Starting phenix.real_space_refine on Thu Jun 26 07:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibg_35343/06_2025/8ibg_35343_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibg_35343/06_2025/8ibg_35343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibg_35343/06_2025/8ibg_35343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibg_35343/06_2025/8ibg_35343.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibg_35343/06_2025/8ibg_35343_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibg_35343/06_2025/8ibg_35343_neut.cif" } resolution = 3.8 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 8 5.49 5 S 151 5.16 5 C 19524 2.51 5 N 5165 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30396 Number of models: 1 Model: "" Number of chains: 28 Chain: "AA" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3077 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 15, 'TRANS': 379} Chain breaks: 2 Chain: "AB" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3137 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain: "AC" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "AD" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1878 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 22, 'TRANS': 213} Chain: "AE" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 830 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain breaks: 3 Chain: "AF" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 855 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "AG" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "AH" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "AI" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 200 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "AJ" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 165 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "AK" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 118 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "Aa" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3076 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain breaks: 3 Chain: "Ab" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3137 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain: "Ac" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "Ad" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1903 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "Ae" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1451 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Chain: "Af" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "Ag" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 622 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 6, 'TRANS': 67} Chain: "Ah" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 512 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 1 Chain: "Ai" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 204 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "Aj" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 345 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Ak" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "AC" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UQ6:plan-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-5': 1} Unresolved non-hydrogen planarities: 15 Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "Ac" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PE': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'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: "Ag" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 115 Time building chain proxies: 18.83, per 1000 atoms: 0.62 Number of scatterers: 30396 At special positions: 0 Unit cell: (145.2, 144.1, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 151 16.00 P 8 15.00 O 5542 8.00 N 5165 7.00 C 19524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYSAA 338 " - pdb=" SG CYSAA 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 222 " - pdb=" SG CYSAE 238 " distance=2.05 Simple disulfide: pdb=" SG CYSAH 51 " - pdb=" SG CYSAH 65 " distance=2.02 Simple disulfide: pdb=" SG CYSAa 338 " - pdb=" SG CYSAa 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAe 222 " - pdb=" SG CYSAe 238 " distance=2.05 Simple disulfide: pdb=" SG CYSAh 35 " - pdb=" SG CYSAh 79 " distance=1.85 Simple disulfide: pdb=" SG CYSAh 51 " - pdb=" SG CYSAh 65 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 3.8 seconds 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7060 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 14 sheets defined 58.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'AA' and resid 78 through 82 Processing helix chain 'AA' and resid 88 through 97 Processing helix chain 'AA' and resid 107 through 116 Processing helix chain 'AA' and resid 139 through 152 removed outlier: 3.566A pdb=" N GLUAA 145 " --> pdb=" O PROAA 141 " (cutoff:3.500A) Processing helix chain 'AA' and resid 157 through 176 removed outlier: 3.716A pdb=" N ASPAA 176 " --> pdb=" O METAA 172 " (cutoff:3.500A) Processing helix chain 'AA' and resid 178 through 192 removed outlier: 3.811A pdb=" N ALAAA 189 " --> pdb=" O ASPAA 185 " (cutoff:3.500A) Processing helix chain 'AA' and resid 195 through 199 Processing helix chain 'AA' and resid 204 through 210 Processing helix chain 'AA' and resid 212 through 224 Processing helix chain 'AA' and resid 225 through 227 No H-bonds generated for 'chain 'AA' and resid 225 through 227' Processing helix chain 'AA' and resid 238 through 249 Processing helix chain 'AA' and resid 300 through 312 Processing helix chain 'AA' and resid 361 through 363 No H-bonds generated for 'chain 'AA' and resid 361 through 363' Processing helix chain 'AA' and resid 364 through 380 Processing helix chain 'AA' and resid 384 through 397 Processing helix chain 'AA' and resid 401 through 404 Processing helix chain 'AA' and resid 405 through 419 Processing helix chain 'AA' and resid 425 through 435 Processing helix chain 'AA' and resid 437 through 449 Processing helix chain 'AA' and resid 467 through 473 Processing helix chain 'AB' and resid 68 through 72 removed outlier: 3.542A pdb=" N GLUAB 72 " --> pdb=" O SERAB 69 " (cutoff:3.500A) Processing helix chain 'AB' and resid 78 through 86 Processing helix chain 'AB' and resid 95 through 106 removed outlier: 3.663A pdb=" N VALAB 106 " --> pdb=" O GLYAB 102 " (cutoff:3.500A) Processing helix chain 'AB' and resid 129 through 143 Processing helix chain 'AB' and resid 147 through 166 removed outlier: 4.714A pdb=" N SERAB 156 " --> pdb=" O ALAAB 152 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLNAB 157 " --> pdb=" O ALAAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 168 through 182 removed outlier: 3.931A pdb=" N ARGAB 172 " --> pdb=" O ASNAB 168 " (cutoff:3.500A) Processing helix chain 'AB' and resid 201 through 213 Processing helix chain 'AB' and resid 214 through 216 No H-bonds generated for 'chain 'AB' and resid 214 through 216' Processing helix chain 'AB' and resid 226 through 237 removed outlier: 3.596A pdb=" N LEUAB 230 " --> pdb=" O SERAB 226 " (cutoff:3.500A) Processing helix chain 'AB' and resid 280 through 293 removed outlier: 3.829A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 307 through 317 removed outlier: 3.563A pdb=" N ALAAB 314 " --> pdb=" O SERAB 310 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYSAB 315 " --> pdb=" O GLNAB 311 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLYAB 316 " --> pdb=" O SERAB 312 " (cutoff:3.500A) Processing helix chain 'AB' and resid 346 through 363 Processing helix chain 'AB' and resid 367 through 387 Processing helix chain 'AB' and resid 388 through 404 Processing helix chain 'AB' and resid 408 through 419 Processing helix chain 'AB' and resid 420 through 434 Processing helix chain 'AC' and resid 10 through 19 removed outlier: 3.607A pdb=" N ILEAC 14 " --> pdb=" O LEUAC 10 " (cutoff:3.500A) Processing helix chain 'AC' and resid 29 through 31 No H-bonds generated for 'chain 'AC' and resid 29 through 31' Processing helix chain 'AC' and resid 32 through 53 Processing helix chain 'AC' and resid 61 through 72 Processing helix chain 'AC' and resid 75 through 104 Processing helix chain 'AC' and resid 105 through 108 removed outlier: 3.577A pdb=" N THRAC 108 " --> pdb=" O GLYAC 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 105 through 108' Processing helix chain 'AC' and resid 109 through 133 Processing helix chain 'AC' and resid 136 through 152 removed outlier: 3.508A pdb=" N LEUAC 150 " --> pdb=" O ILEAC 146 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SERAC 151 " --> pdb=" O THRAC 147 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALAAC 152 " --> pdb=" O ASNAC 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 156 through 166 Processing helix chain 'AC' and resid 171 through 202 removed outlier: 3.552A pdb=" N ARGAC 177 " --> pdb=" O ALAAC 173 " (cutoff:3.500A) Proline residue: AC 186 - end of helix Processing helix chain 'AC' and resid 212 through 215 removed outlier: 4.576A pdb=" N ALAAC 215 " --> pdb=" O ASNAC 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 212 through 215' Processing helix chain 'AC' and resid 224 through 244 Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 284 removed outlier: 4.428A pdb=" N PHEAC 276 " --> pdb=" O TRPAC 272 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALAAC 277 " --> pdb=" O TYRAC 273 " (cutoff:3.500A) Processing helix chain 'AC' and resid 286 through 304 removed outlier: 3.506A pdb=" N ILEAC 298 " --> pdb=" O LEUAC 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAC 301 " --> pdb=" O SERAC 297 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALAAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 305 through 308 removed outlier: 3.963A pdb=" N HISAC 308 " --> pdb=" O PROAC 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 305 through 308' Processing helix chain 'AC' and resid 318 through 341 removed outlier: 3.759A pdb=" N GLYAC 340 " --> pdb=" O THRAC 336 " (cutoff:3.500A) Processing helix chain 'AC' and resid 346 through 364 Processing helix chain 'AC' and resid 364 through 377 Processing helix chain 'AD' and resid 106 through 120 Processing helix chain 'AD' and resid 121 through 124 Processing helix chain 'AD' and resid 131 through 136 Processing helix chain 'AD' and resid 141 through 151 Processing helix chain 'AD' and resid 181 through 188 Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 206 through 216 Processing helix chain 'AD' and resid 262 through 279 Processing helix chain 'AD' and resid 281 through 317 Proline