Starting phenix.real_space_refine on Thu May 29 09:47:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ib7_35334/05_2025/8ib7_35334_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ib7_35334/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ib7_35334/05_2025/8ib7_35334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ib7_35334/05_2025/8ib7_35334.map" model { file = "/net/cci-nas-00/data/ceres_data/8ib7_35334/05_2025/8ib7_35334_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ib7_35334/05_2025/8ib7_35334_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'UQ6:plan-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-5': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 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: {'UQ6:plan-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-5': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 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: 20.22, per 1000 atoms: 0.63 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: 9.96 Conformation dependent library (CDL) restraints added in 4.4 seconds 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: 3.70 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: 11.92 Time building geometry restraints manager: 11.12 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 324 or resid 401 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: 2.910 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: 1.270 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 74.730 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.210 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.150 ------------------------------------------------------------------------------- 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 : 29.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (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 TRP 0.025 0.002 TRPAC 141 HIS 0.009 0.001 HISAC 196 PHE 0.049 0.002 PHEAC 183 TYR 0.049 0.002 TYRAe 235 ARG 0.007 0.001 ARGAE 250 Details of bonding type rmsd hydrogen bonds : bond 0.18930 ( 1787) hydrogen bonds : angle 7.73515 ( 5124) SS BOND : bond 0.01529 ( 7) SS BOND : angle 2.83120 ( 14) covalent geometry : bond 0.01020 (32648) covalent geometry : angle 1.26119 (44282) 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 : 3.386 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: 0.7229 (mp) REVERT: AC 299 LEU cc_start: 0.8593 (mt) cc_final: 0.7796 (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: 0.6039 (p90) REVERT: AD 170 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7624 (mtmm) REVERT: AD 255 TYR cc_start: 0.5740 (m-80) cc_final: 0.5223 (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: 0.7218 (mm-30) REVERT: AI 18 THR cc_start: 0.8702 (m) cc_final: 0.8365 (p) REVERT: AI 20 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7195 (mtm-85) REVERT: Aa 364 SER cc_start: 0.8740 (m) cc_final: 0.8368 (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: 0.8081 (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: 0.8331 (p) REVERT: Ac 203 THR cc_start: 0.8492 (t) cc_final: 0.8219 (p) REVERT: Ac 269 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8703 (mtmm) REVERT: Ac 313 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8397 (ttt180) REVERT: Ad 141 THR cc_start: 0.7390 (p) cc_final: 0.7098 (p) REVERT: Ad 166 MET cc_start: 0.8331 (mtt) cc_final: 0.7585 (mmt) REVERT: Ag 60 TYR cc_start: 0.8961 (t80) cc_final: 0.8663 (t80) REVERT: Ag 66 GLU cc_start: 0.8616 (tp30) cc_final: 0.8315 (tp30) REVERT: Ak 38 TRP cc_start: 0.6510 (t60) cc_final: 0.6273 (t60) outliers start: 6 outliers final: 2 residues processed: 1215 average time/residue: 0.4937 time to fit residues: 925.6641 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 : 3.462 ------------------------------------------------------------------------------- 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 323 optimal weight: 0.7980 chunk 290 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 300 optimal weight: 20.0000 chunk 116 optimal weight: 0.9980 chunk 182 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 347 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** AA 452 GLN ** AA 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 139 ASN AB 304 ASN AC 308 HIS AD 119 GLN 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 284 ASN Ab 290 GLN ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 312 GLN Ad 90 HIS 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.152891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.116273 restraints weight = 55685.878| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.99 r_work: 0.3504 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.466 32661 Z= 0.165 Angle : 0.718 17.888 44296 Z= 0.354 Chirality : 0.044 0.242 4785 Planarity : 0.005 0.048 5608 Dihedral : 11.653 164.930 4800 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.98 % Allowed : 12.50 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.13), residues: 3880 helix: 0.80 (0.11), residues: 2065 sheet: -0.21 (0.28), residues: 376 loop : -0.42 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPAC 165 HIS 0.009 0.001 HISAD 98 PHE 0.025 0.002 PHEAD 273 TYR 0.035 0.002 TYRAD 236 ARG 0.009 0.001 ARGAf 100 Details of bonding type rmsd hydrogen bonds : bond 0.05130 ( 1787) hydrogen bonds : angle 5.21713 ( 5124) SS BOND : bond 0.00542 ( 7) SS BOND : angle 5.05305 ( 14) covalent geometry : bond 0.00368 (32648) covalent geometry : angle 0.71260 (44282) Misc. bond : bond 0.32492 ( 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 928 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 829 time to evaluate : 3.841 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: AA 164 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7913 (mm-30) REVERT: AA 179 MET cc_start: 0.7309 (mtm) cc_final: 0.7051 (mtm) REVERT: AA 247 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7922 (tm-30) REVERT: AA 368 MET cc_start: 0.8968 (tpt) cc_final: 0.8709 (tpt) REVERT: AA 412 ASP cc_start: 0.8291 (t0) cc_final: 0.8057 (t70) REVERT: AA 469 ASN cc_start: 0.8619 (m-40) cc_final: 0.8247 (m110) REVERT: AB 37 ASP cc_start: 0.8383 (t0) cc_final: 0.8069 (p0) REVERT: AB 215 SER cc_start: 0.8854 (m) cc_final: 0.8628 (t) REVERT: AC 94 LEU cc_start: 0.8403 (tp) cc_final: 0.8131 (mp) REVERT: AC 129 MET cc_start: 0.7276 (ptp) cc_final: 0.6833 (ptp) REVERT: AC 138 MET cc_start: 0.8354 (mmt) cc_final: 0.7867 (mmm) REVERT: AC 226 ILE cc_start: 0.8709 (tp) cc_final: 0.8506 (tt) REVERT: AC 240 MET cc_start: 0.9408 (mmm) cc_final: 0.9201 (mmm) REVERT: AC 249 MET cc_start: 0.5741 (tpp) cc_final: 0.5470 (tpp) REVERT: AC 269 LYS cc_start: 0.8609 (ttmm) cc_final: 0.8323 (ttmm) REVERT: AC 322 GLN cc_start: 0.7751 (mt0) cc_final: 0.7512 (mt0) REVERT: AC 375 LYS cc_start: 0.7588 (tmtt) cc_final: 0.7155 (ttmt) REVERT: AD 118 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8069 (mmtt) REVERT: AD 249 TYR cc_start: 0.7131 (p90) cc_final: 0.6777 (p90) REVERT: AD 279 GLU cc_start: 0.8103 (tt0) cc_final: 0.7348 (tt0) REVERT: AD 318 LYS cc_start: 0.8124 (mptt) cc_final: 0.7573 (mttt) REVERT: AE 146 VAL cc_start: 0.6670 (OUTLIER) cc_final: 0.6267 (p) REVERT: AE 165 MET cc_start: 0.4857 (tpt) cc_final: 0.4652 (ptm) REVERT: AF 22 TYR cc_start: 0.8896 (t80) cc_final: 0.8531 (t80) REVERT: AF 29 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8437 (ttmm) REVERT: AF 33 MET cc_start: 0.8396 (mmt) cc_final: 0.8179 (mmt) REVERT: AF 46 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7569 (mm-30) REVERT: AF 99 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8654 (pt) REVERT: AG 8 LEU cc_start: 0.8771 (mt) cc_final: 0.8371 (mt) REVERT: AG 25 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7830 (mtm180) REVERT: AG 65 GLN cc_start: 0.8263 (pp30) cc_final: 0.7969 (pp30) REVERT: AG 74 ASN cc_start: 0.8063 (t0) cc_final: 0.7835 (t0) REVERT: AG 77 MET cc_start: 0.7752 (mmm) cc_final: 0.7513 (mmm) REVERT: AG 79 GLU cc_start: 0.4804 (tp30) cc_final: 0.4367 (mp0) REVERT: AH 33 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8315 (pp20) REVERT: AH 70 PHE cc_start: 0.8554 (m-10) cc_final: 0.8337 (m-10) REVERT: AI 20 ARG cc_start: 0.7424 (mtm180) cc_final: 0.6581 (mtm-85) REVERT: AJ 32 PHE cc_start: 0.8015 (t80) cc_final: 0.7716 (t80) REVERT: Aa 70 THR cc_start: 0.8564 (m) cc_final: 0.7867 (p) REVERT: Aa 87 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8484 (t0) REVERT: Aa 99 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7877 (mttp) REVERT: Aa 131 TYR cc_start: 0.8959 (m-80) cc_final: 0.8654 (m-80) REVERT: Aa 166 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: Aa 179 MET cc_start: 0.6271 (mtm) cc_final: 0.5909 (mtm) REVERT: Aa 342 GLN cc_start: 0.8314 (mp10) cc_final: 0.8111 (mp10) REVERT: Aa 363 MET cc_start: 0.8937 (mmm) cc_final: 0.8588 (mmm) REVERT: Aa 364 SER cc_start: 0.9041 (m) cc_final: 0.8200 (t) REVERT: Aa 368 MET cc_start: 0.9008 (tpt) cc_final: 0.8556 (tpt) REVERT: Ab 82 LEU cc_start: 0.8968 (tp) cc_final: 0.8640 (tp) REVERT: Ab 124 GLU cc_start: 0.8825 (pp20) cc_final: 0.8247 (pp20) REVERT: Ab 148 ARG cc_start: 0.7049 (ptm-80) cc_final: 0.6760 (ptt90) REVERT: Ab 179 ASP cc_start: 0.8972 (t70) cc_final: 0.8695 (t0) REVERT: Ab 231 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8633 (mttm) REVERT: Ab 260 GLU cc_start: 0.8198 (pt0) cc_final: 0.7953 (pt0) REVERT: Ab 309 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7798 (mm) REVERT: Ac 162 GLU cc_start: 0.6701 (mp0) cc_final: 0.6340 (mp0) REVERT: Ac 221 HIS cc_start: 0.8320 (t70) cc_final: 0.7738 (t70) REVERT: Ac 269 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8777 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9147 (mt) cc_final: 0.8607 (tt) REVERT: Ac 356 ILE cc_start: 0.8818 (mm) cc_final: 0.8593 (tp) REVERT: Ac 368 ILE cc_start: 0.8941 (mt) cc_final: 0.8720 (mm) REVERT: Ac 375 LYS cc_start: 0.7369 (tmtt) cc_final: 0.7067 (mttt) REVERT: Ad 166 MET cc_start: 0.7915 (mtt) cc_final: 0.7107 (mmt) REVERT: Ad 210 TYR cc_start: 0.8540 (t80) cc_final: 0.8153 (t80) REVERT: Ad 284 HIS cc_start: 0.7716 (t70) cc_final: 0.7511 (t-90) REVERT: Af 33 MET cc_start: 0.8240 (mmt) cc_final: 