc_final: 0.7933 (t80) REVERT: Aa 153 ASN cc_start: 0.7950 (m-40) cc_final: 0.7240 (t0) REVERT: Aa 170 ARG cc_start: 0.8390 (ptm-80) cc_final: 0.7912 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: Aa 364 SER cc_start: 0.9054 (m) cc_final: 0.8364 (t) REVERT: Aa 368 MET cc_start: 0.8975 (tpt) cc_final: 0.8649 (tpt) REVERT: Aa 430 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7650 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8108 (m-30) cc_final: 0.7531 (m-30) REVERT: Ac 49 LEU cc_start: 0.8649 (tp) cc_final: 0.8446 (tp) REVERT: Ac 269 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8753 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9234 (mt) cc_final: 0.8450 (tt) REVERT: Ac 375 LYS cc_start: 0.7728 (tmtt) cc_final: 0.7057 (mtpt) REVERT: Ad 164 MET cc_start: 0.6975 (ptm) cc_final: 0.6397 (ppp) REVERT: Ad 166 MET cc_start: 0.8254 (mtt) cc_final: 0.7423 (mmt) REVERT: Ad 310 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8010 (mmtm) REVERT: Ae 122 THR cc_start: 0.8656 (m) cc_final: 0.8369 (p) REVERT: Ae 165 MET cc_start: 0.7328 (mtm) cc_final: 0.7027 (mtm) REVERT: Ae 197 ASP cc_start: 0.6476 (t0) cc_final: 0.6161 (t0) REVERT: Af 33 MET cc_start: 0.8502 (mmt) cc_final: 0.8280 (mmm) REVERT: Af 40 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8685 (mt-10) REVERT: Af 80 GLN cc_start: 0.8661 (mt0) cc_final: 0.8400 (mt0) REVERT: Af 86 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7997 (tm-30) REVERT: Af 92 GLU cc_start: 0.8568 (tt0) cc_final: 0.8316 (tm-30) REVERT: Af 97 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7835 (mt-10) REVERT: Af 103 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8110 (mmtm) REVERT: Af 107 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8368 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9270 (tp) cc_final: 0.9016 (tp) REVERT: Ag 68 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8264 (mm-30) REVERT: Ag 78 TYR cc_start: 0.6665 (m-80) cc_final: 0.6311 (m-80) REVERT: Aj 15 PHE cc_start: 0.7783 (m-10) cc_final: 0.7180 (m-10) REVERT: Aj 16 ARG cc_start: 0.7121 (ttm-80) cc_final: 0.6826 (ttm-80) REVERT: Aj 44 TYR cc_start: 0.8792 (t80) cc_final: 0.8555 (t80) REVERT: Aj 53 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.6346 (m100) outliers start: 117 outliers final: 88 residues processed: 734 average time/residue: 0.1924 time to fit residues: 228.4850 Evaluate side-chains 707 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 612 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 63 GLN Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 136 LEU Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 388 VAL Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 241 THR Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 189 ASN Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 288 MET Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 133 VAL Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 43 LEU Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 417 LEU Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Aa residue 462 ILE Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 257 GLU Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 111 GLU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 249 MET Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 355 SER Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 16 SER Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 236 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 272 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 225 optimal weight: 0.9980 chunk 354 optimal weight: 2.9990 chunk 357 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AC 15 ASN AC 137 GLN AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.148300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111110 restraints weight = 56165.949| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.94 r_work: 0.3416 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.005 0.460 32661 Z= 0.144 Angle : 0.642 15.957 44296 Z= 0.304 Chirality : 0.042 0.187 4785 Planarity : 0.004 0.066 5608 Dihedral : 10.611 134.780 4796 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.62 % Allowed : 18.86 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.12 (0.14), residues: 3880 helix: 1.56 (0.11), residues: 2054 sheet: -0.36 (0.27), residues: 372 loop : -0.01 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAe 110 TYR 0.023 0.001 TYRAF 84 PHE 0.031 0.001 PHEAj 32 TRP 0.021 0.001 TRPAK 34 HIS 0.009 0.001 HISAA 402 Details of bonding type rmsd covalent geometry : bond 0.00335 (32648) covalent geometry : angle 0.64188 (44282) SS BOND : bond 0.00131 ( 7) SS BOND : angle 0.76932 ( 14) hydrogen bonds : bond 0.04042 ( 1787) hydrogen bonds : angle 4.68807 ( 5124) Misc. bond : bond 0.27688 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 667 time to evaluate : 0.895 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: AA 76 ASP cc_start: 0.8259 (t0) cc_final: 0.8018 (t0) REVERT: AA 247 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8030 (tm-30) REVERT: AA 341 PHE cc_start: 0.8748 (t80) cc_final: 0.8502 (t80) REVERT: AA 463 GLU cc_start: 0.8040 (tt0) cc_final: 0.7760 (tt0) REVERT: AA 469 ASN cc_start: 0.8609 (m-40) cc_final: 0.8108 (m110) REVERT: AB 37 ASP cc_start: 0.8430 (t0) cc_final: 0.7681 (p0) REVERT: AB 75 ASN cc_start: 0.8967 (t0) cc_final: 0.8519 (p0) REVERT: AB 104 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8753 (mt-10) REVERT: AB 126 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8478 (pt) REVERT: AB 155 ARG cc_start: 0.8263 (mtm180) cc_final: 0.8039 (mtt90) REVERT: AB 241 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6336 (ttp-110) REVERT: AC 15 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7449 (t0) REVERT: AC 89 MET cc_start: 0.8341 (tpp) cc_final: 0.8035 (tpp) REVERT: AC 94 LEU cc_start: 0.8241 (tp) cc_final: 0.8029 (mp) REVERT: AC 113 TRP cc_start: 0.8562 (t-100) cc_final: 0.8313 (t-100) REVERT: AC 129 MET cc_start: 0.7029 (ptp) cc_final: 0.6575 (ptp) REVERT: AC 138 MET cc_start: 0.8549 (mmt) cc_final: 0.8028 (mmm) REVERT: AC 223 TYR cc_start: 0.9137 (m-80) cc_final: 0.8832 (m-80) REVERT: AC 235 MET cc_start: 0.9043 (tmm) cc_final: 0.8664 (tmm) REVERT: AC 240 MET cc_start: 0.9283 (mmm) cc_final: 0.9026 (mmm) REVERT: AC 249 MET cc_start: 0.6992 (tpp) cc_final: 0.6561 (tpp) REVERT: AC 257 MET cc_start: 0.7683 (ptp) cc_final: 0.7274 (ptp) REVERT: AC 269 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8284 (ttmm) REVERT: AC 375 LYS cc_start: 0.7595 (tmtt) cc_final: 0.7056 (ttmt) REVERT: AD 103 SER cc_start: 0.8400 (m) cc_final: 0.8048 (p) REVERT: AD 104 SER cc_start: 0.8938 (p) cc_final: 0.8417 (m) REVERT: AD 110 ILE cc_start: 0.8634 (mt) cc_final: 0.8350 (mm) REVERT: AD 279 GLU cc_start: 0.8195 (tt0) cc_final: 0.7719 (tt0) REVERT: AE 115 TYR cc_start: 0.7045 (m-10) cc_final: 0.6460 (m-10) REVERT: AE 167 PHE cc_start: 0.7774 (m-80) cc_final: 0.6930 (m-80) REVERT: AF 46 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7632 (mm-30) REVERT: AF 86 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8346 (mt-10) REVERT: AF 99 ILE cc_start: 0.9074 (mm) cc_final: 0.8612 (pt) REVERT: AG 25 ARG cc_start: 0.8274 (mtp180) cc_final: 0.7987 (mtm180) REVERT: AG 33 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8075 (tptt) REVERT: AG 47 LEU cc_start: 0.9093 (mm) cc_final: 0.8555 (tp) REVERT: AH 86 LYS cc_start: 0.8460 (mttp) cc_final: 0.8258 (mttp) REVERT: AI 20 ARG cc_start: 0.7532 (mtm180) cc_final: 0.6391 (mtm-85) REVERT: Aa 153 ASN cc_start: 0.7952 (m-40) cc_final: 0.7154 (t0) REVERT: Aa 166 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: Aa 170 ARG cc_start: 0.8314 (ptm-80) cc_final: 0.7860 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: Aa 250 LEU cc_start: 0.9001 (tt) cc_final: 0.8783 (tp) REVERT: Aa 364 SER cc_start: 0.8990 (m) cc_final: 0.8277 (t) REVERT: Aa 368 MET cc_start: 0.8965 (tpt) cc_final: 0.8707 (tpt) REVERT: Aa 430 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7608 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8082 (m-30) cc_final: 0.7501 (m-30) REVERT: Ac 89 MET cc_start: 0.8364 (mmm) cc_final: 0.8069 (tpp) REVERT: Ac 162 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6604 (pt0) REVERT: Ac 235 MET cc_start: 0.8764 (tmm) cc_final: 0.8548 (tmm) REVERT: Ac 269 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8721 (mtmm) REVERT: Ac 294 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8137 (mt) REVERT: Ac 299 LEU cc_start: 0.9240 (mt) cc_final: 0.8418 (tt) REVERT: Ac 373 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: Ac 375 LYS cc_start: 0.7539 (tmtt) cc_final: 0.6782 (mtpt) REVERT: Ad 164 MET cc_start: 0.7086 (ptm) cc_final: 0.6500 (ppp) REVERT: Ad 166 MET cc_start: 0.8111 (mtt) cc_final: 0.7337 (mmt) REVERT: Ad 310 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8029 (mmmt) REVERT: Ae 111 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.6157 (mttm) REVERT: Ae 122 THR cc_start: 0.8500 (m) cc_final: 0.8270 (p) REVERT: Ae 134 SER cc_start: 0.8165 (t) cc_final: 0.7560 (m) REVERT: Ae 163 LYS cc_start: 0.3300 (tptp) cc_final: 0.2801 (mmtt) REVERT: Ae 165 MET cc_start: 0.7393 (mtm) cc_final: 0.7159 (mtp) REVERT: Ae 197 ASP cc_start: 0.6334 (t0) cc_final: 0.6037 (t0) REVERT: Ae 220 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.5107 (mm) REVERT: Af 33 MET cc_start: 0.8479 (mmt) cc_final: 0.8231 (mmm) REVERT: Af 40 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8764 (mt-10) REVERT: Af 80 GLN cc_start: 0.8696 (mt0) cc_final: 0.8377 (mt0) REVERT: Af 92 GLU cc_start: 0.8535 (tt0) cc_final: 0.8225 (tm-30) REVERT: Af 97 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7826 (mt-10) REVERT: Af 103 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8083 (mmtm) REVERT: Af 107 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8388 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9220 (tp) cc_final: 0.8946 (tp) REVERT: Ag 60 TYR cc_start: 0.8994 (t80) cc_final: 0.8590 (t80) REVERT: Aj 15 PHE cc_start: 0.7495 (m-10) cc_final: 0.6867 (m-10) REVERT: Aj 16 ARG cc_start: 0.6913 (ttm-80) cc_final: 0.6672 (ttm-80) REVERT: Aj 53 TRP cc_start: 0.7009 (OUTLIER) cc_final: 0.6259 (m100) outliers start: 120 outliers final: 74 residues processed: 742 average time/residue: 0.1800 time to fit residues: 217.0158 Evaluate side-chains 708 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 622 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 402 HIS Chi-restraints excluded: chain AA residue 440 MET Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 241 ARG Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AB residue 432 VAL Chi-restraints excluded: chain AC residue 15 ASN Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 189 ASN Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 43 LEU Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 249 MET Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 373 GLU Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 111 LYS Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 325 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 360 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 369 optimal weight: 9.9990 chunk 379 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 367 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 377 optimal weight: 0.0980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AC 15 ASN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 85 ASN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 242 HIS Aj 48 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105331 restraints weight = 56732.853| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.06 r_work: 0.3317 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.352 32661 Z= 0.169 Angle : 0.663 16.340 44296 Z= 0.313 Chirality : 0.042 0.168 4785 Planarity : 0.004 0.038 5608 Dihedral : 10.513 132.602 4796 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.71 % Allowed : 19.34 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.14 (0.14), residues: 3880 helix: 1.59 (0.11), residues: 2058 sheet: -0.53 (0.26), residues: 402 loop : 0.04 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGAe 110 TYR 0.025 0.001 TYRAD 236 PHE 0.024 0.001 PHEAd 273 TRP 0.016 0.001 TRPAK 34 HIS 0.017 0.001 HISAA 402 Details of bonding type rmsd covalent geometry : bond 0.00399 (32648) covalent geometry : angle 0.66307 (44282) SS BOND : bond 0.00138 ( 7) SS BOND : angle 0.73645 ( 14) hydrogen bonds : bond 0.04077 ( 1787) hydrogen bonds : angle 4.68072 ( 5124) Misc. bond : bond 0.20721 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 650 time to evaluate : 1.289 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: AA 76 ASP cc_start: 0.8276 (t0) cc_final: 0.8031 (t0) REVERT: AA 94 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8458 (tm-30) REVERT: AA 247 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8081 (tm-30) REVERT: AA 341 PHE cc_start: 0.8799 (t80) cc_final: 0.8560 (t80) REVERT: AA 469 ASN cc_start: 0.8575 (m-40) cc_final: 0.8055 (m110) REVERT: AB 104 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8803 (mt-10) REVERT: AB 126 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8399 (pt) REVERT: AB 155 ARG cc_start: 0.8282 (mtm180) cc_final: 0.8038 (mtt90) REVERT: AB 241 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6515 (ttp-110) REVERT: AC 89 MET cc_start: 0.8312 (tpp) cc_final: 0.7990 (tpp) REVERT: AC 94 LEU cc_start: 0.8247 (tp) cc_final: 0.8016 (mp) REVERT: AC 113 TRP cc_start: 0.8532 (t-100) cc_final: 0.8251 (t-100) REVERT: AC 138 MET cc_start: 0.8576 (mmt) cc_final: 0.7994 (mmm) REVERT: AC 223 TYR cc_start: 0.9169 (m-80) cc_final: 0.8856 (m-80) REVERT: AC 235 MET cc_start: 0.9035 (tmm) cc_final: 0.8652 (tmm) REVERT: AC 249 MET cc_start: 0.7269 (tpp) cc_final: 0.6791 (tpp) REVERT: AC 269 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8277 (ttmm) REVERT: AC 344 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7885 (mm-30) REVERT: AC 375 LYS cc_start: 0.7606 (tmtt) cc_final: 0.7094 (ttmt) REVERT: AD 103 SER cc_start: 0.8402 (m) cc_final: 0.8025 (p) REVERT: AD 104 SER cc_start: 0.8888 (p) cc_final: 0.8439 (m) REVERT: AD 110 ILE cc_start: 0.8518 (mt) cc_final: 0.8221 (mm) REVERT: AD 143 GLU cc_start: 0.8402 (tp30) cc_final: 0.8116 (pm20) REVERT: AD 279 GLU cc_start: 0.8211 (tt0) cc_final: 0.7619 (tt0) REVERT: AD 288 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8246 (mmm) REVERT: AE 90 ASP cc_start: 0.8781 (p0) cc_final: 0.8359 (p0) REVERT: AE 115 TYR cc_start: 0.6946 (m-10) cc_final: 0.6318 (m-10) REVERT: AE 165 MET cc_start: 0.5807 (tpt) cc_final: 0.5180 (ptm) REVERT: AE 167 PHE cc_start: 0.7755 (m-80) cc_final: 0.6288 (m-80) REVERT: AE 271 VAL cc_start: 0.7302 (t) cc_final: 0.6955 (m) REVERT: AF 46 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7643 (mm-30) REVERT: AF 86 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8418 (mt-10) REVERT: AF 99 ILE cc_start: 0.9027 (mm) cc_final: 0.8567 (pt) REVERT: AF 106 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8453 (mm-30) REVERT: AG 47 LEU cc_start: 0.9127 (mm) cc_final: 0.8535 (tp) REVERT: AH 86 LYS cc_start: 0.8462 (mttp) cc_final: 0.8220 (mttp) REVERT: AI 20 ARG cc_start: 0.7653 (mtm180) cc_final: 0.6429 (mtm-85) REVERT: Aa 153 ASN cc_start: 0.8030 (m-40) cc_final: 0.7114 (t0) REVERT: Aa 170 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7808 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: Aa 364 SER cc_start: 0.8944 (m) cc_final: 0.8148 (t) REVERT: Aa 367 ASP cc_start: 0.8776 (t0) cc_final: 0.8570 (t0) REVERT: Aa 368 MET cc_start: 0.8966 (tpt) cc_final: 0.8475 (tpt) REVERT: Aa 430 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7782 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7665 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8069 (m-30) cc_final: 0.7483 (m-30) REVERT: Ac 89 MET cc_start: 0.8432 (mmm) cc_final: 0.8028 (tpp) REVERT: Ac 269 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8677 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9242 (mt) cc_final: 0.8427 (tt) REVERT: Ac 375 LYS cc_start: 0.7492 (tmtt) cc_final: 0.6687 (mtpt) REVERT: Ad 164 MET cc_start: 0.7083 (ptm) cc_final: 0.6528 (ppp) REVERT: Ad 166 MET cc_start: 0.8119 (mtt) cc_final: 0.7328 (mmt) REVERT: Ad 263 MET cc_start: 0.8554 (ttp) cc_final: 0.8156 (tmm) REVERT: Ad 310 LYS cc_start: 0.8308 (mmtt) cc_final: 0.8061 (mmmt) REVERT: Ae 111 LYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5923 (mttm) REVERT: Ae 131 ASN cc_start: 0.7580 (t0) cc_final: 0.7350 (t0) REVERT: Ae 134 SER cc_start: 0.8074 (t) cc_final: 0.7505 (m) REVERT: Ae 197 ASP cc_start: 0.6299 (t0) cc_final: 0.6014 (t0) REVERT: Ae 220 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4961 (mm) REVERT: Af 33 MET cc_start: 0.8429 (mmt) cc_final: 0.8095 (mmm) REVERT: Af 40 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8831 (mt-10) REVERT: Af 46 GLU cc_start: 0.8058 (tp30) cc_final: 0.7690 (tp30) REVERT: Af 80 GLN cc_start: 0.8771 (mt0) cc_final: 0.8396 (mt0) REVERT: Af 92 GLU cc_start: 0.8552 (tt0) cc_final: 0.8177 (tm-30) REVERT: Af 97 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7880 (mt-10) REVERT: Af 103 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8059 (mmtm) REVERT: Af 107 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8440 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9199 (tp) cc_final: 0.8902 (tp) REVERT: Ag 60 TYR