residue: AD 301 - end of helix removed outlier: 3.866A pdb=" N VALAD 313 " --> pdb=" O HISAD 309 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEUAD 314 " --> pdb=" O LYSAD 310 " (cutoff:3.500A) Processing helix chain 'AE' and resid 108 through 139 Processing helix chain 'AE' and resid 168 through 172 Processing helix chain 'AF' and resid 15 through 26 Processing helix chain 'AF' and resid 26 through 31 removed outlier: 3.501A pdb=" N LEUAF 30 " --> pdb=" O GLYAF 26 " (cutoff:3.500A) Processing helix chain 'AF' and resid 33 through 38 removed outlier: 3.668A pdb=" N THRAF 37 " --> pdb=" O METAF 33 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEUAF 38 " --> pdb=" O ARGAF 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 33 through 38' Processing helix chain 'AF' and resid 41 through 51 Processing helix chain 'AF' and resid 52 through 72 Processing helix chain 'AF' and resid 77 through 81 Processing helix chain 'AF' and resid 90 through 110 removed outlier: 4.160A pdb=" N TYRAF 94 " --> pdb=" O TYRAF 90 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLUAF 97 " --> pdb=" O PROAF 93 " (cutoff:3.500A) Processing helix chain 'AG' and resid 33 through 72 removed outlier: 3.985A pdb=" N ASNAG 37 " --> pdb=" O LYSAG 33 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARGAG 48 " --> pdb=" O GLUAG 44 " (cutoff:3.500A) Proline residue: AG 51 - end of helix removed outlier: 3.535A pdb=" N LEUAG 58 " --> pdb=" O VALAG 54 " (cutoff:3.500A) Processing helix chain 'AH' and resid 26 through 38 Processing helix chain 'AH' and resid 38 through 58 removed outlier: 3.631A pdb=" N ARGAH 58 " --> pdb=" O ARGAH 54 " (cutoff:3.500A) Processing helix chain 'AH' and resid 65 through 84 Processing helix chain 'AJ' and resid 18 through 37 removed outlier: 3.843A pdb=" N ARGAJ 34 " --> pdb=" O LEUAJ 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 22 through 37 Processing helix chain 'Aa' and resid 78 through 82 Processing helix chain 'Aa' and resid 88 through 97 Processing helix chain 'Aa' and resid 107 through 117 Processing helix chain 'Aa' and resid 139 through 152 removed outlier: 3.535A pdb=" N GLUAa 145 " --> pdb=" O PROAa 141 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEUAa 147 " --> pdb=" O VALAa 143 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 161 through 176 removed outlier: 3.717A pdb=" N ASPAa 176 " --> pdb=" O METAa 172 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 178 through 187 Processing helix chain 'Aa' and resid 204 through 210 Processing helix chain 'Aa' and resid 212 through 224 Processing helix chain 'Aa' and resid 225 through 227 No H-bonds generated for 'chain 'Aa' and resid 225 through 227' Processing helix chain 'Aa' and resid 238 through 249 Processing helix chain 'Aa' and resid 300 through 312 Processing helix chain 'Aa' and resid 361 through 363 No H-bonds generated for 'chain 'Aa' and resid 361 through 363' Processing helix chain 'Aa' and resid 364 through 382 Processing helix chain 'Aa' and resid 384 through 397 Processing helix chain 'Aa' and resid 401 through 404 Processing helix chain 'Aa' and resid 405 through 419 Processing helix chain 'Aa' and resid 425 through 435 Processing helix chain 'Aa' and resid 437 through 449 Processing helix chain 'Aa' and resid 467 through 475 Processing helix chain 'Ab' and resid 68 through 72 Processing helix chain 'Ab' and resid 78 through 86 Processing helix chain 'Ab' and resid 95 through 107 Processing helix chain 'Ab' and resid 129 through 143 Processing helix chain 'Ab' and resid 147 through 165 removed outlier: 4.667A pdb=" N SERAb 156 " --> pdb=" O ALAAb 152 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLNAb 157 " --> pdb=" O ALAAb 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILEAb 160 " --> pdb=" O SERAb 156 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 168 through 182 removed outlier: 3.895A pdb=" N ARGAb 172 " --> pdb=" O ASNAb 168 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 201 through 213 Processing helix chain 'Ab' and resid 214 through 216 No H-bonds generated for 'chain 'Ab' and resid 214 through 216' Processing helix chain 'Ab' and resid 226 through 238 removed outlier: 5.188A pdb=" N GLNAb 236 " --> pdb=" O GLNAb 232 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHEAb 237 " --> pdb=" O VALAb 233 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 239 through 241 No H-bonds generated for 'chain 'Ab' and resid 239 through 241' Processing helix chain 'Ab' and resid 280 through 294 removed outlier: 3.829A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 307 through 315 Processing helix chain 'Ab' and resid 346 through 363 Processing helix chain 'Ab' and resid 367 through 387 Processing helix chain 'Ab' and resid 388 through 404 Processing helix chain 'Ab' and resid 408 through 419 Processing helix chain 'Ab' and resid 420 through 434 Processing helix chain 'Ac' and resid 10 through 19 removed outlier: 3.609A pdb=" N ILEAc 14 " --> pdb=" O LEUAc 10 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 28 through 31 Processing helix chain 'Ac' and resid 32 through 53 Processing helix chain 'Ac' and resid 61 through 72 Processing helix chain 'Ac' and resid 75 through 104 Processing helix chain 'Ac' and resid 105 through 108 removed outlier: 3.578A pdb=" N THRAc 108 " --> pdb=" O GLYAc 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 105 through 108' Processing helix chain 'Ac' and resid 109 through 133 Processing helix chain 'Ac' and resid 136 through 152 removed outlier: 3.508A pdb=" N LEUAc 150 " --> pdb=" O ILEAc 146 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALAAc 152 " --> pdb=" O ASNAc 148 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 166 Processing helix chain 'Ac' and resid 171 through 202 removed outlier: 3.550A pdb=" N ARGAc 177 " --> pdb=" O ALAAc 173 " (cutoff:3.500A) Proline residue: Ac 186 - end of helix Processing helix chain 'Ac' and resid 212 through 215 removed outlier: 4.575A pdb=" N ALAAc 215 " --> pdb=" O ASNAc 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 212 through 215' Processing helix chain 'Ac' and resid 224 through 244 Processing helix chain 'Ac' and resid 252 through 257 Processing helix chain 'Ac' and resid 271 through 273 No H-bonds generated for 'chain 'Ac' and resid 271 through 273' Processing helix chain 'Ac' and resid 274 through 284 removed outlier: 3.502A pdb=" N TYRAc 278 " --> pdb=" O PHEAc 274 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 286 through 304 removed outlier: 3.505A pdb=" N ILEAc 298 " --> pdb=" O LEUAc 294 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 307 No H-bonds generated for 'chain 'Ac' and resid 305 through 307' Processing helix chain 'Ac' and resid 318 through 341 removed outlier: 3.760A pdb=" N GLYAc 340 " --> pdb=" O THRAc 336 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 346 through 364 Processing helix chain 'Ac' and resid 364 through 378 Processing helix chain 'Ad' and resid 106 through 120 Processing helix chain 'Ad' and resid 121 through 124 Processing helix chain 'Ad' and resid 131 through 136 Processing helix chain 'Ad' and resid 141 through 152 Processing helix chain 'Ad' and resid 181 through 189 removed outlier: 3.568A pdb=" N ARGAd 186 " --> pdb=" O PROAd 182 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 199 through 204 Processing helix chain 'Ad' and resid 206 through 217 Processing helix chain 'Ad' and resid 237 through 241 removed outlier: 3.623A pdb=" N ALAAd 241 " --> pdb=" O PROAd 238 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 262 through 279 Processing helix chain 'Ad' and resid 281 through 313 Proline residue: Ad 301 - end of helix removed outlier: 4.503A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 314 through 316 No H-bonds generated for 'chain 'Ad' and resid 314 through 316' Processing helix chain 'Ae' and resid 104 through 140 removed outlier: 4.376A pdb=" N ALAAe 109 " --> pdb=" O GLUAe 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N METAe 140 " --> pdb=" O PHEAe 136 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 149 Processing helix chain 'Ae' and resid 155 through 159 removed outlier: 3.513A pdb=" N ASPAe 158 " --> pdb=" O LYSAe 155 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILEAe 159 " --> pdb=" O LEUAe 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 155 through 159' Processing helix chain 'Ae' and resid 180 through 190 Processing helix chain 'Ae' and resid 200 through 205 Processing helix chain 'Af' and resid 15 through 26 removed outlier: 3.721A pdb=" N GLYAf 26 " --> pdb=" O TYRAf 22 " (cutoff:3.500A) Processing helix chain 'Af' and resid 34 through 38 removed outlier: 3.686A pdb=" N LEUAf 38 " --> pdb=" O ASPAf 35 " (cutoff:3.500A) Processing helix chain 'Af' and resid 41 through 50 Processing helix chain 'Af' and resid 52 through 72 Processing helix chain 'Af' and resid 77 through 81 Processing helix chain 'Af' and resid 90 through 111 removed outlier: 4.178A pdb=" N TYRAf 94 " --> pdb=" O TYRAf 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUAf 97 " --> pdb=" O PROAf 93 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 21 through 24 Processing helix chain 'Ag' and resid 29 through 72 removed outlier: 3.851A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 4.959A pdb=" N LEUAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARGAg 48 " --> pdb=" O GLUAg 44 " (cutoff:3.500A) Proline residue: Ag 51 - end of helix Processing helix chain 'Ah' and resid 26 through 37 removed outlier: 3.526A pdb=" N THRAh 30 " --> pdb=" O ASPAh 26 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLUAh 33 " --> pdb=" O THRAh 29 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 38 through 54 Processing helix chain 'Ah' and resid 64 through 84 removed outlier: 4.350A pdb=" N GLUAh 68 " --> pdb=" O ASPAh 64 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHEAh 70 " --> pdb=" O THRAh 66 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHEAh 72 " --> pdb=" O GLUAh 68 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALAAh 75 " --> pdb=" O ASPAh 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYSAh 83 " --> pdb=" O CYSAh 79 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 9 through 15 Processing helix chain 'Aj' and resid 17 through 48 removed outlier: 4.276A pdb=" N ARGAj 34 " --> pdb=" O LEUAj 30 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 37 Proline residue: Ak 19 - end of helix Processing sheet with id=AA1, first strand: chain 'AA' and resid 49 through 52 removed outlier: 3.536A pdb=" N SERAA 51 " --> pdb=" O VALAA 59 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARGAA 58 " --> pdb=" O LEUAA 231 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALAAA 233 " --> pdb=" O ARGAA 58 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALAAA 60 " --> pdb=" O ALAAA 233 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLYAA 235 " --> pdb=" O ALAAA 60 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLUAA 62 " --> pdb=" O GLYAA 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 342 through 348 removed outlier: 3.546A pdb=" N ARGAA 276 " --> pdb=" O SERAG 16 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SERAG 16 " --> pdb=" O ARGAA 276 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARGAA 278 " --> pdb=" O VALAG 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 39 through 42 removed outlier: 6.529A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARGAI 77 " --> pdb=" O VALAI 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.737A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLYAB 442 " --> pdb=" O ILEAB 258 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLUAB 260 " --> pdb=" O GLYAB 442 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLYAB 334 " --> pdb=" O SERAB 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AC' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'AE' and resid 163 through 165 Processing sheet with id=AA7, first strand: chain 'AE' and resid 225 through 226 removed outlier: 6.660A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Aa' and resid 50 through 52 removed outlier: 6.418A pdb=" N ARGAa 58 " --> pdb=" O LEUAa 231 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALAAa 233 " --> pdb=" O ARGAa 58 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALAAa 60 " --> pdb=" O ALAAa 233 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLYAa 235 " --> pdb=" O ALAAa 60 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLUAa 62 " --> pdb=" O GLYAa 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Aa' and resid 342 through 348 Processing sheet with id=AB1, first strand: chain 'Ab' and resid 41 through 42 removed outlier: 6.311A pdb=" N VALAb 48 " --> pdb=" O LEUAb 220 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLYAb 222 " --> pdb=" O VALAb 48 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALAAb 50 " --> pdb=" O GLYAb 222 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VALAi 68 " --> pdb=" O VALAb 112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARGAi 77 " --> pdb=" O VALAi 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Ab' and resid 256 through 261 removed outlier: 6.893A pdb=" N GLYAb 256 " --> pdb=" O METAb 438 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ALAAb 440 " --> pdb=" O GLYAb 256 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILEAb 258 " --> pdb=" O ALAAb 440 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLYAb 442 " --> pdb=" O ILEAb 258 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLUAb 260 " --> pdb=" O GLYAb 442 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ac' and resid 23 through 24 Processing sheet with id=AB4, first strand: chain 'Ae' and resid 174 through 175 Processing sheet with id=AB5, first strand: chain 'Ae' and resid 225 through 226 1735 hydrogen bonds defined for protein. 4980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.00 Time building geometry restraints manager: 9.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 10061 1.37 - 1.55: 20761 1.55 - 1.74: 39 1.74 - 1.93: 255 1.93 - 2.11: 21 Bond restraints: 31137 Sorted by residual: bond pdb=" C ASPAI 44 " pdb=" N VALAI 45 " ideal model delta sigma weight residual 1.332 1.517 -0.186 9.20e-03 1.18e+04 4.07e+02 bond pdb=" C ASPAi 44 " pdb=" N VALAi 45 " ideal model delta sigma weight residual 1.332 1.516 -0.184 9.20e-03 1.18e+04 3.99e+02 bond pdb=" N PROAd 221 " pdb=" CD PROAd 221 " ideal model delta sigma weight residual 1.473 1.732 -0.259 1.40e-02 5.10e+03 3.43e+02 bond pdb=" C VALAi 45 " pdb=" N LYSAi 46 " ideal model delta sigma weight residual 1.331 1.533 -0.203 1.29e-02 6.01e+03 2.47e+02 bond pdb=" C VALAI 45 " pdb=" N LYSAI 46 " ideal model delta sigma weight residual 1.329 1.532 -0.203 1.40e-02 5.10e+03 2.10e+02 ... (remaining 31132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 40667 3.21 - 6.43: 1315 6.43 - 9.64: 225 9.64 - 12.85: 36 12.85 - 16.07: 9 Bond angle restraints: 42252 Sorted by residual: angle pdb=" CA ASPAI 44 " pdb=" C ASPAI 44 " pdb=" N VALAI 45 " ideal model delta sigma weight residual 119.52 106.97 12.55 7.90e-01 1.60e+00 2.52e+02 angle pdb=" N ILEAC 115 " pdb=" CA ILEAC 115 " pdb=" C ILEAC 115 " ideal model delta sigma weight residual 110.62 99.16 11.46 1.02e+00 9.61e-01 1.26e+02 angle pdb=" N TRPAk 38 " pdb=" CA TRPAk 38 " pdb=" C TRPAk 38 " ideal model delta sigma weight residual 110.24 126.05 -15.81 1.47e+00 4.63e-01 1.16e+02 angle pdb=" N ASNAb 303 " pdb=" CA ASNAb 303 " pdb=" C ASNAb 303 " ideal model delta sigma weight residual 112.88 100.17 12.71 1.29e+00 6.01e-01 9.71e+01 angle pdb=" N THRAb 306 " pdb=" CA THRAb 306 " pdb=" C THRAb 306 " ideal model delta sigma weight residual 111.33 123.22 -11.89 1.21e+00 6.83e-01 9.66e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.30: 18092 31.30 - 62.60: 314 62.60 - 93.90: 57 93.90 - 125.21: 2 125.21 - 156.51: 4 Dihedral angle restraints: 18469 sinusoidal: 7501 harmonic: 10968 Sorted by residual: dihedral pdb=" CB CYSAh 35 " pdb=" SG CYSAh 35 " pdb=" SG CYSAh 79 " pdb=" CB CYSAh 79 " ideal model delta sinusoidal sigma weight residual 93.00 176.19 -83.19 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYSAH 51 " pdb=" SG CYSAH 51 " pdb=" SG CYSAH 65 " pdb=" CB CYSAH 65 " ideal model delta sinusoidal sigma weight residual 93.00 154.47 -61.47 1 1.00e+01 1.00e-02 5.02e+01 dihedral pdb=" C11 U10Ac 404 " pdb=" C12 U10Ac 404 " pdb=" C13 U10Ac 404 " pdb=" C14 U10Ac 404 " ideal model delta sinusoidal sigma weight residual 126.68 -76.81 -156.51 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 18466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 4341 0.119 - 0.238: 217 0.238 - 0.358: 28 0.358 - 0.477: 3 0.477 - 0.596: 1 Chirality restraints: 4590 Sorted by residual: chirality pdb=" CA ARGAk 39 " pdb=" N ARGAk 39 " pdb=" C ARGAk 39 " pdb=" CB ARGAk 39 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA GLUAa 47 " pdb=" N GLUAa 47 " pdb=" C GLUAa 47 " pdb=" CB GLUAa 47 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CA HISAe 200 " pdb=" N HISAe 200 " pdb=" C HISAe 200 " pdb=" CB HISAe 200 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 4587 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10Ac 404 " -0.096 2.00e-02 2.50e+03 8.37e-02 1.23e+02 pdb=" C1M U10Ac 404 " 0.100 2.00e-02 2.50e+03 pdb=" C2 U10Ac 404 " -0.103 2.00e-02 2.50e+03 pdb=" C3 U10Ac 404 " 0.050 2.00e-02 2.50e+03 pdb=" C4 U10Ac 404 " 0.092 2.00e-02 2.50e+03 pdb=" C5 U10Ac 404 " -0.082 2.00e-02 2.50e+03 pdb=" C6 U10Ac 404 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HECAd 401 " -0.020 2.00e-02 2.50e+03 5.84e-02 7.68e+01 pdb=" C2C HECAd 401 " 0.160 2.00e-02 2.50e+03 pdb=" C3C HECAd 401 " -0.023 2.00e-02 2.50e+03 pdb=" C4C HECAd 401 " -0.002 2.00e-02 2.50e+03 pdb=" CAC HECAd 401 " -0.032 2.00e-02 2.50e+03 pdb=" CHC HECAd 401 " -0.030 2.00e-02 2.50e+03 pdb=" CHD HECAd 401 " 0.003 2.00e-02 2.50e+03 pdb=" CMC HECAd 401 " -0.047 2.00e-02 2.50e+03 pdb=" NC HECAd 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASPAI 44 " 0.022 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C ASPAI 44 " -0.081 2.00e-02 2.50e+03 pdb=" O ASPAI 44 " 0.034 2.00e-02 2.50e+03 pdb=" N VALAI 45 " 0.025 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 671 2.61 - 3.19: 31455 3.19 - 3.76: 51879 3.76 - 4.33: 73863 4.33 - 4.90: 112625 Nonbonded interactions: 270493 Sorted by model distance: nonbonded pdb=" OG1 THRAa 68 " pdb=" OE1 GLUAb 387 " model vdw 2.042 3.040 nonbonded pdb=" N LEUAa 120 " pdb=" O HISAb 298 " model vdw 2.043 3.120 nonbonded pdb=" NE2 HISAC 83 " pdb="FE HEMAC 401 " model vdw 2.062 3.080 nonbonded pdb=" O PROAC 266 " pdb=" CB PROAe 237 " model vdw 2.065 3.440 nonbonded pdb=" O METAE 140 " pdb=" NH2 ARGAc 177 " model vdw 2.069 3.120 ... (remaining 270488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 45 through 156 or resid 160 through 253 or resid 267 thro \ ugh 476)) selection = (chain 'Aa' and resid 45 through 476) } ncs_group { reference = chain 'AB' selection = chain 'Ab' } ncs_group { reference = (chain 'AC' and (resid 8 through 380 or resid 401 through 402)) selection = (chain 'Ac' and (resid 8 through 380 or resid 401 through 402)) } ncs_group { reference = chain 'AD' selection = (chain 'Ad' and (resid 89 through 324 or resid 401)) } ncs_group { reference = chain 'AF' selection = (chain 'Af' and resid 14 through 110) } ncs_group { reference = (chain 'AG' and resid 4 through 77) selection = (chain 'Ag' and resid 4 through 77) } ncs_group { reference = (chain 'AH' and (resid 25 through 56 or resid 61 through 88)) selection = (chain 'Ah' and resid 25 through 88) } ncs_group { reference = (chain 'AI' and resid 42 through 78) selection = (chain 'Ai' and (resid 42 through 46 or resid 57 through 78)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 64.840 Find NCS groups from input model: 1.550 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.288 31150 Z= 0.674 Angle : 1.375 46.163 42266 Z= 0.900 Chirality : 0.061 0.596 4590 Planarity : 0.007 0.084 5364 Dihedral : 13.100 156.508 11388 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 41.