0.7999 (mmm) REVERT: Af 46 GLU cc_start: 0.8480 (tp30) cc_final: 0.8201 (tp30) REVERT: Af 80 GLN cc_start: 0.8526 (mt0) cc_final: 0.8229 (mt0) REVERT: Af 84 TYR cc_start: 0.7815 (t80) cc_final: 0.7514 (t80) REVERT: Af 92 GLU cc_start: 0.8636 (tt0) cc_final: 0.8324 (tm-30) REVERT: Af 97 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7929 (mt-10) REVERT: Af 103 LYS cc_start: 0.8652 (mmmt) cc_final: 0.7809 (mmtm) REVERT: Af 106 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7835 (mt-10) REVERT: Ag 22 PHE cc_start: 0.8492 (m-80) cc_final: 0.8186 (m-80) REVERT: Ag 47 LEU cc_start: 0.9128 (tp) cc_final: 0.8919 (tp) REVERT: Ag 60 TYR cc_start: 0.8960 (t80) cc_final: 0.8602 (t80) REVERT: Ag 77 MET cc_start: 0.8224 (ttm) cc_final: 0.7771 (mtt) REVERT: Ah 89 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7578 (pttm) REVERT: Aj 15 PHE cc_start: 0.7436 (m-10) cc_final: 0.7167 (m-80) REVERT: Ak 38 TRP cc_start: 0.6162 (t60) cc_final: 0.5872 (t60) outliers start: 99 outliers final: 48 residues processed: 884 average time/residue: 0.4269 time to fit residues: 597.3976 Evaluate side-chains 716 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 662 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 201 VAL Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 379 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 69 SER 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 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 AD residue 259 THR 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 48 ILE 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 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 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 Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE 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 89 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 366 optimal weight: 0.6980 chunk 289 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 312 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** AA 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 75 ASN AB 139 ASN AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 219 HIS AJ 46 HIS Aa 87 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 280 ASN Ab 298 HIS Ad 205 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 = 0.4111 r_free = 0.4111 target = 0.151653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115139 restraints weight = 56240.772| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.96 r_work: 0.3475 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.417 32661 Z= 0.148 Angle : 0.644 16.173 44296 Z= 0.313 Chirality : 0.042 0.206 4785 Planarity : 0.004 0.041 5608 Dihedral : 11.100 150.413 4796 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.31 % Allowed : 15.85 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3880 helix: 1.25 (0.11), residues: 2066 sheet: -0.05 (0.28), residues: 372 loop : -0.21 (0.17), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAD 276 HIS 0.007 0.001 HISAd 205 PHE 0.029 0.002 PHEAD 273 TYR 0.030 0.002 TYRAg 78 ARG 0.008 0.001 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 1787) hydrogen bonds : angle 4.87334 ( 5124) SS BOND : bond 0.00323 ( 7) SS BOND : angle 0.75009 ( 14) covalent geometry : bond 0.00338 (32648) covalent geometry : angle 0.64387 (44282) Misc. bond : bond 0.30758 ( 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 819 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 709 time to evaluate : 3.679 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 164 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7976 (mm-30) REVERT: AA 179 MET cc_start: 0.7405 (mtm) cc_final: 0.7128 (mtm) REVERT: AA 247 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7963 (tm-30) REVERT: AA 411 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6884 (tm-30) REVERT: AA 463 GLU cc_start: 0.7916 (tt0) cc_final: 0.7700 (tt0) REVERT: AA 469 ASN cc_start: 0.8558 (m-40) cc_final: 0.8177 (m110) REVERT: AB 37 ASP cc_start: 0.8376 (t0) cc_final: 0.7923 (p0) REVERT: AB 75 ASN cc_start: 0.8942 (t0) cc_final: 0.8510 (p0) REVERT: AB 318 HIS cc_start: 0.7390 (t-90) cc_final: 0.7185 (t-90) REVERT: AC 89 MET cc_start: 0.8554 (tpp) cc_final: 0.8212 (tpp) REVERT: AC 129 MET cc_start: 0.7253 (ptp) cc_final: 0.6841 (ptp) REVERT: AC 138 MET cc_start: 0.8474 (mmt) cc_final: 0.7905 (mmm) REVERT: AC 235 MET cc_start: 0.9051 (tmm) cc_final: 0.8807 (tmm) REVERT: AC 240 MET cc_start: 0.9415 (mmm) cc_final: 0.9101 (mmm) REVERT: AC 249 MET cc_start: 0.6041 (tpp) cc_final: 0.5655 (tpp) REVERT: AC 257 MET cc_start: 0.7691 (ptp) cc_final: 0.7100 (ptp) REVERT: AC 269 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8236 (ttmm) REVERT: AC 375 LYS cc_start: 0.7551 (tmtt) cc_final: 0.6998 (ttmt) REVERT: AD 166 MET cc_start: 0.7048 (mpp) cc_final: 0.6545 (mmm) REVERT: AD 196 ASP cc_start: 0.8096 (p0) cc_final: 0.7803 (p0) REVERT: AD 279 GLU cc_start: 0.8260 (tt0) cc_final: 0.7624 (tt0) REVERT: AF 29 LYS cc_start: 0.8906 (mttt) cc_final: 0.8494 (ttmm) REVERT: AF 46 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7606 (mm-30) REVERT: AF 86 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8295 (mt-10) REVERT: AF 99 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8644 (pt) REVERT: AG 8 LEU cc_start: 0.8899 (mt) cc_final: 0.8674 (mt) REVERT: AG 47 LEU cc_start: 0.9045 (mm) cc_final: 0.8470 (tp) REVERT: AG 74 ASN cc_start: 0.8111 (t0) cc_final: 0.7889 (t0) REVERT: AG 77 MET cc_start: 0.7664 (mmm) cc_final: 0.7360 (mmm) REVERT: AH 33 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (pp20) REVERT: AI 20 ARG cc_start: 0.7526 (mtm180) cc_final: 0.6688 (mtm-85) REVERT: Aa 87 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8493 (t0) REVERT: Aa 131 TYR cc_start: 0.8945 (m-80) cc_final: 0.8605 (m-80) REVERT: Aa 174 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: Aa 179 MET cc_start: 0.6439 (mtm) cc_final: 0.6066 (mtm) REVERT: Aa 222 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7090 (ttp-110) REVERT: Aa 363 MET cc_start: 0.8936 (mmm) cc_final: 0.8736 (mmm) REVERT: Aa 364 SER cc_start: 0.9043 (m) cc_final: 0.8241 (t) REVERT: Aa 368 MET cc_start: 0.8997 (tpt) cc_final: 0.8575 (tpt) REVERT: Ab 82 LEU cc_start: 0.8946 (tp) cc_final: 0.8698 (tp) REVERT: Ab 109 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8503 (mtmt) REVERT: Ab 148 ARG cc_start: 0.6980 (ptm-80) cc_final: 0.6709 (ptt90) REVERT: Ab 179 ASP cc_start: 0.9031 (t70) cc_final: 0.8768 (t0) REVERT: Ab 204 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7586 (mm-30) REVERT: Ab 231 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8676 (mtpp) REVERT: Ab 382 TYR cc_start: 0.8268 (t80) cc_final: 0.8017 (t80) REVERT: Ac 49 LEU cc_start: 0.8420 (tp) cc_final: 0.8177 (tp) REVERT: Ac 171 ASP cc_start: 0.7383 (p0) cc_final: 0.7096 (t70) REVERT: Ac 221 HIS cc_start: 0.8452 (t70) cc_final: 0.8059 (t70) REVERT: Ac 269 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8734 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9170 (mt) cc_final: 0.8511 (tt) REVERT: Ac 356 ILE cc_start: 0.8784 (mm) cc_final: 0.8558 (tp) REVERT: Ac 375 LYS cc_start: 0.7339 (tmtt) cc_final: 0.6935 (mttt) REVERT: Ad 164 MET cc_start: 0.6765 (ptm) cc_final: 0.6034 (ppp) REVERT: Ad 166 MET cc_start: 0.8056 (mtt) cc_final: 0.7105 (mmt) REVERT: Ad 284 HIS cc_start: 0.7666 (t-90) cc_final: 0.7380 (t-90) REVERT: Ad 310 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7666 (mmtm) REVERT: Ae 122 THR cc_start: 0.8460 (m) cc_final: 0.8198 (p) REVERT: Ae 130 LYS cc_start: 0.7530 (ttpt) cc_final: 0.7267 (ptmt) REVERT: Ae 163 LYS cc_start: 0.3739 (tptp) cc_final: 0.3110 (mmtt) REVERT: Af 33 MET cc_start: 0.8313 (mmt) cc_final: 0.8058 (mmm) REVERT: Af 46 GLU cc_start: 0.8330 (tp30) cc_final: 0.8100 (tp30) REVERT: Af 80 GLN cc_start: 0.8656 (mt0) cc_final: 0.8376 (mt0) REVERT: Af 84 TYR cc_start: 0.8092 (t80) cc_final: 0.7740 (t80) REVERT: Af 92 GLU cc_start: 0.8635 (tt0) cc_final: 0.8314 (tm-30) REVERT: Af 97 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7895 (mt-10) REVERT: Af 103 LYS cc_start: 0.8672 (mmmt) cc_final: 0.7470 (mmtm) REVERT: Af 106 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7573 (mt-10) REVERT: Ag 47 LEU cc_start: 0.9135 (tp) cc_final: 0.8891 (tp) REVERT: Ag 60 TYR cc_start: 0.8938 (t80) cc_final: 0.8587 (t80) REVERT: Ag 77 MET cc_start: 0.8591 (ttm) cc_final: 0.8079 (mtt) REVERT: Ag 78 TYR cc_start: 0.6496 (m-80) cc_final: 0.6125 (m-80) REVERT: Ah 49 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8138 (mm-30) REVERT: Ah 89 LYS cc_start: 0.7684 (mtmt) cc_final: 0.7430 (pttm) REVERT: Aj 15 PHE cc_start: 0.7499 (m-10) cc_final: 0.7070 (m-80) REVERT: Aj 53 TRP cc_start: 0.6897 (OUTLIER) cc_final: 0.6129 (m100) outliers start: 110 outliers final: 61 residues processed: 774 average time/residue: 0.4281 time to fit residues: 534.8298 Evaluate side-chains 705 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 639 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 93 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 354 LEU 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 128 SER Chi-restraints excluded: chain AB residue 132 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 278 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 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 189 ASN 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 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 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 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 174 GLU Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Ab residue 65 VAL 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 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 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 191 GLU Chi-restraints excluded: chain Ae residue 242 HIS 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 Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 372 optimal weight: 3.9990 chunk 362 optimal weight: 6.9990 chunk 344 optimal weight: 20.0000 chunk 202 optimal weight: 0.1980 chunk 169 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 15 