cc_start: 0.8935 (t80) cc_final: 0.8480 (t80) REVERT: Ag 68 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8645 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7497 (m-10) cc_final: 0.6805 (m-10) REVERT: Aj 53 TRP cc_start: 0.6998 (OUTLIER) cc_final: 0.6299 (m100) outliers start: 123 outliers final: 90 residues processed: 728 average time/residue: 0.2001 time to fit residues: 236.7138 Evaluate side-chains 721 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 623 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 63 GLN Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 136 LEU Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 130 ILE Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 241 ARG Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AB residue 432 VAL Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 241 THR Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 160 ASP Chi-restraints excluded: chain AD residue 189 ASN Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 288 MET Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 82 ASP Chi-restraints excluded: chain AE residue 117 VAL Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 32 LEU Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 43 ARG Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 14 VAL Chi-restraints excluded: chain AI residue 43 LEU Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 32 LEU Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 266 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 417 LEU Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 257 GLU Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 355 SER Chi-restraints excluded: chain Ad residue 128 ASP Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 111 LYS Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 57 SER Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 66 optimal weight: 10.0000 chunk 382 optimal weight: 7.9990 chunk 356 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 0.0060 chunk 71 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 304 ASN AC 15 ASN AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109624 restraints weight = 56701.168| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.93 r_work: 0.3335 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.340 32661 Z= 0.137 Angle : 0.657 16.949 44296 Z= 0.308 Chirality : 0.042 0.209 4785 Planarity : 0.004 0.039 5608 Dihedral : 10.368 129.402 4796 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.31 % Allowed : 19.86 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.25 (0.14), residues: 3880 helix: 1.68 (0.11), residues: 2054 sheet: -0.37 (0.26), residues: 394 loop : 0.05 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAG 40 TYR 0.025 0.001 TYRAD 236 PHE 0.028 0.001 PHEAj 32 TRP 0.017 0.001 TRPAK 34 HIS 0.006 0.001 HISAe 239 Details of bonding type rmsd covalent geometry : bond 0.00320 (32648) covalent geometry : angle 0.65652 (44282) SS BOND : bond 0.00574 ( 7) SS BOND : angle 1.54974 ( 14) hydrogen bonds : bond 0.03935 ( 1787) hydrogen bonds : angle 4.60383 ( 5124) Misc. bond : bond 0.22988 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 667 time to evaluate : 1.187 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: AA 76 ASP cc_start: 0.8210 (t0) cc_final: 0.7977 (t0) REVERT: AA 94 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8465 (tm-30) REVERT: AA 247 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8040 (tm-30) REVERT: AA 341 PHE cc_start: 0.8774 (t80) cc_final: 0.8566 (t80) REVERT: AA 377 MET cc_start: 0.7692 (mmm) cc_final: 0.7078 (mmm) REVERT: AA 435 GLU cc_start: 0.8638 (pp20) cc_final: 0.8153 (mt-10) REVERT: AA 469 ASN cc_start: 0.8579 (m-40) cc_final: 0.8055 (m110) REVERT: AB 104 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8774 (mt-10) REVERT: AB 126 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8452 (pt) REVERT: AB 155 ARG cc_start: 0.8283 (mtm180) cc_final: 0.8063 (mtt90) REVERT: AC 14 ILE cc_start: 0.7621 (mm) cc_final: 0.7060 (tp) REVERT: AC 113 TRP cc_start: 0.8455 (t-100) cc_final: 0.8176 (t-100) REVERT: AC 138 MET cc_start: 0.8633 (mmt) cc_final: 0.8033 (mmm) REVERT: AC 223 TYR cc_start: 0.9175 (m-80) cc_final: 0.8857 (m-80) REVERT: AC 235 MET cc_start: 0.9071 (tmm) cc_final: 0.8651 (tmm) REVERT: AC 249 MET cc_start: 0.7391 (tpp) cc_final: 0.6981 (tpp) REVERT: AC 344 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7985 (mm-30) REVERT: AC 375 LYS cc_start: 0.7635 (tmtt) cc_final: 0.7110 (ttmt) REVERT: AD 103 SER cc_start: 0.8403 (m) cc_final: 0.7944 (p) REVERT: AD 110 ILE cc_start: 0.8466 (mt) cc_final: 0.8166 (mm) REVERT: AD 143 GLU cc_start: 0.8429 (tp30) cc_final: 0.8179 (pm20) REVERT: AD 166 MET cc_start: 0.5495 (mmm) cc_final: 0.5058 (mmm) REVERT: AD 279 GLU cc_start: 0.8192 (tt0) cc_final: 0.7616 (tt0) REVERT: AD 288 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8258 (mmm) REVERT: AE 90 ASP cc_start: 0.8820 (p0) cc_final: 0.8412 (p0) REVERT: AE 115 TYR cc_start: 0.6867 (m-10) cc_final: 0.6269 (m-10) REVERT: AE 165 MET cc_start: 0.5719 (tpt) cc_final: 0.5120 (ptm) REVERT: AE 167 PHE cc_start: 0.7853 (m-80) cc_final: 0.6394 (m-80) REVERT: AE 271 VAL cc_start: 0.7322 (t) cc_final: 0.6978 (m) REVERT: AF 46 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7657 (mm-30) REVERT: AF 53 GLU cc_start: 0.7698 (tp30) cc_final: 0.7439 (tp30) REVERT: AF 86 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8458 (mt-10) REVERT: AF 99 ILE cc_start: 0.9051 (mm) cc_final: 0.8569 (pt) REVERT: AF 106 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8543 (mm-30) REVERT: AG 45 ARG cc_start: 0.7062 (mmt90) cc_final: 0.6808 (mmm-85) REVERT: AG 47 LEU cc_start: 0.9124 (mm) cc_final: 0.8537 (tp) REVERT: AG 79 GLU cc_start: 0.4457 (mm-30) cc_final: 0.4203 (mm-30) REVERT: AI 20 ARG cc_start: 0.7624 (mtm180) cc_final: 0.6393 (mtm-85) REVERT: Aa 166 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: Aa 170 ARG cc_start: 0.8290 (ptm-80) cc_final: 0.7803 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: Aa 364 SER cc_start: 0.8982 (m) cc_final: 0.8168 (t) REVERT: Aa 367 ASP cc_start: 0.8770 (t0) cc_final: 0.8565 (t0) REVERT: Aa 368 MET cc_start: 0.8941 (tpt) cc_final: 0.8556 (tpt) REVERT: Aa 430 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: Ab 134 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8410 (mtm) REVERT: Ab 204 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7673 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8040 (m-30) cc_final: 0.7460 (m-30) REVERT: Ac 89 MET cc_start: 0.8407 (mmm) cc_final: 0.8096 (tpp) REVERT: Ac 137 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6527 (tp-100) REVERT: Ac 269 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8678 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9252 (mt) cc_final: 0.8478 (tt) REVERT: Ac 373 GLU cc_start: 0.7701 (tt0) cc_final: 0.7495 (tt0) REVERT: Ac 375 LYS cc_start: 0.7395 (tmtt) cc_final: 0.6489 (mtpt) REVERT: Ad 164 MET cc_start: 0.7152 (ptm) cc_final: 0.6610 (ppp) REVERT: Ad 166 MET cc_start: 0.8029 (mtt) cc_final: 0.7317 (mmt) REVERT: Ad 177 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8783 (ttpt) REVERT: Ad 263 MET cc_start: 0.8554 (ttp) cc_final: 0.8144 (tmm) REVERT: Ad 310 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7979 (mmmt) REVERT: Ae 110 ARG cc_start: 0.7789 (mtm110) cc_final: 0.6810 (ptp90) REVERT: Ae 111 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.5968 (mttm) REVERT: Ae 131 ASN cc_start: 0.7514 (t0) cc_final: 0.7147 (t0) REVERT: Ae 134 SER cc_start: 0.7894 (t) cc_final: 0.7450 (p) REVERT: Ae 197 ASP cc_start: 0.6507 (t0) cc_final: 0.6185 (t0) REVERT: Ae 220 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4933 (mm) REVERT: Af 33 MET cc_start: 0.8401 (mmt) cc_final: 0.8088 (mmm) REVERT: Af 40 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8781 (mt-10) REVERT: Af 46 GLU cc_start: 0.8056 (tp30) cc_final: 0.7663 (tp30) REVERT: Af 74 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8470 (mm-40) REVERT: Af 80 GLN cc_start: 0.8784 (mt0) cc_final: 0.8397 (mt0) REVERT: Af 92 GLU cc_start: 0.8547 (tt0) cc_final: 0.8158 (tm-30) REVERT: Af 97 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7801 (mt-10) REVERT: Af 103 LYS cc_start: 0.8714 (mmmt) cc_final: 0.7992 (mmtm) REVERT: Af 107 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8452 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9165 (tp) cc_final: 0.8864 (tp) REVERT: Ag 60 TYR cc_start: 0.8945 (t80) cc_final: 0.8568 (t80) REVERT: Ah 89 LYS cc_start: 0.7714 (pttt) cc_final: 0.7476 (pttm) REVERT: Aj 15 PHE cc_start: 0.7435 (m-10) cc_final: 0.6785 (m-10) REVERT: Aj 16 ARG cc_start: 0.6505 (ttm-80) cc_final: 0.6294 (ttm-80) REVERT: Aj 53 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.6194 (m100) outliers start: 110 outliers final: 77 residues processed: 740 average time/residue: 0.1913 time to fit residues: 229.9455 Evaluate side-chains 705 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 617 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 130 ILE Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 432 VAL Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 160 ASP Chi-restraints excluded: chain AD residue 189 ASN Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 288 MET Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 82 ASP Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 42 VAL Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 208 VAL Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 266 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 400 VAL Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 126 ILE Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 134 MET Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 355 SER Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 111 LYS Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 74 GLN Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 16 SER Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 57 SER Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 318 optimal weight: 0.4980 chunk 338 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 280 optimal weight: 0.7980 chunk 279 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 354 optimal weight: 2.9990 chunk 378 optimal weight: 8.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 ASN AC 32 ASN AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 153 ASN Ab 303 ASN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.110978 restraints weight = 56519.447| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.91 r_work: 0.3347 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.331 32661 Z= 0.138 Angle : 0.662 18.270 44296 Z= 0.311 Chirality : 0.042 0.219 4785 Planarity : 0.004 0.051 5608 Dihedral : 10.302 127.030 4795 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.16 % Allowed : 20.49 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.30 (0.14), residues: 3880 helix: 1.72 (0.11), residues: 2054 sheet: -0.35 (0.26), residues: 398 loop : 0.07 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGAc 282 TYR 0.022 0.001 TYRAg 78 PHE 0.030 0.001 PHEAd 273 TRP 0.017 0.001 TRPAc 141 HIS 0.006 0.001 HISAe 219 Details of bonding type rmsd covalent geometry : bond 0.00323 (32648) covalent geometry : angle 0.66207 (44282) SS BOND : bond 0.00315 ( 7) SS BOND : angle 1.48539 ( 14) hydrogen bonds : bond 0.03881 ( 1787) hydrogen bonds : angle 4.56648 ( 5124) Misc. bond : bond 0.21597 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 642 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 76 ASP cc_start: 