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 96.00 % Rotamer: Outliers : 0.41 % Allowed : 2.82 % Favored : 96.77 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.01 (0.12), residues: 3721 helix: -1.09 (0.10), residues: 1960 sheet: -0.59 (0.27), residues: 362 loop : -1.70 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPAC 141 HIS 0.015 0.001 HISAe 200 PHE 0.049 0.002 PHEAc 183 TYR 0.049 0.002 TYRAE 235 ARG 0.008 0.001 ARGAE 250 Details of bonding type rmsd hydrogen bonds : bond 0.20000 ( 1735) hydrogen bonds : angle 7.90660 ( 4980) SS BOND : bond 0.07077 ( 7) SS BOND : angle 13.96925 ( 14) covalent geometry : bond 0.00994 (31137) covalent geometry : angle 1.35186 (42252) Misc. bond : bond 0.15350 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1312 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 249 HIS cc_start: 0.6522 (m170) cc_final: 0.5884 (m170) REVERT: AA 358 PHE cc_start: 0.9001 (p90) cc_final: 0.8668 (p90) REVERT: AA 440 MET cc_start: 0.7721 (ptp) cc_final: 0.7431 (ptp) REVERT: AB 69 SER cc_start: 0.7927 (p) cc_final: 0.7700 (t) REVERT: AB 172 ARG cc_start: 0.8185 (mtm-85) cc_final: 0.7684 (ttm-80) REVERT: AB 231 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8419 (mtpt) REVERT: AB 309 LEU cc_start: 0.7562 (mt) cc_final: 0.7250 (mt) REVERT: AB 438 MET cc_start: 0.8679 (ttt) cc_final: 0.8403 (ttt) REVERT: AC 35 SER cc_start: 0.8194 (p) cc_final: 0.7857 (p) REVERT: AC 121 PHE cc_start: 0.7608 (m-80) cc_final: 0.7350 (m-80) REVERT: AC 240 MET cc_start: 0.8212 (mmm) cc_final: 0.7899 (mmt) REVERT: AC 294 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7934 (tt) REVERT: AC 347 PHE cc_start: 0.7321 (m-80) cc_final: 0.6975 (m-10) REVERT: AF 43 ASP cc_start: 0.8526 (m-30) cc_final: 0.8301 (m-30) REVERT: AF 89 PHE cc_start: 0.7849 (m-10) cc_final: 0.7310 (m-80) REVERT: AG 40 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7826 (tmm160) REVERT: AG 60 TYR cc_start: 0.7824 (t80) cc_final: 0.7585 (t80) REVERT: AG 64 ASN cc_start: 0.8067 (m-40) cc_final: 0.7754 (m-40) REVERT: AH 42 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.6923 (t) REVERT: AH 61 THR cc_start: 0.4609 (t) cc_final: 0.4291 (t) REVERT: AH 86 LYS cc_start: 0.7792 (pttp) cc_final: 0.7380 (mtmm) REVERT: AI 67 THR cc_start: 0.8744 (m) cc_final: 0.8420 (t) REVERT: Aa 449 PHE cc_start: 0.8398 (m-80) cc_final: 0.8071 (m-80) REVERT: Aa 475 MET cc_start: 0.7436 (mmm) cc_final: 0.7001 (tpp) REVERT: Aa 477 TRP cc_start: 0.6875 (m-10) cc_final: 0.6105 (t60) REVERT: Ab 170 GLN cc_start: 0.8114 (mp10) cc_final: 0.7844 (mp10) REVERT: Ab 213 PHE cc_start: 0.7977 (t80) cc_final: 0.7744 (t80) REVERT: Ac 20 ASP cc_start: 0.7927 (m-30) cc_final: 0.7655 (m-30) REVERT: Ac 94 LEU cc_start: 0.8684 (tp) cc_final: 0.8292 (tt) REVERT: Ac 138 MET cc_start: 0.5224 (tpt) cc_final: 0.4755 (mmm) REVERT: Ac 212 ASN cc_start: 0.6851 (t0) cc_final: 0.6338 (t0) REVERT: Ac 223 TYR cc_start: 0.7542 (m-80) cc_final: 0.7287 (m-80) REVERT: Ac 256 TYR cc_start: 0.6740 (m-80) cc_final: 0.6493 (m-80) REVERT: Ac 265 PRO cc_start: 0.7753 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: Ac 333 LEU cc_start: 0.9014 (mt) cc_final: 0.8773 (tt) REVERT: Ac 376 MET cc_start: 0.8706 (mmm) cc_final: 0.8389 (mmm) REVERT: Ad 134 HIS cc_start: 0.5769 (m170) cc_final: 0.5546 (m-70) REVERT: Ad 288 MET cc_start: 0.8070 (mmt) cc_final: 0.7524 (mmt) REVERT: Ae 91 TYR cc_start: 0.7128 (m-80) cc_final: 0.6758 (m-80) REVERT: Ae 182 LYS cc_start: 0.6216 (tttt) cc_final: 0.5882 (mtmm) REVERT: Ae 244 ASP cc_start: 0.2798 (p0) cc_final: 0.1749 (t70) REVERT: Ae 248 ARG cc_start: 0.3593 (mtm180) cc_final: 0.3339 (ptp90) REVERT: Af 69 LEU cc_start: 0.9146 (mt) cc_final: 0.8879 (mt) REVERT: Af 74 GLN cc_start: 0.8567 (mm110) cc_final: 0.7969 (mm-40) outliers start: 13 outliers final: 5 residues processed: 1319 average time/residue: 0.4874 time to fit residues: 981.7777 Evaluate side-chains 748 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 741 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 294 LEU Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain Ab residue 168 ASN Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 252 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 chunk 286 optimal weight: 0.0010 chunk 111 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 103 ASN AA 173 GLN AA 249 HIS ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 397 ASN AB 167 GLN AB 210 GLN ** AB 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN AD 240 GLN AD 282 HIS ** AD 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 80 HIS AE 135 GLN ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 227 ASN AE 242 HIS AF 23 ASN AF 80 GLN AH 74 HIS Aa 49 GLN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 128 HIS Aa 240 GLN ** Aa 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 397 ASN Aa 402 HIS Ab 118 ASN ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 211 ASN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 261 GLN ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN Ab 415 GLN Ac 44 GLN Ac 267 HIS Ac 308 HIS ** Ac 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 309 HIS ** Ae 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 74 GLN Ag 37 ASN Ah 34 HIS Ah 87 ASN Ak 16 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100410 restraints weight = 73149.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102028 restraints weight = 42402.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103624 restraints weight = 29884.237| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.703 31150 Z= 0.227 Angle : 0.771 14.540 42266 Z= 0.391 Chirality : 0.046 0.236 4590 Planarity : 0.006 0.107 5364 Dihedral : 10.684 136.288 4415 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.08 % Allowed : 16.01 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: -0.01 (0.14), residues: 3721 helix: 0.62 (0.11), residues: 1994 sheet: -0.22 (0.27), residues: 366 loop : -0.76 (0.17), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPAC 165 HIS 0.011 0.002 HISAE 219 PHE 0.034 0.002 PHEAC 95 TYR 0.024 0.002 TYRAD 255 ARG 0.007 0.001 ARGAa 104 Details of bonding type rmsd hydrogen bonds : bond 0.05371 ( 1735) hydrogen bonds : angle 5.47404 ( 4980) SS BOND : bond 0.00958 ( 7) SS BOND : angle 3.08332 ( 14) covalent geometry : bond 0.00516 (31137) covalent geometry : angle 0.76907 (42252) Misc. bond : bond 0.44159 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 819 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 120 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8791 (tt) REVERT: AA 134 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8491 (mtpp) REVERT: AA 142 LYS cc_start: 0.9344 (tppt) cc_final: 0.9075 (tttt) REVERT: AA 229 MET cc_start: 0.8712 (mtp) cc_final: 0.8371 (mtp) REVERT: AA 353 LEU cc_start: 0.8372 (mt) cc_final: 0.8107 (mt) REVERT: AA 358 PHE cc_start: 0.9047 (p90) cc_final: 0.8553 (p90) REVERT: AA 411 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8165 (tm-30) REVERT: AA 440 MET cc_start: 0.8517 (ptp) cc_final: 0.8180 (ptp) REVERT: AA 463 GLU cc_start: 0.7278 (tt0) cc_final: 0.7029 (tt0) REVERT: AB 69 SER cc_start: 0.8535 (p) cc_final: 0.8328 (t) REVERT: AB 77 LEU cc_start: 0.9406 (mt) cc_final: 0.9137 (mp) REVERT: AB 271 ILE cc_start: 0.8543 (mt) cc_final: 0.8152 (pt) REVERT: AB 407 MET cc_start: 0.8224 (mpp) cc_final: 0.7936 (mpp) REVERT: AC 82 MET cc_start: 0.8362 (tpp) cc_final: 0.8153 (tpp) REVERT: AC 95 PHE cc_start: 0.7272 (m-80) cc_final: 0.6997 (m-80) REVERT: AC 216 ASP cc_start: 0.8625 (t0) cc_final: 0.8230 (t0) REVERT: AC 223 TYR cc_start: 0.8244 (m-80) cc_final: 0.7613 (m-80) REVERT: AC 376 MET cc_start: 0.8719 (mmm) cc_final: 0.8518 (tpp) REVERT: AD 134 HIS cc_start: 0.5943 (m90) cc_final: 0.5649 (m90) REVERT: AD 174 TYR cc_start: 0.7576 (m-80) cc_final: 0.7149 (m-80) REVERT: AD 244 MET cc_start: 0.7600 (tmm) cc_final: 0.7155 (tmm) REVERT: AE 82 ASP cc_start: 0.7551 (m-30) cc_final: 0.7210 (t0) REVERT: AE 87 ASP cc_start: 0.8378 (t0) cc_final: 0.8064 (t0) REVERT: AE 89 SER cc_start: 0.8395 (m) cc_final: 0.8142 (p) REVERT: AF 54 ASP cc_start: 0.8405 (m-30) cc_final: 0.8077 (m-30) REVERT: AF 57 ASN cc_start: 0.8258 (m110) cc_final: 0.7739 (p0) REVERT: AF 92 GLU cc_start: 0.8156 (tp30) cc_final: 0.7830 (tp30) REVERT: AF 103 LYS cc_start: 0.9291 (mtmm) cc_final: 0.8911 (mtmm) REVERT: AF 104 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8247 (mt-10) REVERT: AF 110 LYS cc_start: 0.6811 (mtmt) cc_final: 0.6567 (mtmt) REVERT: AG 60 TYR cc_start: 0.7832 (t80) cc_final: 0.7552 (t80) REVERT: AG 64 ASN cc_start: 0.8532 (m-40) cc_final: 0.7945 (m-40) REVERT: AH 86 LYS cc_start: 0.8864 (pttp) cc_final: 0.8199 (mtmm) REVERT: Aa 76 ASP cc_start: 0.7695 (t0) cc_final: 0.7468 (t0) REVERT: Aa 165 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8704 (ttm110) REVERT: Aa 209 ARG cc_start: 0.8486 (mtm180) cc_final: 0.7628 (mtm180) REVERT: Aa 274 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: Aa 392 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8311 (mtmm) REVERT: Aa 449 PHE cc_start: 0.8553 (m-80) cc_final: 0.8173 (m-80) REVERT: Aa 450 TYR cc_start: 0.8318 (t80) cc_final: 0.7292 (t80) REVERT: Ab 135 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7470 (tp30) REVERT: Ab 161 ASP cc_start: 0.8933 (t0) cc_final: 0.8486 (t0) REVERT: Ab 384 MET cc_start: 0.8028 (mtm) cc_final: 0.7645 (mtm) REVERT: Ac 20 ASP cc_start: 0.8406 (m-30) cc_final: 0.8066 (m-30) REVERT: Ac 89 MET cc_start: 0.8568 (tpp) cc_final: 0.8240 (tpp) REVERT: Ac 138 MET cc_start: 0.6504 (tpt) cc_final: 0.5420 (tpt) REVERT: Ac 200 LEU cc_start: 0.9310 (tp) cc_final: 0.9047 (tt) REVERT: Ac 212 ASN cc_start: 0.7899 (t0) cc_final: 0.7314 (t0) REVERT: Ac 214 ASP cc_start: 0.8650 (m-30) cc_final: 0.8385 (m-30) REVERT: Ac 216 ASP cc_start: 0.9097 (t0) cc_final: 0.8884 (t0) REVERT: Ac 256 TYR cc_start: 0.7748 (m-80) cc_final: 0.7301 (m-80) REVERT: Ac 265 PRO cc_start: 0.8654 (Cg_endo) cc_final: 0.8389 (Cg_exo) REVERT: Ac 272 TRP cc_start: 0.8825 (p-90) cc_final: 0.8026 (p-90) REVERT: Ac 273 TYR cc_start: 0.7993 (p90) cc_final: 0.7777 (p90) REVERT: Ac 369 SER cc_start: 0.9009 (p) cc_final: 0.8478 (t) REVERT: Ac 373 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7156 (mt-10) REVERT: Ad 102 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9041 (tt) REVERT: Ad 114 PHE cc_start: 0.9082 (t80) cc_final: 0.8769 (t80) REVERT: Ad 255 TYR cc_start: 0.8051 (m-80) cc_final: 0.7702 (m-80) REVERT: Ad 273 PHE cc_start: 0.9067 (t80) cc_final: 0.8586 (t80) REVERT: Ad 288 MET cc_start: 0.8320 (mmt) cc_final: 0.7831 (mmt) REVERT: Ad 292 MET cc_start: 0.8892 (tmm) cc_final: 0.8528 (tmm) REVERT: Ae 156 LEU cc_start: 0.5534 (tp) cc_final: 0.5200 (tp) REVERT: Ae 170 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7960 (tpt170) REVERT: Ae 244 ASP cc_start: 0.3159 (p0) cc_final: 0.2018 (t0) REVERT: Ae 248 ARG cc_start: 0.4277 (mtm180) cc_final: 0.3772 (ptp-170) REVERT: Af 33 MET cc_start: 0.8546 (mmm) cc_final: 0.8063 (mmm) REVERT: Af 60 MET cc_start: 0.8976 (tpp) cc_final: 0.8630 (tpp) REVERT: Af 83 LYS cc_start: 0.8572 (mptt) cc_final: 0.8267 (mptt) REVERT: Af 89 PHE cc_start: 0.7780 (m-10) cc_final: 0.7514 (m-10) REVERT: Ag 24 GLN cc_start: 0.8791 (pt0) cc_final: 0.8580 (pt0) REVERT: Ag 39 LEU cc_start: 0.8869 (tp) cc_final: 0.8657 (tp) REVERT: Ag 43 ARG cc_start: 0.7696 (ptm160) cc_final: 0.7293 (ttp80) REVERT: Ah 55 VAL cc_start: 0.6416 (t) cc_final: 0.6207 (t) REVERT: Ah 70 PHE cc_start: 0.8407 (m-80) cc_final: 0.7891 (m-80) REVERT: Ah 80 VAL cc_start: 0.8963 (t) cc_final: 0.8313 (t) REVERT: Ai 62 ARG cc_start: 