optimal weight: 0.0470 chunk 147 optimal weight: 8.9990 chunk 379 optimal weight: 9.9990 overall best weight: 2.8484 ------------------------------------------------------------------------------- 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 249 HIS AA 452 GLN AB 139 ASN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 242 HIS AJ 46 HIS AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 290 GLN Ab 291 HIS Ac 44 GLN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 282 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119358 restraints weight = 57389.321| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.95 r_work: 0.3429 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.659 32661 Z= 0.280 Angle : 0.753 17.354 44296 Z= 0.365 Chirality : 0.046 0.223 4785 Planarity : 0.005 0.042 5608 Dihedral : 11.150 136.199 4796 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.07 % Allowed : 16.27 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 3880 helix: 1.21 (0.11), residues: 2052 sheet: -0.38 (0.27), residues: 370 loop : -0.22 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPAj 53 HIS 0.012 0.002 HISAc 196 PHE 0.028 0.002 PHEAj 32 TYR 0.022 0.002 TYRAg 78 ARG 0.009 0.001 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 1787) hydrogen bonds : angle 4.98892 ( 5124) SS BOND : bond 0.00363 ( 7) SS BOND : angle 1.56659 ( 14) covalent geometry : bond 0.00651 (32648) covalent geometry : angle 0.75258 (44282) Misc. bond : bond 0.44537 ( 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 813 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 678 time to evaluate : 3.687 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: 0.9144 (mm) cc_final: 0.8899 (mm) REVERT: AA 164 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7805 (mt-10) REVERT: AA 247 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8034 (tm-30) REVERT: AA 368 MET cc_start: 0.8875 (tpt) cc_final: 0.8590 (tpt) REVERT: AA 469 ASN cc_start: 0.8673 (m-40) cc_final: 0.8335 (m110) REVERT: AB 37 ASP cc_start: 0.8346 (t0) cc_final: 0.7930 (p0) REVERT: AB 241 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6206 (ttp-110) REVERT: AC 15 ASN cc_start: 0.7215 (t0) cc_final: 0.6774 (t0) REVERT: AC 20 ASP cc_start: 0.8447 (m-30) cc_final: 0.8244 (m-30) REVERT: AC 89 MET cc_start: 0.8683 (tpp) cc_final: 0.8431 (tpp) REVERT: AC 129 MET cc_start: 0.7552 (ptp) cc_final: 0.7210 (ptp) REVERT: AC 138 MET cc_start: 0.8442 (mmt) cc_final: 0.8100 (mmm) REVERT: AC 235 MET cc_start: 0.9001 (tmm) cc_final: 0.8649 (tmm) REVERT: AC 249 MET cc_start: 0.6924 (tpp) cc_final: 0.6533 (tpp) REVERT: AC 257 MET cc_start: 0.7840 (ptp) cc_final: 0.7382 (ptp) REVERT: AC 269 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8261 (ttmm) REVERT: AC 375 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7151 (ttmt) REVERT: AD 103 SER cc_start: 0.8362 (m) cc_final: 0.8012 (p) REVERT: AD 279 GLU cc_start: 0.8233 (tt0) cc_final: 0.7641 (tt0) REVERT: AD 296 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8071 (mmp) REVERT: AE 115 TYR cc_start: 0.7321 (m-10) cc_final: 0.6774 (m-10) REVERT: AF 46 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7755 (mm-30) REVERT: AF 74 GLN cc_start: 0.8535 (mt0) cc_final: 0.8255 (mt0) REVERT: AF 86 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8365 (mt-10) REVERT: AF 99 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8691 (pt) REVERT: AG 25 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7356 (mtm180) REVERT: AG 47 LEU cc_start: 0.9072 (mm) cc_final: 0.8545 (tp) REVERT: AG 64 ASN cc_start: 0.8533 (t0) cc_final: 0.8180 (m-40) REVERT: AG 72 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7577 (mmm160) REVERT: AG 77 MET cc_start: 0.7683 (mmm) cc_final: 0.7390 (mmm) REVERT: AH 33 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: AI 20 ARG cc_start: 0.7731 (mtm180) cc_final: 0.6718 (mtm-85) REVERT: Aa 153 ASN cc_start: 0.8015 (m-40) cc_final: 0.7360 (t0) REVERT: Aa 170 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.7875 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: Aa 220 LEU cc_start: 0.8891 (mt) cc_final: 0.8536 (mt) REVERT: Aa 364 SER cc_start: 0.9039 (m) cc_final: 0.8310 (t) REVERT: Aa 368 MET cc_start: 0.9026 (tpt) cc_final: 0.8503 (tpt) REVERT: Aa 475 MET cc_start: 0.8876 (tpt) cc_final: 0.8292 (tpt) REVERT: Ab 124 GLU cc_start: 0.8816 (pp20) cc_final: 0.8562 (pp20) REVERT: Ab 128 SER cc_start: 0.8289 (m) cc_final: 0.7579 (t) REVERT: Ab 204 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7703 (mm-30) REVERT: Ab 407 MET cc_start: 0.8387 (mmt) cc_final: 0.8027 (tpt) REVERT: Ab 437 SER cc_start: 0.9080 (m) cc_final: 0.8723 (p) REVERT: Ac 20 ASP cc_start: 0.8141 (m-30) cc_final: 0.7550 (m-30) REVERT: Ac 269 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8894 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9255 (mt) cc_final: 0.8470 (tt) REVERT: Ac 356 ILE cc_start: 0.8868 (mm) cc_final: 0.8644 (tp) REVERT: Ac 375 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7221 (mttt) REVERT: Ad 166 MET cc_start: 0.8359 (mtt) cc_final: 0.7481 (mmt) REVERT: Ad 310 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8087 (mmtm) REVERT: Af 33 MET cc_start: 0.8589 (mmt) cc_final: 0.8376 (mmm) REVERT: Af 40 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8649 (mt-10) REVERT: Af 46 GLU cc_start: 0.8378 (tp30) cc_final: 0.8066 (tp30) REVERT: Af 86 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7992 (tm-30) REVERT: Af 92 GLU cc_start: 0.8636 (tt0) cc_final: 0.8379 (tm-30) REVERT: Af 97 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7908 (mt-10) REVERT: Af 103 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8015 (mmtm) REVERT: Ag 47 LEU cc_start: 0.9316 (tp) cc_final: 0.9062 (tp) REVERT: Ag 60 TYR cc_start: 0.9049 (t80) cc_final: 0.8459 (t80) REVERT: Ag 68 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8302 (mm-30) REVERT: Ag 77 MET cc_start: 0.8482 (ttm) cc_final: 0.8085 (mtt) REVERT: Ag 78 TYR cc_start: 0.6463 (m-80) cc_final: 0.6121 (m-80) REVERT: Ah 49 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7881 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7888 (m-10) cc_final: 0.7485 (m-80) REVERT: Aj 44 TYR cc_start: 0.8786 (t80) cc_final: 0.8519 (t80) REVERT: Aj 53 TRP cc_start: 0.7165 (OUTLIER) cc_final: 0.6373 (m100) outliers start: 135 outliers final: 92 residues processed: 763 average time/residue: 0.4368 time to fit residues: 529.2812 Evaluate side-chains 714 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 616 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 63 GLN Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 202 GLU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 69 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 139 ASN Chi-restraints excluded: chain AB residue 192 CYS Chi-restraints excluded: chain AB residue 233 VAL 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 149 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 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 AC residue 357 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 293 LEU Chi-restraints excluded: chain AD residue 296 MET Chi-restraints excluded: chain AE residue 117 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 55 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 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 79 SER Chi-restraints excluded: chain Aa residue 114 GLU 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 462 ILE Chi-restraints excluded: chain Ab residue 65 VAL Chi-restraints excluded: chain Ab residue 92 LYS 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 Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 194 ILE Chi-restraints excluded: chain Ac residue 198 LEU 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 128 ASP Chi-restraints excluded: chain Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 253 LEU Chi-restraints excluded: chain Ae residue 82 ASP 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 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 42 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 216 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 336 optimal weight: 0.8980 chunk 311 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 331 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** AC 137 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 181 ASN ** Ab 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 242 HIS Ah 37 GLN 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 = 0.148194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110837 restraints weight = 56078.046| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.93 r_work: 0.3412 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.453 32661 Z= 0.146 Angle : 0.652 17.056 44296 Z= 0.310 Chirality : 0.043 0.389 4785 Planarity : 0.004 0.041 5608 Dihedral : 10.777 133.959 4796 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.01 % Allowed : 18.68 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3880 helix: 1.45 (0.11), residues: 2057 sheet: -0.23 (0.28), residues: 362 loop : -0.13 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPAK 34 HIS 0.006 0.001 HISAe 239 PHE 0.030 0.001 PHEAj 32 TYR 0.030 0.001 TYRAD 236 ARG 0.009 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1787) hydrogen bonds : angle 4.72776 ( 5124) SS BOND : bond 0.00083 ( 7) SS BOND : angle 0.80933 ( 14) covalent geometry : bond 0.00338 (32648) covalent geometry : angle 0.65235 (44282) Misc. bond : bond 0.28967 ( 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 790 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 690 time to evaluate : 3.610 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: AA 96 LEU cc_start: 0.9077 (mm) cc_final: 0.8848 (mm) REVERT: AA 110 GLU cc_start: 0.7707 (pt0) cc_final: 0.7282 (pm20) REVERT: AA 164 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7897 (mt-10) REVERT: AA 238 GLU cc_start: 0.8544 (mp0) cc_final: 0.8310 (mp0) REVERT: AA 247 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8029 (tm-30) REVERT: AA 368 MET cc_start: 0.8875 (tpt) cc_final: 0.8414 (tpt) REVERT: AA 411 