0.8179 (t0) cc_final: 0.7951 (t0) REVERT: AA 94 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8462 (tm-30) REVERT: AA 247 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8021 (tm-30) REVERT: AA 341 PHE cc_start: 0.8784 (t80) cc_final: 0.8542 (t80) REVERT: AA 377 MET cc_start: 0.7735 (mmm) cc_final: 0.7179 (mmm) REVERT: AA 435 GLU cc_start: 0.8639 (pp20) cc_final: 0.8194 (mt-10) REVERT: AA 469 ASN cc_start: 0.8577 (m-40) cc_final: 0.8065 (m110) REVERT: AB 104 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8746 (mt-10) REVERT: AB 126 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8444 (pt) REVERT: AB 155 ARG cc_start: 0.8313 (mtm180) cc_final: 0.8102 (mtt90) REVERT: AC 14 ILE cc_start: 0.7668 (mm) cc_final: 0.7060 (tp) REVERT: AC 42 MET cc_start: 0.7486 (mtt) cc_final: 0.7127 (mtm) REVERT: AC 94 LEU cc_start: 0.8191 (tp) cc_final: 0.7897 (mp) REVERT: AC 113 TRP cc_start: 0.8430 (t-100) cc_final: 0.8161 (t-100) REVERT: AC 138 MET cc_start: 0.8583 (mmt) cc_final: 0.8051 (mmm) REVERT: AC 223 TYR cc_start: 0.9183 (m-80) cc_final: 0.8881 (m-80) REVERT: AC 235 MET cc_start: 0.9112 (tmm) cc_final: 0.8596 (tmm) REVERT: AC 249 MET cc_start: 0.7450 (tpp) cc_final: 0.7056 (tpp) REVERT: AC 344 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7979 (mm-30) REVERT: AC 375 LYS cc_start: 0.7643 (tmtt) cc_final: 0.7090 (ttmt) REVERT: AD 103 SER cc_start: 0.8376 (m) cc_final: 0.7946 (p) REVERT: AD 110 ILE cc_start: 0.8383 (mt) cc_final: 0.8169 (mm) REVERT: AD 115 GLN cc_start: 0.8612 (tp40) cc_final: 0.7786 (tt0) REVERT: AD 143 GLU cc_start: 0.8398 (tp30) cc_final: 0.8185 (pm20) REVERT: AD 166 MET cc_start: 0.5827 (mmm) cc_final: 0.5319 (mmm) REVERT: AD 279 GLU cc_start: 0.8194 (tt0) cc_final: 0.7626 (tt0) REVERT: AD 288 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8265 (mmm) REVERT: AE 115 TYR cc_start: 0.6865 (m-10) cc_final: 0.6238 (m-10) REVERT: AE 165 MET cc_start: 0.5869 (tpt) cc_final: 0.5343 (ptm) REVERT: AE 271 VAL cc_start: 0.7260 (t) cc_final: 0.6880 (m) REVERT: AF 46 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7659 (mm-30) REVERT: AF 86 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8465 (mt-10) REVERT: AF 99 ILE cc_start: 0.9063 (mm) cc_final: 0.8575 (pt) REVERT: AF 106 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8549 (mm-30) REVERT: AG 25 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7669 (mtm180) REVERT: AG 45 ARG cc_start: 0.7132 (mmt90) cc_final: 0.6860 (mmm-85) REVERT: AG 47 LEU cc_start: 0.9085 (mm) cc_final: 0.8506 (tp) REVERT: AG 79 GLU cc_start: 0.4454 (mm-30) cc_final: 0.4164 (mm-30) REVERT: AI 20 ARG cc_start: 0.7638 (mtm180) cc_final: 0.6396 (mtm-85) REVERT: Aa 91 TYR cc_start: 0.8222 (t80) cc_final: 0.7718 (t80) REVERT: Aa 164 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8576 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: Aa 170 ARG cc_start: 0.8309 (ptm-80) cc_final: 0.7820 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: Aa 364 SER cc_start: 0.8943 (m) cc_final: 0.8156 (t) REVERT: Aa 368 MET cc_start: 0.8942 (tpt) cc_final: 0.8554 (tpt) REVERT: Aa 430 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7798 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7671 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8014 (m-30) cc_final: 0.7435 (m-30) REVERT: Ac 89 MET cc_start: 0.8394 (mmm) cc_final: 0.8137 (tpp) REVERT: Ac 137 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6499 (tp-100) REVERT: Ac 221 HIS cc_start: 0.8693 (t70) cc_final: 0.8229 (t-90) REVERT: Ac 269 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8691 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9240 (mt) cc_final: 0.8477 (tt) REVERT: Ac 375 LYS cc_start: 0.7412 (tmtt) cc_final: 0.6464 (mtpt) REVERT: Ad 164 MET cc_start: 0.7097 (ptm) cc_final: 0.6555 (ppp) REVERT: Ad 166 MET cc_start: 0.7998 (mtt) cc_final: 0.7335 (mmt) REVERT: Ad 177 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8786 (ttpt) REVERT: Ad 263 MET cc_start: 0.8555 (ttp) cc_final: 0.8134 (tmm) REVERT: Ad 292 MET cc_start: 0.7938 (tmm) cc_final: 0.7705 (tmm) REVERT: Ad 309 HIS cc_start: 0.7383 (t70) cc_final: 0.6955 (t70) REVERT: Ad 310 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8047 (mmmt) REVERT: Ae 110 ARG cc_start: 0.7861 (mtm110) cc_final: 0.6905 (ptp90) REVERT: Ae 111 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.5940 (mttm) REVERT: Ae 131 ASN cc_start: 0.7569 (t0) cc_final: 0.7204 (t0) REVERT: Ae 134 SER cc_start: 0.7800 (t) cc_final: 0.7393 (p) REVERT: Ae 220 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5518 (mm) REVERT: Af 33 MET cc_start: 0.8414 (mmt) cc_final: 0.8094 (mmm) REVERT: Af 40 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8754 (mt-10) REVERT: Af 46 GLU cc_start: 0.8058 (tp30) cc_final: 0.7656 (tp30) REVERT: Af 74 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8546 (mm-40) REVERT: Af 92 GLU cc_start: 0.8548 (tt0) cc_final: 0.8158 (tm-30) REVERT: Af 97 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7800 (mt-10) REVERT: Af 103 LYS cc_start: 0.8719 (mmmt) cc_final: 0.7998 (mmtm) REVERT: Af 107 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8358 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9126 (tp) cc_final: 0.8838 (tp) REVERT: Ag 60 TYR cc_start: 0.8898 (t80) cc_final: 0.8587 (t80) REVERT: Aj 15 PHE cc_start: 0.7343 (m-10) cc_final: 0.6637 (m-80) REVERT: Aj 53 TRP cc_start: 0.6691 (OUTLIER) cc_final: 0.6089 (m100) REVERT: Ak 38 TRP cc_start: 0.5860 (t60) cc_final: 0.5580 (t60) outliers start: 105 outliers final: 79 residues processed: 707 average time/residue: 0.1820 time to fit residues: 210.8950 Evaluate side-chains 722 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 633 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AB residue 432 VAL Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 