0.5326 (mtt180) cc_final: 0.5047 (mtm180) REVERT: Ai 78 PHE cc_start: 0.6575 (m-80) cc_final: 0.6323 (m-80) REVERT: Ak 23 MET cc_start: 0.7587 (mmp) cc_final: 0.6594 (mtm) outliers start: 130 outliers final: 67 residues processed: 889 average time/residue: 0.4289 time to fit residues: 597.4658 Evaluate side-chains 735 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 665 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 143 VAL Chi-restraints excluded: chain AA residue 182 VAL Chi-restraints excluded: chain AA residue 190 THR Chi-restraints excluded: chain AA residue 208 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 306 VAL Chi-restraints excluded: chain AA residue 311 ILE Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AB residue 38 LEU Chi-restraints excluded: chain AB residue 48 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 161 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 211 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 41 THR Chi-restraints excluded: chain AF residue 75 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AG residue 38 VAL Chi-restraints excluded: chain AG residue 54 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 144 VAL Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 274 GLU Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 435 GLU Chi-restraints excluded: chain Ab residue 47 LEU Chi-restraints excluded: chain Ab residue 104 GLU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 129 ASP Chi-restraints excluded: chain Ab residue 272 VAL Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 102 LEU Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ae residue 122 THR Chi-restraints excluded: chain Ae residue 132 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 65 CYS Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ai residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 348 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 174 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 345 optimal weight: 0.7980 chunk 329 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 240 GLN AD 309 HIS ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 175 ASN Aa 207 ASN Aa 249 HIS ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN Ac 68 HIS Ac 267 HIS Ac 308 HIS Ac 345 HIS ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.128073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096477 restraints weight = 74166.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.099630 restraints weight = 39066.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101057 restraints weight = 24431.630| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.514 31150 Z= 0.198 Angle : 0.708 16.496 42266 Z= 0.354 Chirality : 0.044 0.192 4590 Planarity : 0.005 0.069 5364 Dihedral : 9.922 131.147 4406 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.58 % Allowed : 18.17 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.44 (0.14), residues: 3721 helix: 0.95 (0.11), residues: 2009 sheet: -0.24 (0.27), residues: 380 loop : -0.42 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPAD 96 HIS 0.006 0.001 HISAA 249 PHE 0.028 0.002 PHEAC 95 TYR 0.019 0.002 TYRAg 57 ARG 0.006 0.001 ARGAH 45 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 1735) hydrogen bonds : angle 5.10631 ( 4980) SS BOND : bond 0.00573 ( 7) SS BOND : angle 1.84901 ( 14) covalent geometry : bond 0.00458 (31137) covalent geometry : angle 0.70782 (42252) Misc. bond : bond 0.36147 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 713 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 91 TYR cc_start: 0.8657 (t80) cc_final: 0.8341 (t80) REVERT: AA 98 PHE cc_start: 0.8424 (m-10) cc_final: 0.8191 (m-80) REVERT: AA 134 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8412 (mtpp) REVERT: AA 149 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7303 (t0) REVERT: AA 250 LEU cc_start: 0.8938 (mt) cc_final: 0.8688 (tt) REVERT: AA 363 MET cc_start: 0.8978 (mmt) cc_final: 0.8766 (mmt) REVERT: AA 411 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8203 (tm-30) REVERT: AB 69 SER cc_start: 0.8696 (p) cc_final: 0.8369 (t) REVERT: AB 77 LEU cc_start: 0.9424 (mt) cc_final: 0.9169 (mp) REVERT: AB 172 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7581 (ttm110) REVERT: AB 203 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: AB 271 ILE cc_start: 0.8458 (mt) cc_final: 0.8074 (pt) REVERT: AB 370 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8770 (t70) REVERT: AC 31 TRP cc_start: 0.8257 (m-90) cc_final: 0.7477 (m-90) REVERT: AC 82 MET cc_start: 0.8456 (tpp) cc_final: 0.8173 (tpp) REVERT: AC 89 MET cc_start: 0.8540 (mmt) cc_final: 0.8203 (mtt) REVERT: AC 90 PHE cc_start: 0.8394 (t80) cc_final: 0.8131 (t80) REVERT: AC 91 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7722 (t80) REVERT: AC 95 PHE cc_start: 0.7486 (m-80) cc_final: 0.6408 (m-80) REVERT: AC 344 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7911 (tm-30) REVERT: AD 96 TRP cc_start: 0.7077 (m-90) cc_final: 0.6688 (m-90) REVERT: AD 134 HIS cc_start: 0.5989 (m90) cc_final: 0.5775 (m90) REVERT: AD 146 LYS cc_start: 0.9352 (ttpp) cc_final: 0.8875 (pttt) REVERT: AD 174 TYR cc_start: 0.7607 (m-80) cc_final: 0.7089 (m-80) REVERT: AD 181 ASN cc_start: 0.7603 (t0) cc_final: 0.7229 (t0) REVERT: AD 244 MET cc_start: 0.7650 (tmm) cc_final: 0.7356 (tmm) REVERT: AD 308 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7422 (ttt90) REVERT: AE 82 ASP cc_start: 0.7731 (m-30) cc_final: 0.7333 (t0) REVERT: AF 40 GLU cc_start: 0.8316 (mp0) cc_final: 0.8021 (mp0) REVERT: AF 42 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7916 (mm-30) REVERT: AF 45 LYS cc_start: 0.9451 (mtpp) cc_final: 0.9055 (mtpp) REVERT: AF 79 ASP cc_start: 0.8738 (p0) cc_final: 0.8424 (p0) REVERT: AF 85 GLU cc_start: 0.8331 (pm20) cc_final: 0.7357 (pm20) REVERT: AF 108 TRP cc_start: 0.8635 (t-100) cc_final: 0.8172 (t-100) REVERT: AF 110 LYS cc_start: 0.6744 (mtmt) cc_final: 0.6503 (mtmt) REVERT: AG 40 ARG cc_start: 0.8683 (tmm160) cc_final: 0.8180 (tmm160) REVERT: AG 60 TYR cc_start: 0.7880 (t80) cc_final: 0.7629 (t80) REVERT: AG 64 ASN cc_start: 0.8739 (m-40) cc_final: 0.8285 (m-40) REVERT: AG 65 GLN cc_start: 0.8339 (pp30) cc_final: 0.8082 (pp30) REVERT: AH 45 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7116 (mmt180) REVERT: Aa 63 GLN cc_start: 0.8444 (tt0) cc_final: 0.7918 (tp40) REVERT: Aa 76 ASP cc_start: 0.7704 (t0) cc_final: 0.7421 (t0) REVERT: Aa 79 SER cc_start: 0.9244 (OUTLIER) cc_final: 0.8268 (t) REVERT: Aa 81 TYR cc_start: 0.8851 (m-80) cc_final: 0.8517 (m-80) REVERT: Aa 165 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8893 (ttm110) REVERT: Aa 174 GLU cc_start: 0.8560 (mm-30) cc_final: 0.7212 (tm-30) REVERT: Aa 274 GLU cc_start: 0.8468 (tt0) cc_final: 0.8236 (tt0) REVERT: Aa 392 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8155 (mtmm) REVERT: Aa 449 PHE cc_start: 0.8487 (m-80) cc_final: 0.8210 (m-80) REVERT: Aa 450 TYR cc_start: 0.8368 (t80) cc_final: 0.7311 (t80) REVERT: Ab 104 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8404 (pp20) REVERT: Ab 309 LEU cc_start: 0.7566 (mt) cc_final: 0.7264 (mp) REVERT: Ab 311 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8519 (pp30) REVERT: Ab 407 MET cc_start: 0.8206 (mmp) cc_final: 0.7956 (tpp) REVERT: Ac 20 ASP cc_start: 0.8513 (m-30) cc_final: 0.8195 (m-30) REVERT: Ac 216 ASP cc_start: 0.9048 (t0) cc_final: 0.8787 (t0) REVERT: Ac 256 TYR cc_start: 0.7952 (m-80) cc_final: 0.7278 (m-80) REVERT: Ad 102 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9236 (tt) REVERT: Ad 106 ASP cc_start: 0.8085 (t0) cc_final: 0.7849 (t0) REVERT: Ad 273 PHE cc_start: 0.8986 (t80) cc_final: 0.8351 (t80) REVERT: Ad 288 MET cc_start: 0.8401 (mmt) cc_final: 0.7903 (mmt) REVERT: Ad 292 MET cc_start: 0.8986 (tmm) cc_final: 0.8540 (tmm) REVERT: Ae 93 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6843 (mtp85) REVERT: Ae 140 MET cc_start: 0.8674 (mtp) cc_final: 0.8233 (mmm) REVERT: Af 33 MET cc_start: 0.8604 (mmm) cc_final: 0.8164 (mmm) REVERT: Af 60 MET cc_start: 0.9181 (tpp) cc_final: 0.8720 (tpp) REVERT: Af 74 GLN cc_start: 0.8663 (mm110) cc_final: 0.8418 (mm110) REVERT: Af 83 LYS cc_start: 0.8538 (mptt) cc_final: 0.8226 (mptt) REVERT: Af 89 PHE cc_start: 0.7835 (m-10) cc_final: 0.7381 (m-10) REVERT: Ag 37 ASN cc_start: 0.8696 (m-40) cc_final: 0.8369 (t0) REVERT: Ag 39 LEU cc_start: 0.8959 (tp) cc_final: 0.8711 (tp) REVERT: Ag 43 ARG cc_start: 0.7728 (ptm160) cc_final: 0.7344 (ttp80) REVERT: Ah 70 PHE cc_start: 0.8347 (m-80) cc_final: 0.7874 (m-80) REVERT: Ai 67 THR cc_start: 0.8688 (m) cc_final: 0.8200 (p) REVERT: Ak 23 MET cc_start: 0.7570 (mmp) cc_final: 0.6713 (mtm) outliers start: 146 outliers final: 84 residues processed: 795 average time/residue: 0.4270 time to fit residues: 539.2348 Evaluate side-chains 724 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 630 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 149 ASP Chi-restraints excluded: chain AA residue 182 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 370 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 94 LEU Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AG residue 38 VAL Chi-restraints excluded: chain AH residue 45 ARG Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 52 ILE Chi-restraints excluded: chain Aa residue 75 ILE Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 104 GLU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 301 ARG Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 387 GLU Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ad residue 89 LEU Chi-restraints excluded: chain Ad residue 102 LEU Chi-restraints excluded: chain Ad residue 116 VAL Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 154 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 252 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ad residue 300 LEU Chi-restraints excluded: chain Ae residue 93 ARG Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 33 GLU Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 19 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 76 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 355 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 240 GLN ** AD 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 23 ASN ** AF 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 227 HIS Ab 311 GLN Ab 365 ASN Ac 267 HIS Ac 308 HIS ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.128998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098483 restraints weight = 74089.