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7143 (tm-30) REVERT: AA 463 GLU cc_start: 0.7977 (tt0) cc_final: 0.7740 (tt0) REVERT: AA 469 ASN cc_start: 0.8625 (m-40) cc_final: 0.8139 (m110) REVERT: AB 37 ASP cc_start: 0.8397 (t0) cc_final: 0.7731 (p0) REVERT: AB 75 ASN cc_start: 0.8945 (t0) cc_final: 0.8485 (p0) REVERT: AB 126 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8471 (pt) REVERT: AB 203 GLU cc_start: 0.8482 (mp0) cc_final: 0.8264 (mp0) REVERT: AC 15 ASN cc_start: 0.7248 (t0) cc_final: 0.6911 (t0) REVERT: AC 20 ASP cc_start: 0.8410 (m-30) cc_final: 0.8200 (m-30) REVERT: AC 89 MET cc_start: 0.8577 (tpp) cc_final: 0.7944 (tpp) REVERT: AC 113 TRP cc_start: 0.8577 (t-100) cc_final: 0.8312 (t-100) REVERT: AC 129 MET cc_start: 0.6978 (ptp) cc_final: 0.6622 (ptp) REVERT: AC 138 MET cc_start: 0.8374 (mmt) cc_final: 0.7905 (mmm) REVERT: AC 223 TYR cc_start: 0.9129 (m-80) cc_final: 0.8861 (m-80) REVERT: AC 235 MET cc_start: 0.9047 (tmm) cc_final: 0.8747 (tmm) REVERT: AC 249 MET cc_start: 0.7028 (tpp) cc_final: 0.6604 (tpp) REVERT: AC 257 MET cc_start: 0.7687 (ptp) cc_final: 0.7353 (ptp) REVERT: AC 269 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8227 (ttmm) REVERT: AC 375 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7134 (ttmt) REVERT: AD 103 SER cc_start: 0.8315 (m) cc_final: 0.7996 (p) REVERT: AD 104 SER cc_start: 0.8923 (p) cc_final: 0.8424 (m) REVERT: AD 110 ILE cc_start: 0.8558 (mt) cc_final: 0.8242 (mm) REVERT: AD 255 TYR cc_start: 0.5530 (m-10) cc_final: 0.5329 (m-10) REVERT: AD 272 THR cc_start: 0.8716 (m) cc_final: 0.8342 (p) REVERT: AD 279 GLU cc_start: 0.8159 (tt0) cc_final: 0.7626 (tt0) REVERT: AD 296 MET cc_start: 0.8356 (mmt) cc_final: 0.7896 (mmp) REVERT: AE 115 TYR cc_start: 0.7006 (m-10) cc_final: 0.6421 (m-10) REVERT: AE 167 PHE cc_start: 0.7736 (m-80) cc_final: 0.6933 (m-80) REVERT: AF 46 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7659 (mm-30) REVERT: AF 86 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8318 (mt-10) REVERT: AF 99 ILE cc_start: 0.9084 (mm) cc_final: 0.8619 (pt) REVERT: AF 106 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8581 (mm-30) REVERT: AG 25 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7268 (mtm180) REVERT: AG 33 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8126 (tptt) REVERT: AG 47 LEU cc_start: 0.9090 (mm) cc_final: 0.8571 (tp) REVERT: AI 20 ARG cc_start: 0.7552 (mtm180) cc_final: 0.6391 (mtm-85) REVERT: Aa 153 ASN cc_start: 0.7934 (m-40) cc_final: 0.7154 (t0) REVERT: Aa 164 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8577 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: Aa 170 ARG cc_start: 0.8302 (ptm-80) cc_final: 0.7848 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: Aa 304 LEU cc_start: 0.9043 (mt) cc_final: 0.8005 (mt) REVERT: Aa 364 SER cc_start: 0.8963 (m) cc_final: 0.8228 (t) REVERT: Aa 368 MET cc_start: 0.8931 (tpt) cc_final: 0.8674 (tpt) REVERT: Aa 430 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: Aa 475 MET cc_start: 0.8739 (tpt) cc_final: 0.8364 (tpt) REVERT: Ab 204 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7608 (mm-30) REVERT: Ab 437 SER cc_start: 0.8986 (m) cc_final: 0.8655 (p) REVERT: Ac 20 ASP cc_start: 0.8098 (m-30) cc_final: 0.7516 (m-30) REVERT: Ac 221 HIS cc_start: 0.8557 (t70) cc_final: 0.7887 (t70) REVERT: Ac 269 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8688 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9238 (mt) cc_final: 0.8449 (tt) REVERT: Ac 375 LYS cc_start: 0.7541 (tmtt) cc_final: 0.6800 (mtpt) REVERT: Ad 164 MET cc_start: 0.7075 (ptm) cc_final: 0.6475 (ppp) REVERT: Ad 166 MET cc_start: 0.8138 (mtt) cc_final: 0.7228 (mmt) REVERT: Ad 310 LYS cc_start: 0.8287 (mmtt) cc_final: 0.8004 (mmmt) REVERT: Ae 82 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8522 (t0) REVERT: Ae 122 THR cc_start: 0.8509 (m) cc_final: 0.8281 (p) REVERT: Ae 134 SER cc_start: 0.8133 (t) cc_final: 0.7507 (m) REVERT: Ae 163 LYS cc_start: 0.3104 (tptp) cc_final: 0.2792 (mmtt) REVERT: Ae 243 TYR cc_start: 0.3922 (m-80) cc_final: 0.3671 (m-80) REVERT: Af 33 MET cc_start: 0.8457 (mmt) cc_final: 0.8166 (mmm) REVERT: Af 40 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8770 (mt-10) REVERT: Af 46 GLU cc_start: 0.8355 (tp30) cc_final: 0.8087 (tp30) REVERT: Af 80 GLN cc_start: 0.8727 (mt0) cc_final: 0.8428 (mt0) REVERT: Af 84 TYR cc_start: 0.8527 (t80) cc_final: 0.8311 (t80) REVERT: Af 86 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7873 (tm-30) REVERT: Af 92 GLU cc_start: 0.8557 (tt0) cc_final: 0.8218 (tm-30) REVERT: Af 97 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7891 (mt-10) REVERT: Af 103 LYS cc_start: 0.8653 (mmmt) cc_final: 0.7863 (mmtm) REVERT: Ag 47 LEU cc_start: 0.9204 (tp) cc_final: 0.8911 (tp) REVERT: Ag 77 MET cc_start: 0.8509 (ttm) cc_final: 0.8225 (mtt) REVERT: Ag 78 TYR cc_start: 0.6563 (m-80) cc_final: 0.6323 (m-80) REVERT: Ah 49 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8128 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7553 (m-10) cc_final: 0.6959 (m-10) REVERT: Aj 16 ARG cc_start: 0.6843 (ttm-80) cc_final: 0.6573 (ttm-80) REVERT: Aj 53 TRP cc_start: 0.6997 (OUTLIER) cc_final: 0.6205 (m100) outliers start: 100 outliers final: 64 residues processed: 753 average time/residue: 0.4149 time to fit residues: 506.9763 Evaluate side-chains 702 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 632 time to evaluate : 3.558 ------------------------------------------------------------------------------- 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 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 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 432 VAL 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 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 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 44 GLU 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 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 65 VAL 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 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 Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 82 ASP Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU 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 24 LEU Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Aj residue 52 LEU Chi-restraints excluded: chain Aj residue 53 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 301 optimal weight: 0.4980 chunk 296 optimal weight: 0.9980 chunk 321 optimal weight: 0.0070 chunk 353 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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** AB 139 ASN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 74 GLN AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 303 ASN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 37 GLN Aj 48 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.149336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.111783 restraints weight = 56289.220| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.97 r_work: 0.3440 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.337 32661 Z= 0.125 Angle : 0.638 15.701 44296 Z= 0.299 Chirality : 0.042 0.349 4785 Planarity : 0.004 0.044 5608 Dihedral : 10.472 132.160 4796 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.74 % Allowed : 19.95 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3880 helix: 1.58 (0.11), residues: 2054 sheet: -0.10 (0.28), residues: 362 loop : -0.09 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAK 34 HIS 0.006 0.001 HISAe 239 PHE 0.033 0.001 PHEAj 32 TYR 0.029 0.001 TYRAD 236 ARG 0.011 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1787) hydrogen bonds : angle 4.59398 ( 5124) SS BOND : bond 0.00094 ( 7) SS BOND : angle 0.72091 ( 14) covalent geometry : bond 0.00281 (32648) covalent geometry : angle 0.63820 (44282) Misc. bond : bond 0.22144 ( 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 770 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 679 time to evaluate : 3.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 96 LEU cc_start: 0.9043 (mm) cc_final: 0.8821 (mm) REVERT: AA 164 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7880 (mt-10) REVERT: AA 238 GLU cc_start: 0.8591 (mp0) cc_final: 0.8342 (mp0) REVERT: AA 247 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8019 (tm-30) REVERT: AA 368 MET cc_start: 0.8671 (tpt) cc_final: 0.8391 (mmm) REVERT: AA 411 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7135 (tm-30) REVERT: AA 412 ASP cc_start: 0.8582 (t0) cc_final: 0.8213 (t70) REVERT: AA 463 GLU cc_start: 0.7848 (tt0) cc_final: 0.7644 (tt0) REVERT: AA 469 ASN cc_start: 0.8588 (m-40) cc_final: 0.8091 (m110) REVERT: AB 37 ASP cc_start: 0.8292 (t0) cc_final: 0.7700 (p0) REVERT: AB 75 ASN cc_start: 0.8970 (t0) cc_final: 0.8496 (p0) REVERT: AB 104 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8676 (mt-10) REVERT: AB 126 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8465 (pt) REVERT: AB 203 GLU cc_start: 0.8475 (mp0) cc_final: 0.8231 (mp0) REVERT: AB 390 GLU cc_start: 0.8835 (pp20) cc_final: 0.8626 (pp20) REVERT: AC 89 MET cc_start: 0.8317 (tpp) cc_final: 0.8112 (tpp) REVERT: AC 113 TRP cc_start: 0.8466 (t-100) cc_final: 0.8197 (t-100) REVERT: AC 138 MET cc_start: 0.8349 (mmt) cc_final: 0.7877 (mmm) REVERT: AC 223 TYR cc_start: 0.9125 (m-80) cc_final: 0.8812 (m-80) REVERT: AC 235 MET cc_start: 0.9072 (tmm) cc_final: 0.8660 (tmm) REVERT: AC 249 MET cc_start: 0.7066 (tpp) cc_final: 0.6620 (tpp) REVERT: AC 257 MET cc_start: 0.7716 (ptp) cc_final: 0.7227 (ptp) REVERT: AC 269 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8269 (ttmm) REVERT: AC 344 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7888 (mm-30) REVERT: AC 375 LYS cc_start: 0.7574 (tmtt) cc_final: 0.7014 (ttmt) REVERT: AD 103 SER cc_start: 0.8317 (m) cc_final: 0.8010 (p) REVERT: AD 104 SER cc_start: 0.8924 (p) cc_final: 0.8410 (m) REVERT: AD 209 ASP cc_start: 0.8194 (m-30) cc_final: 0.7671 (m-30) REVERT: AD 279 GLU cc_start: 0.8161 (tt0) cc_final: 0.7685 (tt0) REVERT: AD 296 MET cc_start: 0.8313 (mmt) cc_final: 0.7934 (mmp) REVERT: AE 115 TYR cc_start: 0.6988 (m-10) cc_final: 0.6353 (m-10) REVERT: AE 