189 ASN Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 288 MET Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 82 ASP Chi-restraints excluded: chain AE residue 140 MET Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 32 LEU Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 208 VAL Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 266 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 400 VAL Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 126 ILE Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 257 GLU Chi-restraints excluded: chain Ab residue 303 ASN Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 355 SER Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 111 LYS Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Af residue 74 GLN Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 16 SER Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 57 SER Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 173 optimal weight: 0.0870 chunk 265 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 329 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 118 optimal weight: 0.1980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 153 ASN ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.146038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.109268 restraints weight = 56797.723| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.12 r_work: 0.3344 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.331 32661 Z= 0.178 Angle : 0.815 59.200 44296 Z= 0.427 Chirality : 0.044 0.875 4785 Planarity : 0.005 0.145 5608 Dihedral : 10.313 126.993 4795 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.71 % Rotamer: Outliers : 2.80 % Allowed : 20.94 % Favored : 76.26 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.14), residues: 3880 helix: 1.73 (0.11), residues: 2055 sheet: -0.30 (0.26), residues: 386 loop : 0.06 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGAc 282 TYR 0.020 0.001 TYRAc 224 PHE 0.032 0.001 PHEAj 36 TRP 0.015 0.001 TRPAK 34 HIS 0.007 0.001 HISAe 219 Details of bonding type rmsd covalent geometry : bond 0.00407 (32648) covalent geometry : angle 0.81520 (44282) SS BOND : bond 0.00385 ( 7) SS BOND : angle 1.47302 ( 14) hydrogen bonds : bond 0.03885 ( 1787) hydrogen bonds : angle 4.57015 ( 5124) Misc. bond : bond 0.22597 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 634 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 76 ASP cc_start: 0.8180 (t0) cc_final: 0.7953 (t0) REVERT: AA 94 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8458 (tm-30) REVERT: AA 247 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8033 (tm-30) REVERT: AA 341 PHE cc_start: 0.8774 (t80) cc_final: 0.8567 (t80) REVERT: AA 377 MET cc_start: 0.7731 (mmm) cc_final: 0.7175 (mmm) REVERT: AA 435 GLU cc_start: 0.8647 (pp20) cc_final: 0.8198 (mt-10) REVERT: AA 469 ASN cc_start: 0.8579 (m-40) cc_final: 0.8065 (m110) REVERT: AB 104 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8744 (mt-10) REVERT: AB 126 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8435 (pt) REVERT: AC 14 ILE cc_start: 0.7641 (mm) cc_final: 0.7037 (tp) REVERT: AC 42 MET cc_start: 0.7469 (mtt) cc_final: 0.7104 (mtm) REVERT: AC 94 LEU cc_start: 0.8179 (tp) cc_final: 0.7871 (mp) REVERT: AC 113 TRP cc_start: 0.8423 (t-100) cc_final: 0.8153 (t-100) REVERT: AC 138 MET cc_start: 0.8591 (mmt) cc_final: 0.8055 (mmm) REVERT: AC 223 TYR cc_start: 0.9184 (m-80) cc_final: 0.8881 (m-80) REVERT: AC 235 MET cc_start: 0.9100 (tmm) cc_final: 0.8588 (tmm) REVERT: AC 249 MET cc_start: 0.7461 (tpp) cc_final: 0.7065 (tpp) REVERT: AC 375 LYS cc_start: 0.7636 (tmtt) cc_final: 0.7088 (ttmt) REVERT: AD 90 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7636 (m90) REVERT: AD 103 SER cc_start: 0.8368 (m) cc_final: 0.7940 (p) REVERT: AD 110 ILE cc_start: 0.8391 (mt) cc_final: 0.8177 (mm) REVERT: AD 115 GLN cc_start: 0.8617 (tp40) cc_final: 0.7789 (tt0) REVERT: AD 143 GLU cc_start: 0.8404 (tp30) cc_final: 0.8190 (pm20) REVERT: AD 166 MET cc_start: 0.5724 (mmm) cc_final: 0.5259 (mmm) REVERT: AD 279 GLU cc_start: 0.8189 (tt0) cc_final: 0.7626 (tt0) REVERT: AD 288 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8270 (mmm) REVERT: AE 115 TYR cc_start: 0.6879 (m-10) cc_final: 0.6245 (m-10) REVERT: AE 165 MET cc_start: 0.5845 (tpt) cc_final: 0.5319 (ptm) REVERT: AE 271 VAL cc_start: 0.7261 (t) cc_final: 0.6886 (m) REVERT: AF 46 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7648 (mm-30) REVERT: AF 86 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8460 (mt-10) REVERT: AF 99 ILE cc_start: 0.9060 (mm) cc_final: 0.8570 (pt) REVERT: AF 106 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8544 (mm-30) REVERT: AG 25 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7659 (mtm180) REVERT: AG 45 ARG cc_start: 0.7126 (mmt90) cc_final: 0.6847 (mmm-85) REVERT: AG 47 LEU cc_start: 0.9087 (mm) cc_final: 0.8457 (tp) REVERT: AI 20 ARG cc_start: 0.7622 (mtm180) cc_final: 0.6384 (mtm-85) REVERT: Aa 91 TYR cc_start: 0.8208 (t80) cc_final: 0.7705 (t80) REVERT: Aa 164 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8586 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: Aa 170 ARG cc_start: 0.8295 (ptm-80) cc_final: 0.7810 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: Aa 364 SER cc_start: 0.8921 (m) cc_final: 0.8152 (t) REVERT: Aa 368 MET cc_start: 0.8869 (tpt) cc_final: 0.8556 (tpt) REVERT: Aa 430 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7668 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8014 (m-30) cc_final: 0.7436 (m-30) REVERT: Ac 89 MET cc_start: 0.8392 (mmm) cc_final: 0.8113 (tpp) REVERT: Ac 137 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6503 (tp-100) REVERT: Ac 221 HIS cc_start: 0.8690 (t70) cc_final: 0.8226 (t-90) REVERT: Ac 269 