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099886 restraints weight = 42746.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101554 restraints weight = 32887.018| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.440 31150 Z= 0.154 Angle : 0.664 16.128 42266 Z= 0.326 Chirality : 0.043 0.329 4590 Planarity : 0.005 0.062 5364 Dihedral : 9.655 149.412 4406 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.30 % Allowed : 19.65 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.70 (0.14), residues: 3721 helix: 1.14 (0.12), residues: 1999 sheet: -0.23 (0.27), residues: 380 loop : -0.21 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPAk 38 HIS 0.006 0.001 HISAA 249 PHE 0.022 0.002 PHEAE 136 TYR 0.021 0.002 TYRAC 278 ARG 0.012 0.001 ARGAa 396 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1735) hydrogen bonds : angle 4.87957 ( 4980) SS BOND : bond 0.00449 ( 7) SS BOND : angle 1.43806 ( 14) covalent geometry : bond 0.00359 (31137) covalent geometry : angle 0.66344 (42252) Misc. bond : bond 0.29205 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 700 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 91 TYR cc_start: 0.8714 (t80) cc_final: 0.8474 (t80) REVERT: AB 69 SER cc_start: 0.8687 (p) cc_final: 0.8363 (t) REVERT: AB 77 LEU cc_start: 0.9380 (mt) cc_final: 0.9110 (mp) REVERT: AB 203 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: AB 271 ILE cc_start: 0.8481 (mt) cc_final: 0.8098 (pt) REVERT: AB 429 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8441 (ttmm) REVERT: AC 31 TRP cc_start: 0.8206 (m-90) cc_final: 0.7251 (m-90) REVERT: AC 58 ASP cc_start: 0.7615 (m-30) cc_final: 0.7113 (p0) REVERT: AC 69 ILE cc_start: 0.8547 (mm) cc_final: 0.8099 (mt) REVERT: AC 90 PHE cc_start: 0.8368 (t80) cc_final: 0.8091 (t80) REVERT: AC 91 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7825 (t80) REVERT: AC 95 PHE cc_start: 0.7623 (m-80) cc_final: 0.6495 (m-80) REVERT: AC 181 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: AC 274 PHE cc_start: 0.8197 (t80) cc_final: 0.7921 (t80) REVERT: AD 93 SER cc_start: 0.8581 (m) cc_final: 0.8105 (p) REVERT: AD 146 LYS cc_start: 0.9355 (ttpp) cc_final: 0.8976 (pttt) REVERT: AD 174 TYR cc_start: 0.7528 (m-80) cc_final: 0.7126 (m-80) REVERT: AD 181 ASN cc_start: 0.7661 (t0) cc_final: 0.7241 (t0) REVERT: AD 244 MET cc_start: 0.7472 (tmm) cc_final: 0.7200 (tmm) REVERT: AE 82 ASP cc_start: 0.7844 (m-30) cc_final: 0.7639 (t0) REVERT: AE 92 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6941 (ttm110) REVERT: AF 21 TYR cc_start: 0.8783 (t80) cc_final: 0.7614 (t80) REVERT: AF 42 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7889 (mm-30) REVERT: AF 45 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9041 (mtpp) REVERT: AF 79 ASP cc_start: 0.8676 (p0) cc_final: 0.8334 (p0) REVERT: AF 85 GLU cc_start: 0.8089 (pm20) cc_final: 0.7733 (pm20) REVERT: AG 57 TYR cc_start: 0.8359 (t80) cc_final: 0.8051 (t80) REVERT: AG 60 TYR cc_start: 0.7925 (t80) cc_final: 0.7642 (t80) REVERT: AG 64 ASN cc_start: 0.8721 (m-40) cc_final: 0.8252 (m-40) REVERT: Aa 76 ASP cc_start: 0.7574 (t0) cc_final: 0.7299 (t0) REVERT: Aa 79 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8128 (t) REVERT: Aa 81 TYR cc_start: 0.8811 (m-80) cc_final: 0.8365 (m-80) REVERT: Aa 174 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7406 (tm-30) REVERT: Aa 209 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8257 (mtm-85) REVERT: Aa 274 GLU cc_start: 0.8395 (tt0) cc_final: 0.8121 (tt0) REVERT: Aa 450 TYR cc_start: 0.8178 (t80) cc_final: 0.7239 (t80) REVERT: Aa 468 TYR cc_start: 0.8445 (t80) cc_final: 0.8193 (t80) REVERT: Ac 20 ASP cc_start: 0.8512 (m-30) cc_final: 0.8161 (m-30) REVERT: Ac 141 TRP cc_start: 0.7995 (m100) cc_final: 0.7304 (m100) REVERT: Ac 200 LEU cc_start: 0.9374 (tp) cc_final: 0.9124 (tt) REVERT: Ac 212 ASN cc_start: 0.8081 (t0) cc_final: 0.7486 (t0) REVERT: Ac 216 ASP cc_start: 0.9002 (t0) cc_final: 0.8580 (t0) REVERT: Ac 217 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8491 (mtmm) REVERT: Ac 282 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8402 (ptp90) REVERT: Ac 308 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.8002 (t-90) REVERT: Ad 102 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9275 (tt) REVERT: Ad 273 PHE cc_start: 0.8961 (t80) cc_final: 0.8325 (t80) REVERT: Ad 288 MET cc_start: 0.8347 (mmt) cc_final: 0.7775 (mmt) REVERT: Ad 306 MET cc_start: 0.8842 (ttp) cc_final: 0.8505 (ttt) REVERT: Ae 131 ASN cc_start: 0.6994 (t0) cc_final: 0.6550 (t0) REVERT: Ae 140 MET cc_start: 0.8515 (mtp) cc_final: 0.7937 (mtp) REVERT: Ae 156 LEU cc_start: 0.5152 (tp) cc_final: 0.4927 (tp) REVERT: Ae 244 ASP cc_start: 0.0946 (p0) cc_final: -0.0013 (t70) REVERT: Ae 248 ARG cc_start: 0.3426 (mtm180) cc_final: 0.2881 (ptt180) REVERT: Af 33 MET cc_start: 0.8568 (mmm) cc_final: 0.8075 (mtp) REVERT: Af 53 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7953 (tm-30) REVERT: Af 60 MET cc_start: 0.9143 (tpp) cc_final: 0.8693 (tpp) REVERT: Af 83 LYS cc_start: 0.8561 (mptt) cc_final: 0.8285 (mptt) REVERT: Af 89 PHE cc_start: 0.7992 (m-10) cc_final: 0.7696 (m-10) REVERT: Ag 37 ASN cc_start: 0.8574 (m-40) cc_final: 0.8240 (t0) REVERT: Ag 43 ARG cc_start: 0.7713 (ptm160) cc_final: 0.7326 (ttp80) REVERT: Ag 60 TYR cc_start: 0.9098 (t80) cc_final: 0.8848 (t80) REVERT: Ai 67 THR cc_start: 0.8668 (m) cc_final: 0.8204 (p) REVERT: Ak 23 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6794 (mtm) outliers start: 137 outliers final: 79 residues processed: 780 average time/residue: 0.4270 time to fit residues: 531.9941 Evaluate side-chains 718 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 630 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 109 LEU Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 266 VAL Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 75 ILE Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 308 HIS Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ad residue 102 LEU Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 23 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 101 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 119 HIS ** AA 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 167 GLN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 304 ASN Ab 311 GLN Ab 365 ASN Ac 16 HIS ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 90 HIS ** Af 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 34 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096908 restraints weight = 74399.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097710 restraints weight = 41626.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.099628 restraints weight = 30359.320| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.557 31150 Z= 0.216 Angle : 0.718 18.324 42266 Z= 0.349 Chirality : 0.044 0.210 4590 Planarity : 0.005 0.061 5364 Dihedral : 9.675 160.811 4406 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.87 % Allowed : 19.90 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.68 (0.14), residues: 3721 helix: 1.13 (0.12), residues: 1998 sheet: -0.19 (0.27), residues: 372 loop : -0.25 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPAk 38 HIS 0.031 0.001 HISAc 308 PHE 0.030 0.002 PHEAD 237 TYR 0.016 0.002 TYRAc 224 ARG 0.013 0.001 ARGAA 378 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 1735) hydrogen bonds : angle 4.93786 ( 4980) SS BOND : bond 0.00523 ( 7) SS BOND : angle 1.46978 ( 14) covalent geometry : bond 0.00498 (31137) covalent geometry : angle 0.71808 (42252) Misc. bond : bond 0.34585 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 651 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 98 PHE cc_start: 0.8322 (m-80) cc_final: 0.8020 (m-80) REVERT: AA 219 TYR cc_start: 0.8965 (t80) cc_final: 0.8752 (t80) REVERT: AA 467 ASP cc_start: 0.7586 (p0) cc_final: 0.7377 (p0) REVERT: AB 69 SER cc_start: 0.8816 (p) cc_final: 0.8464 (t) REVERT: AB 77 LEU cc_start: 0.9397 (mt) cc_final: 0.9127 (mp) REVERT: AB 203 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: AB 271 ILE cc_start: 0.8647 (mt) cc_final: 0.8329 (pt) REVERT: AB 429 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (ttmm) REVERT: AC 58 ASP cc_start: 0.7515 (m-30) cc_final: 0.7116 (p0) REVERT: AC 82 MET cc_start: 0.8782 (tpp) cc_final: 0.8427 (tpp) REVERT: AC 90 PHE cc_start: 0.8458 (t80) cc_final: 0.8184 (t80) REVERT: AC 91 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7845 (t80) REVERT: AC 95 PHE cc_start: 0.7706 (m-80) cc_final: 0.6438 (m-80) REVERT: AC 124 MET cc_start: 0.6979 (ttp) cc_final: 0.6331 (tmm) REVERT: AC 181 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: AD 93 SER cc_start: 0.8221 (m) cc_final: 0.7905 (p) REVERT: AD 96 TRP cc_start: 0.7046 (m-90) cc_final: 0.6465 (m-90) REVERT: AD 146 LYS cc_start: 0.9328 (ttpp) cc_final: 0.8959 (pttt) REVERT: AD 174 TYR cc_start: 0.7512 (m-80) cc_final: 0.7250 (m-80) REVERT: AD 181 ASN cc_start: 0.7683 (t0) cc_final: 0.7231 (t0) REVERT: AD 244 MET cc_start: 0.7214 (tmm) cc_final: 0.6850 (tmm) REVERT: AD 308 ARG cc_start: 0.8437 (mtp85) cc_final: 0.7778 (ttt90) REVERT: AE 82 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7828 (t70) REVERT: AE 92 ARG cc_start: 0.7353 (ttm110) cc_final: 0.7006 (ttm110) REVERT: AF 79 ASP cc_start: 0.8649 (p0) cc_final: 0.8252 (p0) REVERT: Aa 76 ASP cc_start: 0.7546 (t0) cc_final: 0.7337 (t0) REVERT: Aa 79 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.8404 (t) REVERT: Aa 81 TYR cc_start: 0.8912 (m-80) cc_final: 0.8371 (m-80) REVERT: Aa 175 ASN cc_start: 0.8159 (t0) cc_final: 0.7711 (p0) REVERT: Aa 274 GLU cc_start: 0.8431 (tt0) cc_final: 0.8164 (tt0) REVERT: Aa 449 PHE cc_start: 0.8686 (m-10) cc_final: 0.8275 (m-10) REVERT: Aa 468 TYR cc_start: 0.8524 (t80) cc_final: 0.8315 (t80) REVERT: Ab 159 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8610 (tptt) REVERT: Ab 311 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8528 (pp30) REVERT: Ac 20 ASP cc_start: 0.8555 (m-30) cc_final: 0.8176 (m-30) REVERT: Ac 141 TRP cc_start: 0.8052 (m100) cc_final: 0.7352 (m100) REVERT: Ac 187 PHE cc_start: 0.7901 (m-80) cc_final: 0.7423 (m-80) REVERT: Ac 216 ASP cc_start: 0.9076 (t0) cc_final: 0.8644 (t0) REVERT: Ac 217 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8538 (mtmm) REVERT: Ac 282 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8260 (ptp90) REVERT: Ac 373 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7453 (mt-10) REVERT: Ac 376 MET cc_start: 0.8718 (mtp) cc_final: 0.8456 (mtp) REVERT: Ad 273 PHE cc_start: 0.8957 (t80) cc_final: 