149 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6419 (ptt) REVERT: AE 167 PHE cc_start: 0.7760 (m-80) cc_final: 0.6922 (m-80) REVERT: AF 86 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8394 (mt-10) REVERT: AF 99 ILE cc_start: 0.9068 (mm) cc_final: 0.8605 (pt) REVERT: AG 25 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7107 (mtm180) REVERT: AG 33 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8188 (tptt) REVERT: AG 44 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8055 (mm-30) REVERT: AG 47 LEU cc_start: 0.9085 (mm) cc_final: 0.8549 (tp) REVERT: AH 33 GLU cc_start: 0.8515 (pm20) cc_final: 0.8281 (pm20) REVERT: AH 86 LYS cc_start: 0.8653 (mttp) cc_final: 0.8437 (mttp) REVERT: AI 20 ARG cc_start: 0.7553 (mtm180) cc_final: 0.6358 (mtm-85) REVERT: Aa 54 ASP cc_start: 0.8576 (m-30) cc_final: 0.8253 (t0) REVERT: Aa 153 ASN cc_start: 0.7951 (m-40) cc_final: 0.7122 (t0) REVERT: Aa 164 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8541 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: Aa 170 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.7815 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: Aa 220 LEU cc_start: 0.8742 (mt) cc_final: 0.8484 (mt) REVERT: Aa 250 LEU cc_start: 0.9075 (tt) cc_final: 0.8821 (tp) REVERT: Aa 364 SER cc_start: 0.8977 (m) cc_final: 0.8263 (t) REVERT: Aa 368 MET cc_start: 0.8914 (tpt) cc_final: 0.8673 (tpt) REVERT: Aa 430 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7609 (mm-30) REVERT: Ac 20 ASP cc_start: 0.7954 (m-30) cc_final: 0.7397 (m-30) REVERT: Ac 221 HIS cc_start: 0.8650 (t70) cc_final: 0.8000 (t70) REVERT: Ac 269 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8671 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9258 (mt) cc_final: 0.8519 (tt) REVERT: Ac 375 LYS cc_start: 0.7525 (tmtt) cc_final: 0.6763 (mtpt) REVERT: Ad 146 LYS cc_start: 0.8555 (tptm) cc_final: 0.8270 (tptt) REVERT: Ad 164 MET cc_start: 0.7029 (ptm) cc_final: 0.6471 (ppp) REVERT: Ad 166 MET cc_start: 0.8061 (mtt) cc_final: 0.7271 (mmt) REVERT: Ad 310 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7929 (mmmt) REVERT: Ae 82 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8530 (t0) REVERT: Ae 122 THR cc_start: 0.8451 (m) cc_final: 0.8232 (p) REVERT: Ae 134 SER cc_start: 0.8055 (t) cc_final: 0.7449 (m) REVERT: Af 33 MET cc_start: 0.8429 (mmt) cc_final: 0.8096 (mmm) REVERT: Af 40 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8744 (mt-10) REVERT: Af 46 GLU cc_start: 0.8352 (tp30) cc_final: 0.7928 (tp30) REVERT: Af 80 GLN cc_start: 0.8644 (mt0) cc_final: 0.8302 (mt0) REVERT: Af 86 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7894 (tm-30) REVERT: Af 92 GLU cc_start: 0.8552 (tt0) cc_final: 0.8193 (tm-30) REVERT: Af 97 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7861 (mt-10) REVERT: Af 103 LYS cc_start: 0.8648 (mmmt) cc_final: 0.7886 (mmtm) REVERT: Af 107 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8432 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9172 (tp) cc_final: 0.8891 (tp) REVERT: Ag 60 TYR cc_start: 0.8938 (t80) cc_final: 0.8536 (t80) REVERT: Ag 77 MET cc_start: 0.8366 (ttm) cc_final: 0.8145 (mtt) REVERT: Ag 78 TYR cc_start: 0.6586 (m-80) cc_final: 0.6324 (m-80) REVERT: Ah 49 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8207 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7454 (m-10) cc_final: 0.6776 (m-80) REVERT: Aj 16 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.6519 (ttm-80) REVERT: Aj 53 TRP cc_start: 0.6896 (OUTLIER) cc_final: 0.6296 (m100) outliers start: 91 outliers final: 58 residues processed: 733 average time/residue: 0.4264 time to fit residues: 502.1916 Evaluate side-chains 693 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 627 time to evaluate : 3.609 ------------------------------------------------------------------------------- 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 304 LEU Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 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 AC residue 49 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 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 AE residue 149 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 44 GLU 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 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 214 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 65 VAL 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 303 ASN 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 Ad residue 152 VAL Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 82 ASP Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 24 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 332 optimal weight: 6.9990 chunk 255 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 348 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 336 optimal weight: 0.0470 chunk 109 optimal weight: 8.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 15 ASN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.143683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104671 restraints weight = 56749.965| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.05 r_work: 0.3347 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.344 32661 Z= 0.195 Angle : 0.678 16.548 44296 Z= 0.320 Chirality : 0.043 0.289 4785 Planarity : 0.004 0.040 5608 Dihedral : 10.478 129.237 4795 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.40 % Allowed : 19.83 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.14), residues: 3880 helix: 1.57 (0.11), residues: 2054 sheet: -0.17 (0.27), residues: 365 loop : -0.08 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAj 53 HIS 0.008 0.001 HISAc 196 PHE 0.025 0.002 PHEAC 347 TYR 0.031 0.002 TYRAD 236 ARG 0.009 0.001 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 1787) hydrogen bonds : angle 4.65759 ( 5124) SS BOND : bond 0.00141 ( 7) SS BOND : angle 0.59379 ( 14) covalent geometry : bond 0.00462 (32648) covalent geometry : angle 0.67812 (44282) Misc. bond : bond 0.22540 ( 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 756 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 643 time to evaluate : 3.834 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 96 LEU cc_start: 0.9122 (mm) cc_final: 0.8892 (mm) REVERT: AA 164 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7830 (mt-10) REVERT: AA 238 GLU cc_start: 0.8674 (mp0) cc_final: 0.8426 (mp0) REVERT: AA 247 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8082 (tm-30) REVERT: AA 368 MET cc_start: 0.8909 (tpt) cc_final: 0.8598 (mmm) REVERT: AA 469 ASN cc_start: 0.8604 (m-40) cc_final: 0.8080 (m110) REVERT: AB 37 ASP cc_start: 0.8399 (t0) cc_final: 0.7730 (p0) REVERT: AB 126 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8437 (pt) REVERT: AB 155 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7864 (mtt90) REVERT: AC 15 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7632 (t0) REVERT: AC 42 MET cc_start: 0.7593 (mtt) cc_final: 0.7235 (mtm) REVERT: AC 113 TRP cc_start: 0.8563 (t-100) cc_final: 0.8253 (t-100) REVERT: AC 138 MET cc_start: 0.8429 (mmt) cc_final: 0.8085 (mmm) REVERT: AC 177 ARG cc_start: 0.6946 (ptp-170) cc_final: 0.6633 (ptp-170) REVERT: AC 223 TYR cc_start: 0.9143 (m-80) cc_final: 0.8857 (m-80) REVERT: AC 235 MET cc_start: 0.9074 (tmm) cc_final: 0.8649 (tmm) REVERT: AC 249 MET cc_start: 0.7355 (tpp) cc_final: 0.6923 (tpp) REVERT: AC 269 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8233 (ttmm) REVERT: AC 375 LYS cc_start: 0.7670 (tmtt) cc_final: 0.7128 (ttmt) REVERT: AD 103 SER cc_start: 0.8398 (m) cc_final: 0.7984 (p) REVERT: AD 110 ILE cc_start: 0.8571 (mt) cc_final: 0.8232 (mm) REVERT: AD 143 GLU cc_start: 0.8336 (tp30) cc_final: 0.8071 (pm20) REVERT: AD 279 GLU cc_start: 0.8220 (tt0) cc_final: 0.7642 (tt0) REVERT: AE 115 TYR cc_start: 0.7059 (m-10) cc_final: 0.6454 (m-10) REVERT: AE 149 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6436 (ptt) REVERT: AE 165 MET cc_start: 0.5655 (tpt) cc_final: 0.5097 (ptm) REVERT: AE 167 PHE cc_start: 0.7780 (m-80) cc_final: 0.6365 (m-80) REVERT: AE 271 VAL cc_start: 0.7252 (t) cc_final: 0.6954 (m) REVERT: AF 86 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8475 (mt-10) REVERT: AF 99 ILE cc_start: 0.9102 (mm) cc_final: 0.8643 (pt) REVERT: AG 25 ARG cc_start: 0.7626 (mtm180) cc_final: 0.7225 (mtm180) REVERT: AG 33 LYS cc_start: 0.8404 (ttpp) cc_final: 0.8163 (tptt) REVERT: AG 47 LEU cc_start: 0.9102 (mm) cc_final: 0.8550 (tp) REVERT: AH 33 GLU cc_start: 0.8585 (pm20) cc_final: 0.8366 (pm20) REVERT: AH 86 LYS cc_start: 0.8729 (mttp) cc_final: 0.8449 (mttp) REVERT: AI 20 ARG cc_start: 0.7575 (mtm180) cc_final: 0.6308 (mtm-85) REVERT: AJ 32 PHE cc_start: 0.8262 (t80) cc_final: 0.7989 (t80) REVERT: Aa 164 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8562 (mm-30) REVERT: Aa 170 ARG cc_start: 0.8349 (ptm-80) cc_final: 0.7820 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: Aa 364 SER cc_start: 0.9026 (m) cc_final: 0.8284 (t) REVERT: Aa 368 MET cc_start: 0.8974 (tpt) cc_final: 0.8438 (tpt) REVERT: Aa 430 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7645 (mm-30) REVERT: Ab 437 SER cc_start: 0.8964 (m) cc_final: 0.8603 (p) REVERT: Ac 20 ASP cc_start: 0.8076 (m-30) cc_final: 0.7502 (m-30) REVERT: Ac 89 MET cc_start: 0.8520 (tpp) cc_final: 0.8225 (tpp) REVERT: Ac 137 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6619 (tp-100) REVERT: Ac 269 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8741 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9248 (mt) cc_final: 0.8461 (tt) REVERT: Ac 373 GLU cc_start: 0.7634 (tt0) cc_final: 0.7370 (tt0) REVERT: Ac 375 LYS cc_start: 0.7586 (tmtt) cc_final: 0.6724 (mtpt) REVERT: Ad 146 LYS cc_start: 0.8533 (tptm) cc_final: 0.8272 (tptt) REVERT: Ad 164 MET cc_start: 0.7150 (ptm) cc_final: 0.6631 (ppp) REVERT: Ad 166 MET cc_start: 0.8147 (mtt) cc_final: 0.7302 (mmt) REVERT: Ad 310 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8091 (mmmt) REVERT: Ae 82 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8605 (t0) REVERT: Ae 122 THR cc_start: 0.8412 (m) cc_final: 0.8209 (p) REVERT: Ae 131 ASN cc_start: 0.7617 (t0) cc_final: 