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8693 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9239 (mt) cc_final: 0.8477 (tt) REVERT: Ac 375 LYS cc_start: 0.7416 (tmtt) cc_final: 0.6471 (mtpt) REVERT: Ad 164 MET cc_start: 0.7092 (ptm) cc_final: 0.6552 (ppp) REVERT: Ad 166 MET cc_start: 0.8009 (mtt) cc_final: 0.7342 (mmt) REVERT: Ad 177 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8786 (ttpt) REVERT: Ad 263 MET cc_start: 0.8555 (ttp) cc_final: 0.8127 (tmm) REVERT: Ad 292 MET cc_start: 0.7914 (tmm) cc_final: 0.7682 (tmm) REVERT: Ad 309 HIS cc_start: 0.7373 (t70) cc_final: 0.6945 (t70) REVERT: Ad 310 LYS cc_start: 0.8244 (mmtt) cc_final: 0.8036 (mmmt) REVERT: Ae 110 ARG cc_start: 0.7860 (mtm110) cc_final: 0.6966 (ptp90) REVERT: Ae 111 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5940 (mttm) REVERT: Ae 130 LYS cc_start: 0.6789 (ttpt) cc_final: 0.6549 (ptmt) REVERT: Ae 131 ASN cc_start: 0.7552 (t0) cc_final: 0.7269 (t0) REVERT: Ae 134 SER cc_start: 0.7772 (t) cc_final: 0.7382 (p) REVERT: Ae 163 LYS cc_start: 0.3496 (tptp) cc_final: 0.3136 (mmtt) REVERT: Af 33 MET cc_start: 0.8400 (mmt) cc_final: 0.8078 (mmm) REVERT: Af 40 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8768 (mt-10) REVERT: Af 46 GLU cc_start: 0.8051 (tp30) cc_final: 0.7645 (tp30) REVERT: Af 92 GLU cc_start: 0.8545 (tt0) cc_final: 0.8148 (tm-30) REVERT: Af 97 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7786 (mt-10) REVERT: Af 103 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8070 (mmtm) REVERT: Af 107 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8365 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9120 (tp) cc_final: 0.8829 (tp) REVERT: Ag 60 TYR cc_start: 0.8908 (t80) cc_final: 0.8603 (t80) REVERT: Aj 15 PHE cc_start: 0.7348 (m-10) cc_final: 0.6668 (m-80) REVERT: Aj 53 TRP cc_start: 0.6686 (OUTLIER) cc_final: 0.6075 (m100) outliers start: 93 outliers final: 79 residues processed: 696 average time/residue: 0.1950 time to fit residues: 223.3000 Evaluate side-chains 708 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 620 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 153 ASN Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 445 CYS Chi-restraints excluded: chain AB residue 51 SER Chi-restraints excluded: chain AB residue 95 SER Chi-restraints excluded: chain AB residue 126 ILE Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AB residue 432 VAL Chi-restraints excluded: chain AC residue 150 LEU Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 189 ILE Chi-restraints excluded: chain AC residue 229 ILE Chi-restraints excluded: chain AC residue 267 HIS Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AD residue 90 HIS Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 288 MET Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 82 ASP Chi-restraints excluded: chain AE residue 140 MET Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 56 VAL Chi-restraints excluded: chain AG residue 78 TYR Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 32 LEU Chi-restraints excluded: chain Aa residue 47 GLU Chi-restraints excluded: chain Aa residue 48 THR Chi-restraints excluded: chain Aa residue 50 VAL Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 166 ASP Chi-restraints excluded: chain Aa residue 174 GLU Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 208 VAL Chi-restraints excluded: chain Aa residue 214 THR Chi-restraints excluded: chain Aa residue 216 LEU Chi-restraints excluded: chain Aa residue 266 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 400 VAL Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 124 GLU Chi-restraints excluded: chain Ab residue 126 ILE Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 257 GLU Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ac residue 355 SER Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 111 LYS Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ae residue 230 ASP Chi-restraints excluded: chain Ag residue 14 VAL Chi-restraints excluded: chain Ag residue 16 SER Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 57 SER Chi-restraints excluded: chain Ah residue 73 LEU Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 302 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 366 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 315 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 153 ASN ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 303 ASN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN ** Af 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.146210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109850 restraints weight = 56789.200| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.21 r_work: 0.3337 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.331 32661 Z= 0.197 Angle : 0.839 59.194 44296 Z= 0.448 Chirality : 0.046 1.182 4785 Planarity : 0.005 0.160 5608 Dihedral : 10.306 126.947 4795 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.71 % Rotamer: Outliers : 2.89 % Allowed : 20.97 % Favored : 76.14 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.06 % 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: 1.31 (0.14), residues: 3880 helix: 1.72 (0.11), residues: 2055 sheet: -0.30 (0.26), residues: 386 loop : 0.06 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGAc 282 TYR 0.019 0.001 TYRAc 224 PHE 0.023 0.001 PHEAj 36 TRP 0.014 0.001 TRPAK 34 HIS 0.011 0.001 HISAe 219 Details of bonding type rmsd covalent geometry : bond 0.00446 (32648) covalent geometry : angle 0.83837 (44282) SS BOND : bond 0.00362 ( 7) SS BOND : angle 1.47089 ( 14) hydrogen bonds : bond 0.03903 ( 1787) hydrogen bonds : angle 4.57346 ( 5124) Misc. bond : bond 0.22557 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8519.15 seconds wall clock time: 146 minutes 41.89 seconds (8801.89 seconds total)