0.8408 (t80) REVERT: Ad 288 MET cc_start: 0.8423 (mmt) cc_final: 0.7905 (mmt) REVERT: Ad 306 MET cc_start: 0.8815 (ttp) cc_final: 0.8379 (ttt) REVERT: Ae 131 ASN cc_start: 0.7143 (t0) cc_final: 0.6738 (t0) REVERT: Ae 156 LEU cc_start: 0.5456 (tp) cc_final: 0.5159 (tp) REVERT: Ae 191 GLU cc_start: 0.7070 (mp0) cc_final: 0.6606 (pm20) REVERT: Ae 244 ASP cc_start: 0.1322 (p0) cc_final: 0.0405 (t0) REVERT: Af 15 ASP cc_start: 0.7716 (t70) cc_final: 0.7262 (p0) REVERT: Af 17 PHE cc_start: 0.8249 (t80) cc_final: 0.7991 (t80) REVERT: Af 33 MET cc_start: 0.8698 (mmm) cc_final: 0.7900 (mmm) REVERT: Af 60 MET cc_start: 0.9256 (tpp) cc_final: 0.8868 (tpp) REVERT: Af 75 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9078 (mp) REVERT: Af 83 LYS cc_start: 0.8680 (mptt) cc_final: 0.8434 (mptt) REVERT: Af 89 PHE cc_start: 0.8234 (m-10) cc_final: 0.8026 (m-10) REVERT: Ag 43 ARG cc_start: 0.7778 (ptm160) cc_final: 0.7398 (ttp80) REVERT: Ag 60 TYR cc_start: 0.9171 (t80) cc_final: 0.8885 (t80) REVERT: Ah 70 PHE cc_start: 0.8382 (m-80) cc_final: 0.8009 (m-80) REVERT: Ai 67 THR cc_start: 0.8740 (m) cc_final: 0.8350 (p) REVERT: Ak 23 MET cc_start: 0.7686 (mmp) cc_final: 0.6812 (mtm) outliers start: 155 outliers final: 105 residues processed: 741 average time/residue: 0.4278 time to fit residues: 508.5254 Evaluate side-chains 728 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 614 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 240 MET Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 202 ARG Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 82 ASP Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 133 ILE Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 104 GLU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 156 SER Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 192 CYS Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 301 ARG Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ac residue 366 MET Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 252 VAL Chi-restraints excluded: chain Ad residue 263 MET Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Af residue 75 ILE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ai residue 68 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 317 optimal weight: 10.0000 chunk 356 optimal weight: 0.0870 chunk 244 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 308 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS AE 178 HIS AF 23 ASN ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 103 ASN Aa 193 GLN ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 267 HIS Ad 90 HIS Ag 13 HIS Ah 34 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093935 restraints weight = 75257.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094752 restraints weight = 41981.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096489 restraints weight = 29744.819| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.653 31150 Z= 0.247 Angle : 0.749 20.080 42266 Z= 0.363 Chirality : 0.044 0.170 4590 Planarity : 0.005 0.079 5364 Dihedral : 9.677 175.110 4406 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.12 % Allowed : 20.81 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.14), residues: 3721 helix: 1.02 (0.12), residues: 2006 sheet: -0.12 (0.28), residues: 362 loop : -0.34 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPAd 311 HIS 0.009 0.001 HISAc 196 PHE 0.028 0.002 PHEAd 114 TYR 0.019 0.002 TYRAG 57 ARG 0.012 0.001 ARGAj 16 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 1735) hydrogen bonds : angle 4.97630 ( 4980) SS BOND : bond 0.00502 ( 7) SS BOND : angle 1.36795 ( 14) covalent geometry : bond 0.00567 (31137) covalent geometry : angle 0.74914 (42252) Misc. bond : bond 0.38080 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 644 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 98 PHE cc_start: 0.8443 (m-80) cc_final: 0.8202 (m-80) REVERT: AA 467 ASP cc_start: 0.7621 (p0) cc_final: 0.7371 (p0) REVERT: AB 69 SER cc_start: 0.8891 (p) cc_final: 0.8578 (t) REVERT: AB 77 LEU cc_start: 0.9425 (mt) cc_final: 0.9133 (mp) REVERT: AB 203 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: AB 271 ILE cc_start: 0.8647 (mt) cc_final: 0.8317 (pt) REVERT: AB 415 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7949 (tm-30) REVERT: AB 429 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8551 (ttmm) REVERT: AC 31 TRP cc_start: 0.8236 (m-90) cc_final: 0.7650 (m-90) REVERT: AC 40 CYS cc_start: 0.8231 (t) cc_final: 0.7694 (t) REVERT: AC 72 ASP cc_start: 0.6931 (t0) cc_final: 0.6709 (t0) REVERT: AC 82 MET cc_start: 0.8785 (tpp) cc_final: 0.8424 (tpp) REVERT: AC 89 MET cc_start: 0.8101 (mtm) cc_final: 0.7806 (mtm) REVERT: AC 90 PHE cc_start: 0.8523 (t80) cc_final: 0.8022 (t80) REVERT: AC 91 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7808 (t80) REVERT: AC 95 PHE cc_start: 0.7674 (m-80) cc_final: 0.6354 (m-80) REVERT: AC 124 MET cc_start: 0.6911 (ttp) cc_final: 0.6677 (tmm) REVERT: AC 181 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: AC 252 ASP cc_start: 0.5141 (t0) cc_final: 0.4912 (t0) REVERT: AC 275 LEU cc_start: 0.8792 (tp) cc_final: 0.8473 (tp) REVERT: AD 96 TRP cc_start: 0.7040 (m-90) cc_final: 0.6469 (m-90) REVERT: AD 146 LYS cc_start: 0.9388 (ttpp) cc_final: 0.8979 (pttt) REVERT: AD 174 TYR cc_start: 0.7597 (m-80) cc_final: 0.7280 (m-80) REVERT: AD 181 ASN cc_start: 0.7712 (t0) cc_final: 0.7224 (t0) REVERT: AD 244 MET cc_start: 0.7104 (tmm) cc_final: 0.6746 (tmm) REVERT: AD 291 LYS cc_start: 0.9031 (tppp) cc_final: 0.8817 (mmmm) REVERT: AD 296 MET cc_start: 0.7104 (mmp) cc_final: 0.5672 (mtt) REVERT: AE 92 ARG cc_start: 0.7394 (ttm110) cc_final: 0.6880 (ttm110) REVERT: AF 79 ASP cc_start: 0.8689 (p0) cc_final: 0.8269 (p0) REVERT: Aa 79 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8488 (t) REVERT: Aa 123 TYR cc_start: 0.8833 (p90) cc_final: 0.8372 (p90) REVERT: Aa 175 ASN cc_start: 0.8138 (t0) cc_final: 0.7838 (p0) REVERT: Aa 209 ARG cc_start: 0.8517 (mtm180) cc_final: 0.8215 (mtm-85) REVERT: Aa 274 GLU cc_start: 0.8452 (tt0) cc_final: 0.8177 (tt0) REVERT: Ab 213 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: Ab 311 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8499 (pp30) REVERT: Ab 407 MET cc_start: 0.8163 (mmp) cc_final: 0.7911 (mmt) REVERT: Ac 20 ASP cc_start: 0.8618 (m-30) cc_final: 0.8254 (m-30) REVERT: Ac 88 SER cc_start: 0.8945 (m) cc_final: 0.8721 (t) REVERT: Ac 121 PHE cc_start: 0.7861 (m-80) cc_final: 0.7416 (m-80) REVERT: Ac 141 TRP cc_start: 0.8075 (m100) cc_final: 0.7401 (m100) REVERT: Ac 187 PHE cc_start: 0.8091 (m-80) cc_final: 0.7445 (m-80) REVERT: Ac 212 ASN cc_start: 0.8278 (t0) cc_final: 0.7776 (p0) REVERT: Ac 216 ASP cc_start: 0.9070 (t0) cc_final: 0.8610 (t0) REVERT: Ac 217 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8567 (mtmm) REVERT: Ac 373 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7488 (mt-10) REVERT: Ad 164 MET cc_start: 0.8813 (tmm) cc_final: 0.8365 (tpp) REVERT: Ad 288 MET cc_start: 0.8527 (mmt) cc_final: 0.7982 (mmt) REVERT: Ae 131 ASN cc_start: 0.7241 (t0) cc_final: 0.6791 (t0) REVERT: Ae 156 LEU cc_start: 0.5259 (tp) cc_final: 0.4973 (tp) REVERT: Ae 170 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7894 (mtp180) REVERT: Af 15 ASP cc_start: 0.7786 (t70) cc_final: 0.7430 (p0) REVERT: Af 33 MET cc_start: 0.8740 (mmm) cc_final: 0.7923 (mmm) REVERT: Af 83 LYS cc_start: 0.8748 (mptt) cc_final: 0.8505 (mptt) REVERT: Af 89 PHE cc_start: 0.8254 (m-10) cc_final: 0.7924 (m-10) REVERT: Ag 43 ARG cc_start: 0.7699 (ptm160) cc_final: 0.6917 (ttp80) REVERT: Ag 60 TYR cc_start: 0.9219 (t80) cc_final: 0.8852 (t80) REVERT: Ah 70 PHE cc_start: 0.8523 (m-80) cc_final: 0.8266 (m-80) REVERT: Ai 67 THR cc_start: 0.8728 (m) cc_final: 0.8349 (p) REVERT: Aj 13 LEU cc_start: 0.7554 (mm) cc_final: 0.7227 (mm) REVERT: Aj 16 ARG cc_start: 0.7118 (ptt-90) cc_final: 0.6886 (ptt-90) REVERT: Ak 23 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6895 (mtm) outliers start: 163 outliers final: 125 residues processed: 736 average time/residue: 0.4113 time to fit residues: 488.5690 Evaluate side-chains 734 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 600 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 139 ASP Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 250 LEU Chi-restraints excluded: chain AA residue 394 ILE Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 141 THR Chi-restraints excluded: chain AB residue 203 GLU Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AB residue 429 LYS Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 181 PHE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 320 ILE Chi-restraints excluded: chain AC residue 329 VAL Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 202 ARG Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 51 LEU Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain AI residue 64 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 230 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 104 GLU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 156 SER Chi-restraints excluded: chain Ab residue 164 VAL Chi-restraints excluded: chain Ab residue 192 CYS Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ab residue 447 THR Chi-restraints excluded: chain Ac residue 37 LEU Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 225 THR Chi-restraints excluded: chain Ac residue 237 LEU Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 361 ILE Chi-restraints excluded: chain Ac residue 366 MET Chi-restraints excluded: chain Ad residue 116 VAL Chi-restraints excluded: chain Ad residue 120 VAL Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 175 PHE Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 263 MET Chi-restraints excluded: chain Ad residue 266 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ae residue 121 THR Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ag residue 74 ASN Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 48 LEU Chi-restraints excluded: chain Ah residue 72 PHE Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Chi-restraints excluded: chain Ak residue 24 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 16 optimal weight: 1.9990 chunk 277 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS ** AD 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN Ac 54 HIS ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 267 HIS Ad 90 HIS Ad 284 HIS Ah 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.127576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097181 restraints weight = 74067.