0.7393 (t0) REVERT: Ae 134 SER cc_start: 0.8107 (t) cc_final: 0.7520 (m) REVERT: Ae 163 LYS cc_start: 0.3650 (tptp) cc_final: 0.3273 (tptp) REVERT: Af 33 MET cc_start: 0.8476 (mmt) cc_final: 0.8172 (mmm) REVERT: Af 40 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8726 (mt-10) REVERT: Af 46 GLU cc_start: 0.8350 (tp30) cc_final: 0.7938 (tp30) REVERT: Af 74 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: Af 86 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7847 (tm-30) REVERT: Af 92 GLU cc_start: 0.8572 (tt0) cc_final: 0.8197 (tm-30) REVERT: Af 97 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7819 (mm-30) REVERT: Af 103 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8053 (mmtm) REVERT: Af 107 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8456 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9232 (tp) cc_final: 0.8965 (tp) REVERT: Ag 60 TYR cc_start: 0.9007 (t80) cc_final: 0.8565 (t80) REVERT: Ag 77 MET cc_start: 0.8300 (ttm) cc_final: 0.8092 (mtt) REVERT: Ag 78 TYR cc_start: 0.6603 (m-80) cc_final: 0.6303 (m-80) REVERT: Ah 49 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8291 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7549 (m-10) cc_final: 0.6877 (m-10) REVERT: Aj 53 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6266 (m100) outliers start: 113 outliers final: 81 residues processed: 718 average time/residue: 0.4294 time to fit residues: 493.4211 Evaluate side-chains 703 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 613 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 304 LEU Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 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 309 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 49 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 205 HIS Chi-restraints excluded: chain AD residue 215 LEU Chi-restraints excluded: chain AE residue 117 VAL Chi-restraints excluded: chain AE residue 149 MET Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 44 GLU 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 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 214 THR Chi-restraints excluded: chain Aa residue 256 VAL Chi-restraints excluded: chain Aa residue 266 THR Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 430 GLU Chi-restraints excluded: chain Ab residue 65 VAL 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 393 LEU Chi-restraints excluded: chain Ab residue 450 LEU Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 237 LEU 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 227 LEU Chi-restraints excluded: chain Ad residue 242 ILE Chi-restraints excluded: chain Ae residue 82 ASP Chi-restraints excluded: chain Ae residue 90 ASP Chi-restraints excluded: chain Ae residue 152 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Af residue 74 GLN Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 24 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 246 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 322 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 260 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 AC 32 ASN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 153 ASN Ac 331 ASN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 GLN Ah 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106578 restraints weight = 56780.688| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.08 r_work: 0.3377 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 32661 Z= 0.140 Angle : 0.655 16.345 44296 Z= 0.307 Chirality : 0.042 0.229 4785 Planarity : 0.004 0.055 5608 Dihedral : 10.361 125.694 4795 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.07 % Allowed : 20.55 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3880 helix: 1.62 (0.11), residues: 2061 sheet: -0.38 (0.26), residues: 396 loop : 0.02 (0.17), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAc 141 HIS 0.007 0.001 HISAe 239 PHE 0.028 0.001 PHEAj 32 TYR 0.026 0.001 TYRAD 236 ARG 0.013 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1787) hydrogen bonds : angle 4.56341 ( 5124) SS BOND : bond 0.00127 ( 7) SS BOND : angle 0.64362 ( 14) covalent geometry : bond 0.00330 (32648) covalent geometry : angle 0.65511 (44282) Misc. bond : bond 0.20379 ( 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 752 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 650 time to evaluate : 4.011 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: AA 96 LEU cc_start: 0.9101 (mm) cc_final: 0.8887 (mm) REVERT: AA 164 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7814 (mt-10) REVERT: AA 238 GLU cc_start: 0.8689 (mp0) cc_final: 0.8417 (mp0) REVERT: AA 247 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8012 (tm-30) REVERT: AA 368 MET cc_start: 0.8895 (tpt) cc_final: 0.8619 (mmm) REVERT: AA 412 ASP cc_start: 0.8559 (t0) cc_final: 0.8203 (t70) REVERT: AA 435 GLU cc_start: 0.8633 (pp20) cc_final: 0.8158 (mt-10) REVERT: AA 469 ASN cc_start: 0.8569 (m-40) cc_final: 0.8073 (m110) REVERT: AB 37 ASP cc_start: 0.8447 (t0) cc_final: 0.7761 (p0) REVERT: AB 126 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8473 (pt) REVERT: AB 155 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7790 (mtt90) REVERT: AC 113 TRP cc_start: 0.8464 (t-100) cc_final: 0.8138 (t-100) REVERT: AC 138 MET cc_start: 0.8314 (mmt) cc_final: 0.7950 (mmm) REVERT: AC 223 TYR cc_start: 0.9156 (m-80) cc_final: 0.8877 (m-80) REVERT: AC 235 MET cc_start: 0.9106 (tmm) cc_final: 0.8815 (tmm) REVERT: AC 249 MET cc_start: 0.7508 (tpp) cc_final: 0.7122 (tpp) REVERT: AC 269 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8235 (ttmm) REVERT: AC 375 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7133 (ttmt) REVERT: AD 90 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7520 (m90) REVERT: AD 103 SER cc_start: 0.8371 (m) cc_final: 0.7989 (p) REVERT: AD 115 GLN cc_start: 0.8674 (tp40) cc_final: 0.7970 (tt0) REVERT: AD 143 GLU cc_start: 0.8367 (tp30) cc_final: 0.8145 (pm20) REVERT: AD 166 MET cc_start: 0.5227 (mmm) cc_final: 0.4915 (mmm) REVERT: AD 279 GLU cc_start: 0.8208 (tt0) cc_final: 0.7734 (tt0) REVERT: AE 115 TYR cc_start: 0.6913 (m-10) cc_final: 0.6274 (m-10) REVERT: AE 149 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6446 (ptt) REVERT: AE 165 MET cc_start: 0.5638 (tpt) cc_final: 0.5223 (ptm) REVERT: AE 271 VAL cc_start: 0.7336 (t) cc_final: 0.6999 (m) REVERT: AF 86 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8460 (mt-10) REVERT: AF 99 ILE cc_start: 0.9066 (mm) cc_final: 0.8582 (pt) REVERT: AF 106 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8497 (mm-30) REVERT: AG 25 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7070 (mtm180) REVERT: AG 44 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: AG 46 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8735 (mm) REVERT: AG 47 LEU cc_start: 0.9079 (mm) cc_final: 0.8387 (tp) REVERT: AG 68 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8542 (pt0) REVERT: AG 69 GLN cc_start: 0.7379 (tm-30) cc_final: 0.7164 (tm-30) REVERT: AH 86 LYS cc_start: 0.8659 (mttp) cc_final: 0.8414 (mtmm) REVERT: AH 87 ASN cc_start: 0.8965 (p0) cc_final: 0.8410 (p0) REVERT: AI 20 ARG cc_start: 0.7582 (mtm180) cc_final: 0.6343 (mtm-85) REVERT: AI 77 ARG cc_start: 0.6891 (tmt170) cc_final: 0.5076 (mtm110) REVERT: Aa 91 TYR cc_start: 0.8330 (t80) cc_final: 0.7779 (t80) REVERT: Aa 164 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8558 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: Aa 170 ARG cc_start: 0.8309 (ptm-80) cc_final: 0.7809 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: Aa 364 SER cc_start: 0.8936 (m) cc_final: 0.8179 (t) REVERT: Aa 368 MET cc_start: 0.8871 (tpt) cc_final: 0.8553 (tpt) REVERT: Aa 430 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7668 (mm-30) REVERT: Ac 20 ASP cc_start: 0.8015 (m-30) cc_final: 0.7450 (m-30) REVERT: Ac 89 MET cc_start: 0.8462 (tpp) cc_final: 0.8147 (tpp) REVERT: Ac 137 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6518 (tp-100) REVERT: Ac 171 ASP cc_start: 0.7310 (t0) cc_final: 0.7028 (t0) REVERT: Ac 269 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8691 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9255 (mt) cc_final: 0.8492 (tt) REVERT: Ac 375 LYS cc_start: 0.7511 (tmtt) cc_final: 0.6605 (mtpt) REVERT: Ad 146 LYS cc_start: 0.8568 (tptm) cc_final: 0.8321 (tptt) REVERT: Ad 164 MET cc_start: 0.7103 (ptm) cc_final: 0.6589 (ppp) REVERT: Ad 166 MET cc_start: 0.8032 (mtt) cc_final: 0.7311 (mmt) REVERT: Ad 309 HIS cc_start: 0.7449 (t70) cc_final: 0.7041 (t70) REVERT: Ad 310 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8087 (mmmt) REVERT: Ae 110 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7274 (ptp90) REVERT: Ae 134 SER cc_start: 0.7927 (t) cc_final: 0.7481 (p) REVERT: Ae 163 LYS cc_start: 0.3626 (tptp) cc_final: 0.3241 (tptp) REVERT: Ae 168 LYS cc_start: 0.6105 (tptt) cc_final: 0.5687 (tptm) REVERT: Af 33 MET cc_start: 0.8421 (mmt) cc_final: 0.8138 (mmm) REVERT: Af 40 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8748 (mt-10) REVERT: Af 46 GLU cc_start: 0.8363 (tp30) cc_final: 0.7922 (tp30) REVERT: Af 80 GLN cc_start: 0.8877 (mt0) cc_final: 0.8676 (mt0) REVERT: Af 92 GLU cc_start: 0.8540 (tt0) cc_final: 0.8147 (tm-30) REVERT: Af 97 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7788 (mm-30) REVERT: Af 103 LYS cc_start: 0.8642 (mmmt) cc_final: 0.7942 (mmtm) REVERT: Af 107 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8430 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9191 (tp) cc_final: 0.8900 (tp) REVERT: Ag 60 TYR cc_start: 0.8951 (t80) cc_final: 0.8557 (t80) REVERT: Ah 49 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8319 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7437 (m-10) cc_final: 0.6792 (m-10) REVERT: Aj 16 ARG cc_start: 0.6586 (ttm-80) cc_final: 0.6375 (ttm-80) REVERT: Aj 53 TRP cc_start: 0.6891 (OUTLIER) cc_final: 0.6263 (m100) outliers start: 102 outliers final: 72 residues processed: 713 average time/residue: 0.4135 time to fit residues: 473.9996 Evaluate side-chains 698 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 616 time to evaluate : 3.322 ------------------------------------------------------------------------------- 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 304 LEU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 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 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 233 LEU 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 AE residue 82 ASP Chi-restraints excluded: chain AE residue 149 MET Chi-restraints excluded: chain AE residue 244 ASP Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AG residue 44 GLU Chi-restraints excluded: chain AG residue 46 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 AI residue 14 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 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 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 65 VAL 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 240 MET Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ab residue 450 LEU Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 271 GLU 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 227 LEU Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 24 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 168 optimal weight: 6.9990 chunk 262 optimal weight: 8.9990 chunk 371 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 241 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 308 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 85 ASN ** Ad 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Ah 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.144933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105944 restraints weight = 56854.862| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.06 r_work: 0.3368 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.333 32661 Z= 0.158 Angle : 0.673 18.423 44296 Z= 0.315 Chirality : 0.042 0.195 4785 Planarity : 0.004 0.051 5608 Dihedral : 10.311 122.842 4795 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.92 % Allowed : 20.97 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3880 helix: 1.65 (0.11), residues: 2057 sheet: -0.41 (0.26), residues: 402 loop : 0.02 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPAc 141 HIS 0.007 0.001 HISAe 239 PHE 0.033 0.001 PHEAC 347 TYR 0.027 0.001 TYRAD 236 ARG 0.013 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 1787) hydrogen bonds : angle 4.57626 ( 5124) SS BOND : bond 0.00123 ( 7) SS BOND : angle 0.63128 ( 14) covalent geometry : bond 0.00376 (32648) covalent geometry : angle 0.67260 (44282) Misc. bond : bond 0.23521 ( 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 749 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 652 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 96 LEU cc_start: 0.9102 (mm) cc_final: 0.8887 (mm) REVERT: AA 164 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7822 (mt-10) REVERT: AA 238 GLU cc_start: 0.8681 (mp0) cc_final: 0.8409 (mp0) REVERT: AA 247 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8053 (tm-30) REVERT: AA 368 MET cc_start: 0.8908 (tpt) cc_final: 0.8601 (mmm) REVERT: AA 412 ASP cc_start: 0.8579 (t0) cc_final: 0.8236 (t70) REVERT: AA 435 GLU cc_start: 0.8644 (pp20) cc_final: 0.8188 (mt-10) REVERT: AA 469 ASN cc_start: 0.8571 (m-40) cc_final: 0.8090 (m110) REVERT: AB 37 ASP cc_start: 0.8505 (t0) cc_final: 0.7781 (p0) REVERT: AB 104 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8774 (mt-10) REVERT: AB 126 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8472 (pt) REVERT: AB 155 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7870 (mtt90) REVERT: AC 113 TRP cc_start: 0.8469 (t-100) cc_final: 0.8132 (t-100) REVERT: AC 138 MET cc_start: 0.8311 (mmt) cc_final: 0.7973 (mmm) REVERT: AC 223 TYR cc_start: 0.9166 (m-80) cc_final: 0.8903 (m-80) REVERT: AC 235 MET cc_start: 0.9128 (tmm) cc_final: 0.8663 (tmm) REVERT: AC 249 MET cc_start: 0.7621 (tpp) cc_final: 0.7236 (tpp) REVERT: AC 269 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8212 (ttmm) REVERT: AC 344 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7932 (mm-30) REVERT: AC 375 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7147 (ttmt) REVERT: AD 103 SER cc_start: 0.8397 (m) cc_final: 0.8083 (p) REVERT: AD 115 GLN cc_start: 0.8592 (tp40) cc_final: 0.7875 (tt0) REVERT: AD 143 GLU cc_start: 0.8388 (tp30) cc_final: 0.8186 (pm20) REVERT: AD 166 MET cc_start: 0.5463 (mmm) cc_final: 0.5159 (mmm) REVERT: AD 251 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8281 (tm-30) REVERT: AD 279 GLU cc_start: 0.8238 (tt0) cc_final: 0.7760 (tt0) REVERT: AD 292 MET cc_start: 0.8562 (tmm) cc_final: 0.8318 (tmm) REVERT: AE 115 TYR cc_start: 0.6820 (m-10) cc_final: 0.6191 (m-10) REVERT: AE 165 MET cc_start: 0.5654 (tpt) cc_final: 0.5239 (ptm) REVERT: AE 271 VAL cc_start: 0.7372 (t) cc_final: 0.7074 (m) REVERT: AF 53 GLU cc_start: 0.7679 (tp30) cc_final: 0.7432 (tp30) REVERT: AF 86 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8427 (mt-10) REVERT: AF 99 ILE cc_start: 0.9074 (mm) cc_final: 0.8590 (pt) REVERT: AF 106 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8551 (mm-30) REVERT: AG 25 ARG cc_start: 0.7472 (mtm180) cc_final: 0.7073 (mtm180) REVERT: AG 44 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: AG 47 LEU cc_start: 0.9104 (mm) cc_final: 0.8533 (tp) REVERT: AG 68 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8539 (pt0) REVERT: AG 69 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7096 (tm-30) REVERT: AH 86 LYS cc_start: 0.8703 (mttp) cc_final: 0.8478 (mtmm) REVERT: AH 87 ASN cc_start: 0.8993 (p0) cc_final: 0.8717 (p0) REVERT: AI 20 ARG cc_start: 0.7516 (mtm180) cc_final: 0.6264 (mtm-85) REVERT: Aa 91 TYR cc_start: 0.8265 (t80) cc_final: 0.7693 (t80) REVERT: Aa 164 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8557 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: Aa 170 ARG cc_start: 0.8337 (ptm-80) cc_final: 0.7530 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: Aa 364 SER cc_start: 0.8944 (m) cc_final: 0.8190 (t) REVERT: Aa 368 MET cc_start: 0.8880 (tpt) cc_final: 0.8485 (tpt) REVERT: Aa 430 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: Ab 204 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7662 (mm-30) REVERT: Ab 437 SER cc_start: 0.9050 (m) cc_final: 0.8691 (p) REVERT: Ac 20 ASP cc_start: 0.7994 (m-30) cc_final: 0.7423 (m-30) REVERT: Ac 137 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6599 (tp-100) REVERT: Ac 171 ASP cc_start: 0.7427 (t0) cc_final: 0.7095 (t0) REVERT: Ac 269 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8718 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9240 (mt) cc_final: 0.8460 (tt) REVERT: Ac 331 ASN cc_start: 0.8905 (p0) cc_final: 0.8666 (p0) REVERT: Ac 375 LYS cc_start: 0.7528 (tmtt) cc_final: 0.6578 (mtpt) REVERT: Ad 146 LYS cc_start: 0.8577 (tptm) cc_final: 0.8311 (tptt) REVERT: Ad 164 MET cc_start: 0.6959 (ptm) cc_final: 0.6429 (ppp) REVERT: Ad 166 MET cc_start: 0.8083 (mtt) cc_final: 0.7350 (mmt) REVERT: Ad 309 HIS cc_start: 0.7477 (t70) cc_final: 0.7064 (t70) REVERT: Ae 110 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7080 (ptp90) REVERT: Ae 134 SER cc_start: 0.7905 (t) cc_final: 0.7467 (p) REVERT: Ae 163 LYS cc_start: 0.3698 (tptp) cc_final: 0.3316 (tptp) REVERT: Ae 168 LYS cc_start: 0.6072 (tptt) cc_final: 0.5832 (tptm) REVERT: Af 33 MET cc_start: 0.8427 (mmt) cc_final: 0.8153 (mmm) REVERT: Af 40 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8759 (mt-10) REVERT: Af 46 GLU cc_start: 0.8382 (tp30) cc_final: 0.7939 (tp30) REVERT: Af 74 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8522 (mm-40) REVERT: Af 80 GLN cc_start: 0.8869 (mt0) cc_final: 0.8602 (mt0) REVERT: Af 92 GLU cc_start: 0.8553 (tt0) cc_final: 0.8163 (tm-30) REVERT: Af 97 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7814 (mm-30) REVERT: Af 103 LYS cc_start: 0.8662 (mmmt) cc_final: 0.7953 (mmtm) REVERT: Af 107 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8438 (tm-30) REVERT: Ag 47 LEU cc_start: 0.9189 (tp) cc_final: 0.8892 (tp) REVERT: Ag 60 TYR cc_start: 0.8954 (t80) cc_final: 0.8568 (t80) REVERT: Ag 78 TYR cc_start: 0.6418 (m-80) cc_final: 0.6057 (m-80) REVERT: Ah 49 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8341 (mm-30) REVERT: Aj 15 PHE cc_start: 0.7348 (m-10) cc_final: 0.6671 (m-10) REVERT: Aj 53 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.6372 (m100) outliers start: 97 outliers final: 82 residues processed: 712 average time/residue: 0.4174 time to fit residues: 484.0983 Evaluate side-chains 706 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 616 time to evaluate : 3.782 ------------------------------------------------------------------------------- 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 304 LEU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 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 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 233 LEU 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 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 AF residue 42 GLU Chi-restraints excluded: chain AG residue 44 GLU 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 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 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 214 THR Chi-restraints excluded: chain Aa residue 230 VAL 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 65 VAL 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 240 MET Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ab residue 450 LEU Chi-restraints excluded: chain Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 271 GLU 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 227 LEU Chi-restraints excluded: chain Ad residue 242 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Af residue 74 GLN Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ag residue 73 LYS Chi-restraints excluded: chain Ah residue 24 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 134 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 368 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 chunk 382 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 15 ASN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 341 GLN ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 87 ASN ** 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** ** Ae 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Ah 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106819 restraints weight = 56865.847| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.17 r_work: 0.3348 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 32661 Z= 0.180 Angle : 0.693 21.284 44296 Z= 0.325 Chirality : 0.043 0.229 4785 Planarity : 0.004 0.050 5608 Dihedral : 10.346 120.142 4795 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.04 % Allowed : 20.94 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3880 helix: 1.61 (0.11), residues: 2067 sheet: -0.38 (0.26), residues: 385 loop : 0.03 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPAc 141 HIS 0.010 0.001 HISAf 73 PHE 0.020 0.001 PHEAa 98 TYR 0.021 0.001 TYRAa 420 ARG 0.012 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1787) hydrogen bonds : angle 4.60564 ( 5124) SS BOND : bond 0.00143 ( 7) SS BOND : angle 0.62708 ( 14) covalent geometry : bond 0.00431 (32648) covalent geometry : angle 0.69339 (44282) Misc. bond : bond 0.23410 ( 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 731 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 630 time to evaluate : 3.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 96 LEU cc_start: 0.9120 (mm) cc_final: 0.8895 (mm) REVERT: AA 164 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7818 (mt-10) REVERT: AA 238 GLU cc_start: 0.8700 (mp0) cc_final: 0.8431 (mp0) REVERT: AA 247 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8048 (tm-30) REVERT: AA 368 MET cc_start: 0.8895 (tpt) cc_final: 0.8370 (tpt) REVERT: AA 412 ASP cc_start: 0.8597 (t0) cc_final: 0.8258 (t70) REVERT: AA 435 GLU cc_start: 0.8650 (pp20) cc_final: 0.8173 (mt-10) REVERT: AA 469 ASN cc_start: 0.8582 (m-40) cc_final: 0.8169 (m110) REVERT: AB 37 ASP cc_start: 0.8487 (t0) cc_final: 0.7714 (p0) REVERT: AB 104 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8799 (mt-10) REVERT: AB 126 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8482 (pt) REVERT: AB 155 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7889 (mtt90) REVERT: AC 113 TRP cc_start: 0.8494 (t-100) cc_final: 0.8145 (t-100) REVERT: AC 138 MET cc_start: 0.8345 (mmt) cc_final: 0.7948 (mmm) REVERT: AC 235 MET cc_start: 0.9070 (tmm) cc_final: 0.8612 (tmm) REVERT: AC 249 MET cc_start: 0.7671 (tpp) cc_final: 0.7320 (tpp) REVERT: AC 344 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7943 (mm-30) REVERT: AC 375 LYS cc_start: 0.7705 (tmtt) cc_final: 0.7162 (ttmt) REVERT: AD 103 SER cc_start: 0.8407 (m) cc_final: 0.8110 (p) REVERT: AD 115 GLN cc_start: 0.8547 (tp40) cc_final: 0.7744 (tt0) REVERT: AD 143 GLU cc_start: 0.8374 (tp30) cc_final: 0.8170 (pm20) REVERT: AD 166 MET cc_start: 0.5477 (mmm) cc_final: 0.5143 (mmm) REVERT: AD 251 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8281 (tm-30) REVERT: AD 279 GLU cc_start: 0.8237 (tt0) cc_final: 0.7756 (tt0) REVERT: AE 115 TYR cc_start: 0.6886 (m-10) cc_final: 0.6228 (m-10) REVERT: AE 271 VAL cc_start: 0.7385 (t) cc_final: 0.7082 (m) REVERT: AF 53 GLU cc_start: 0.7774 (tp30) cc_final: 0.7523 (tp30) REVERT: AF 86 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8436 (mt-10) REVERT: AF 99 ILE cc_start: 0.9078 (mm) cc_final: 0.8584 (pt) REVERT: AF 106 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8546 (mm-30) REVERT: AG 25 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7086 (mtm180) REVERT: AG 47 LEU cc_start: 0.9092 (mm) cc_final: 0.8517 (tp) REVERT: AG 68 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8552 (pt0) REVERT: AG 69 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7057 (tm-30) REVERT: AH 86 LYS cc_start: 0.8691 (mttp) cc_final: 0.8459 (mtmm) REVERT: AH 87 ASN cc_start: 0.8970 (p0) cc_final: 0.8703 (p0) REVERT: AI 20 ARG cc_start: 0.7517 (mtm180) cc_final: 0.6241 (mtm-85) REVERT: Aa 91 TYR cc_start: 0.8306 (t80) cc_final: 0.7739 (t80) REVERT: Aa 164 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8590 (mm-30) REVERT: Aa 166 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7945 (m-30) REVERT: Aa 170 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.7532 (ptm-80) REVERT: Aa 174 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: Aa 179 MET cc_start: 0.6474 (mtm) cc_final: 0.6041 (mtm) REVERT: Aa 364 SER cc_start: 0.8972 (m) cc_final: 0.8218 (t) REVERT: Aa 368 MET cc_start: 0.8875 (tpt) cc_final: 0.8422 (tpt) REVERT: Aa 430 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7813 (mm-30) REVERT: Aa 450 TYR cc_start: 0.8577 (t80) cc_final: 0.8203 (t80) REVERT: Ab 204 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7673 (mm-30) REVERT: Ab 437 SER cc_start: 0.9020 (m) cc_final: 0.8664 (p) REVERT: Ac 20 ASP cc_start: 0.7979 (m-30) cc_final: 0.7420 (m-30) REVERT: Ac 137 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6737 (tp-100) REVERT: Ac 249 MET cc_start: 0.8825 (tpp) cc_final: 0.8620 (tpt) REVERT: Ac 269 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8732 (mtmm) REVERT: Ac 299 LEU cc_start: 0.9247 (mt) cc_final: 0.8459 (tt) REVERT: Ac 331 ASN cc_start: 0.8933 (p0) cc_final: 0.8683 (p0) REVERT: Ac 375 LYS cc_start: 0.7458 (tmtt) cc_final: 0.6480 (mttp) REVERT: Ad 164 MET cc_start: 0.6955 (ptm) cc_final: 0.6530 (ppp) REVERT: Ad 166 MET cc_start: 0.8117 (mtt) cc_final: 0.7317 (mmt) REVERT: Ad 309 HIS cc_start: 0.7516 (t70) cc_final: 0.7104 (t70) REVERT: Ae 110 ARG cc_start: 0.7996 (mtm110) cc_final: 0.7173 (ptp90) REVERT: Ae 134 SER cc_start: 0.7915 (t) cc_final: 0.7482 (p) REVERT: Ae 163 LYS cc_start: 0.3809 (tptp) cc_final: 0.3326 (tptp) REVERT: Ae 168 LYS cc_start: 0.6130 (tptt) cc_final: 0.5866 (tptm) REVERT: Ae 231 PHE cc_start: 0.6674 (m-10) cc_final: 0.6440 (m-10) REVERT: Af 33 MET cc_start: 0.8461 (mmt) cc_final: 0.8143 (mmm) REVERT: Af 40 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8782 (mt-10) REVERT: Af 46 GLU cc_start: 0.8349 (tp30) cc_final: 0.7934 (tp30) REVERT: Af 74 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8477 (mm-40) REVERT: Af 80 GLN cc_start: 0.8910 (mt0) cc_final: 0.8636 (mt0) REVERT: Af 86 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7866 (tm-30) REVERT: Af 92 GLU cc_start: 0.8551 (tt0) cc_final: 0.8165 (tm-30) REVERT: Af 97 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7831 (mm-30) REVERT: Af 103 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8129 (mmtm) REVERT: Af 107 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8470 (tm-30) REVERT: Ag 12 ARG cc_start: 0.9203 (mtp180) cc_final: 0.8879 (mtp180) REVERT: Ag 47 LEU cc_start: 0.9202 (tp) cc_final: 0.8919 (tp) REVERT: Ag 60 TYR cc_start: 0.8985 (t80) cc_final: 0.8545 (t80) REVERT: Ag 78 TYR cc_start: 0.6544 (m-80) cc_final: 0.6127 (m-80) REVERT: Aj 15 PHE cc_start: 0.7401 (m-10) cc_final: 0.6696 (m-10) REVERT: Aj 53 TRP cc_start: 0.6890 (OUTLIER) cc_final: 0.6362 (m100) outliers start: 101 outliers final: 86 residues processed: 694 average time/residue: 0.4083 time to fit residues: 463.5420 Evaluate side-chains 715 residues out of total 3319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 622 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 202 GLU Chi-restraints excluded: chain AA residue 304 LEU Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 381 THR 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 65 VAL 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 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 233 LEU 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 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 40 GLU Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 42 GLU Chi-restraints excluded: chain AG residue 44 GLU 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 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 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 214 THR Chi-restraints excluded: chain Aa residue 230 VAL 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 Aa residue 462 ILE Chi-restraints excluded: chain Ab residue 65 VAL 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 393 LEU Chi-restraints excluded: chain Ab residue 450 LEU Chi-restraints excluded: chain Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 137 GLN Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 271 GLU 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 227 LEU Chi-restraints excluded: chain Ad residue 242 ILE Chi-restraints excluded: chain Ae residue 191 GLU Chi-restraints excluded: chain Af residue 74 GLN Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 24 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 333 optimal weight: 0.7980 chunk 304 optimal weight: 0.9990 chunk 285 optimal weight: 0.5980 chunk 60 optimal weight: 0.0030 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 309 HIS ** AE 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 87 ASN ** 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** ** Ae 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Ah 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107394 restraints weight = 56749.410| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.04 r_work: 0.3390 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.320 32661 Z= 0.135 Angle : 0.674 20.758 44296 Z= 0.316 Chirality : 0.042 0.327 4785 Planarity : 0.004 0.048 5608 Dihedral : 10.223 117.697 4795 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.80 % Allowed : 21.36 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3880 helix: 1.65 (0.11), residues: 2067 sheet: -0.39 (0.26), residues: 396 loop : 0.10 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPAc 141 HIS 0.007 0.001 HISAe 239 PHE 0.021 0.001 PHEAD 273 TYR 0.020 0.001 TYRAG 17 ARG 0.012 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 1787) hydrogen bonds : angle 4.53215 ( 5124) SS BOND : bond 0.00155 ( 7) SS BOND : angle 0.67302 ( 14) covalent geometry : bond 0.00319 (32648) covalent geometry : angle 0.67379 (44282) Misc. bond : bond 0.21553 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17587.30 seconds wall clock time: 305 minutes 17.50 seconds (18317.50 seconds total)