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098714 restraints weight = 41460.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100140 restraints weight = 29115.918| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.451 31150 Z= 0.146 Angle : 0.689 16.378 42266 Z= 0.332 Chirality : 0.043 0.178 4590 Planarity : 0.004 0.081 5364 Dihedral : 9.426 179.638 4406 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.95 % Allowed : 22.66 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.14), residues: 3721 helix: 1.18 (0.12), residues: 2001 sheet: -0.16 (0.27), residues: 374 loop : -0.20 (0.18), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPAa 376 HIS 0.026 0.001 HISAD 309 PHE 0.031 0.001 PHEAc 276 TYR 0.032 0.001 TYRAc 104 ARG 0.010 0.000 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 1735) hydrogen bonds : angle 4.79863 ( 4980) SS BOND : bond 0.00371 ( 7) SS BOND : angle 1.13773 ( 14) covalent geometry : bond 0.00341 (31137) covalent geometry : angle 0.68833 (42252) Misc. bond : bond 0.28248 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 687 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 111 LYS cc_start: 0.8869 (ptpt) cc_final: 0.8654 (ptpt) REVERT: AB 69 SER cc_start: 0.8820 (p) cc_final: 0.8424 (t) REVERT: AB 77 LEU cc_start: 0.9391 (mt) cc_final: 0.9116 (mp) REVERT: AB 203 GLU cc_start: 0.8080 (pt0) cc_final: 0.7800 (tm-30) REVERT: AB 415 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7924 (tm-30) REVERT: AC 31 TRP cc_start: 0.8240 (m-90) cc_final: 0.7452 (m-90) REVERT: AC 37 LEU cc_start: 0.9167 (mt) cc_final: 0.8944 (mm) REVERT: AC 40 CYS cc_start: 0.8147 (t) cc_final: 0.7735 (t) REVERT: AC 90 PHE cc_start: 0.8432 (t80) cc_final: 0.7983 (t80) REVERT: AC 91 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7799 (t80) REVERT: AC 95 PHE cc_start: 0.7730 (m-80) cc_final: 0.6621 (m-80) REVERT: AC 124 MET cc_start: 0.7125 (ttp) cc_final: 0.6857 (tmm) REVERT: AC 252 ASP cc_start: 0.5111 (t0) cc_final: 0.4825 (t0) REVERT: AC 275 LEU cc_start: 0.8807 (tp) cc_final: 0.8471 (tp) REVERT: AC 322 GLN cc_start: 0.8386 (mt0) cc_final: 0.8180 (mt0) REVERT: AD 96 TRP cc_start: 0.6934 (m-90) cc_final: 0.6345 (m-90) REVERT: AD 174 TYR cc_start: 0.7630 (m-80) cc_final: 0.7324 (m-80) REVERT: AD 181 ASN cc_start: 0.7635 (t0) cc_final: 0.7144 (t0) REVERT: AD 244 MET cc_start: 0.7308 (tmm) cc_final: 0.6940 (tmm) REVERT: AD 291 LYS cc_start: 0.9042 (tppp) cc_final: 0.8733 (mmmm) REVERT: AD 296 MET cc_start: 0.7042 (mmp) cc_final: 0.5561 (mtt) REVERT: AE 92 ARG cc_start: 0.7423 (ttm110) cc_final: 0.6901 (ttm110) REVERT: AF 21 TYR cc_start: 0.8812 (t80) cc_final: 0.7515 (t80) REVERT: AF 79 ASP cc_start: 0.8619 (p0) cc_final: 0.8214 (p0) REVERT: AF 92 GLU cc_start: 0.8482 (tp30) cc_final: 0.7914 (tp30) REVERT: AF 101 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8936 (mt-10) REVERT: AF 102 ARG cc_start: 0.9175 (tmm-80) cc_final: 0.8921 (tmm-80) REVERT: Aa 79 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8074 (t) REVERT: Aa 91 TYR cc_start: 0.7943 (t80) cc_final: 0.7640 (t80) REVERT: Aa 123 TYR cc_start: 0.8744 (p90) cc_final: 0.8292 (p90) REVERT: Aa 165 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8866 (ttm110) REVERT: Aa 175 ASN cc_start: 0.8208 (t0) cc_final: 0.7907 (p0) REVERT: Aa 201 VAL cc_start: 0.9367 (t) cc_final: 0.9051 (p) REVERT: Aa 274 GLU cc_start: 0.8393 (tt0) cc_final: 0.8153 (tt0) REVERT: Aa 468 TYR cc_start: 0.8382 (t80) cc_final: 0.8137 (t80) REVERT: Ab 159 LYS cc_start: 0.8948 (tmtt) cc_final: 0.8599 (tptt) REVERT: Ab 213 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: Ab 338 ILE cc_start: 0.8391 (pt) cc_final: 0.7970 (mm) REVERT: Ab 407 MET cc_start: 0.8050 (mmp) cc_final: 0.7809 (tpp) REVERT: Ac 20 ASP cc_start: 0.8581 (m-30) cc_final: 0.8164 (m-30) REVERT: Ac 53 MET cc_start: 0.5364 (ttt) cc_final: 0.5090 (ttt) REVERT: Ac 88 SER cc_start: 0.8876 (m) cc_final: 0.8633 (t) REVERT: Ac 121 PHE cc_start: 0.7793 (m-80) cc_final: 0.7323 (m-80) REVERT: Ac 138 MET cc_start: 0.5967 (tpp) cc_final: 0.4814 (tpp) REVERT: Ac 141 TRP cc_start: 0.8059 (m100) cc_final: 0.7442 (m100) REVERT: Ac 187 PHE cc_start: 0.7960 (m-80) cc_final: 0.7430 (m-80) REVERT: Ac 212 ASN cc_start: 0.8276 (t0) cc_final: 0.7879 (p0) REVERT: Ac 216 ASP cc_start: 0.8989 (t0) cc_final: 0.8459 (t0) REVERT: Ac 217 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8555 (mtmm) REVERT: Ac 233 LEU cc_start: 0.9002 (mm) cc_final: 0.8332 (tt) REVERT: Ac 282 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8453 (ptp90) REVERT: Ad 103 SER cc_start: 0.8843 (m) cc_final: 0.8315 (p) REVERT: Ad 288 MET cc_start: 0.8454 (mmt) cc_final: 0.8045 (mmt) REVERT: Ae 131 ASN cc_start: 0.7108 (t0) cc_final: 0.6693 (t0) REVERT: Ae 140 MET cc_start: 0.9075 (mmm) cc_final: 0.8515 (mmm) REVERT: Ae 156 LEU cc_start: 0.5187 (tp) cc_final: 0.4936 (tp) REVERT: Ae 191 GLU cc_start: 0.7201 (pm20) cc_final: 0.6616 (pm20) REVERT: Af 15 ASP cc_start: 0.7719 (t70) cc_final: 0.7421 (p0) REVERT: Af 33 MET cc_start: 0.8692 (mmm) cc_final: 0.8157 (mtp) REVERT: Af 53 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8071 (tm-30) REVERT: Af 83 LYS cc_start: 0.8713 (mptt) cc_final: 0.8496 (mptt) REVERT: Af 89 PHE cc_start: 0.8243 (m-10) cc_final: 0.7994 (m-10) REVERT: Ag 40 ARG cc_start: 0.8735 (tmm-80) cc_final: 0.8351 (tmm-80) REVERT: Ag 43 ARG cc_start: 0.7671 (ptm160) cc_final: 0.6970 (ttp80) REVERT: Ag 60 TYR cc_start: 0.9191 (t80) cc_final: 0.8848 (t80) REVERT: Ai 67 THR cc_start: 0.8680 (m) cc_final: 0.8336 (p) REVERT: Aj 13 LEU cc_start: 0.7587 (mm) cc_final: 0.7241 (mm) REVERT: Aj 16 ARG cc_start: 0.7180 (ptt-90) cc_final: 0.6817 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8173 (tt0) cc_final: 0.7724 (mm-40) REVERT: Ak 23 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6689 (mtm) outliers start: 126 outliers final: 93 residues processed: 758 average time/residue: 0.5672 time to fit residues: 692.3700 Evaluate side-chains 742 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 643 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 250 LEU Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 113 THR Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 96 LEU Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 51 LEU Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 366 MET Chi-restraints excluded: chain Ad residue 175 PHE Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 263 MET Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ae residue 212 ILE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 280 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 296 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 205 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 264 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 95 HIS ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 267 HIS Ad 90 HIS Ah 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098466 restraints weight = 74215.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099318 restraints weight = 41954.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100829 restraints weight = 29764.437| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.446 31150 Z= 0.151 Angle : 0.711 16.815 42266 Z= 0.340 Chirality : 0.043 0.244 4590 Planarity : 0.004 0.055 5364 Dihedral : 9.357 177.295 4406 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.92 % Allowed : 23.48 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.14), residues: 3721 helix: 1.21 (0.12), residues: 2000 sheet: -0.09 (0.27), residues: 374 loop : -0.20 (0.18), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAa 376 HIS 0.005 0.001 HISAE 219 PHE 0.031 0.002 PHEAc 276 TYR 0.036 0.002 TYRAc 104 ARG 0.013 0.001 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 1735) hydrogen bonds : angle 4.78554 ( 4980) SS BOND : bond 0.00377 ( 7) SS BOND : angle 1.01481 ( 14) covalent geometry : bond 0.00356 (31137) covalent geometry : angle 0.71099 (42252) Misc. bond : bond 0.27732 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 668 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 229 MET cc_start: 0.8658 (mtp) cc_final: 0.8331 (mtp) REVERT: AA 271 THR cc_start: 0.8922 (m) cc_final: 0.8604 (p) REVERT: AB 69 SER cc_start: 0.8828 (p) cc_final: 0.8441 (t) REVERT: AB 77 LEU cc_start: 0.9386 (mt) cc_final: 0.9101 (mp) REVERT: AB 415 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7920 (tm-30) REVERT: AC 31 TRP cc_start: 0.8233 (m-90) cc_final: 0.7381 (m-90) REVERT: AC 40 CYS cc_start: 0.8009 (t) cc_final: 0.7654 (t) REVERT: AC 90 PHE cc_start: 0.8433 (t80) cc_final: 0.7994 (t80) REVERT: AC 91 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7757 (t80) REVERT: AC 95 PHE cc_start: 0.7734 (m-80) cc_final: 0.6620 (m-80) REVERT: AC 124 MET cc_start: 0.7075 (ttp) cc_final: 0.6853 (tmm) REVERT: AC 226 ILE cc_start: 0.8599 (tp) cc_final: 0.8264 (tt) REVERT: AC 252 ASP cc_start: 0.5140 (t0) cc_final: 0.4847 (t0) REVERT: AC 275 LEU cc_start: 0.8793 (tp) cc_final: 0.8453 (tp) REVERT: AC 278 TYR cc_start: 0.7580 (t80) cc_final: 0.7330 (t80) REVERT: AC 322 GLN cc_start: 0.8403 (mt0) cc_final: 0.8149 (mt0) REVERT: AD 96 TRP cc_start: 0.7023 (m-90) cc_final: 0.6436 (m-90) REVERT: AD 146 LYS cc_start: 0.9298 (ttpp) cc_final: 0.9042 (pttt) REVERT: AD 174 TYR cc_start: 0.7584 (m-80) cc_final: 0.7339 (m-80) REVERT: AD 181 ASN cc_start: 0.7661 (t0) cc_final: 0.7155 (t0) REVERT: AD 244 MET cc_start: 0.7167 (tmm) cc_final: 0.6792 (tmm) REVERT: AD 291 LYS cc_start: 0.9032 (tppp) cc_final: 0.8817 (mmmm) REVERT: AD 296 MET cc_start: 0.7198 (mmp) cc_final: 0.5867 (mtt) REVERT: AE 92 ARG cc_start: 0.7549 (ttm110) cc_final: 0.7089 (ttm110) REVERT: AF 79 ASP cc_start: 0.8564 (p0) cc_final: 0.8147 (p0) REVERT: AF 92 GLU cc_start: 0.8470 (tp30) cc_final: 0.7882 (tp30) REVERT: AF 101 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8973 (mt-10) REVERT: AH 82 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7908 (t-170) REVERT: Aa 63 GLN cc_start: 0.8677 (tt0) cc_final: 0.8446 (tp40) REVERT: Aa 79 SER cc_start: 0.9046 (m) cc_final: 0.8128 (t) REVERT: Aa 123 TYR cc_start: 0.8742 (p90) cc_final: 0.8304 (p90) REVERT: Aa 175 ASN cc_start: 0.8233 (t0) cc_final: 0.7872 (p0) REVERT: Aa 201 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9013 (p) REVERT: Aa 209 ARG cc_start: 0.8307 (mtm180) cc_final: 0.7564 (mtm180) REVERT: Aa 274 GLU cc_start: 0.8377 (tt0) cc_final: 0.8157 (tt0) REVERT: Aa 344 PHE cc_start: 0.9221 (p90) cc_final: 0.9010 (p90) REVERT: Ab 159 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8653 (tptt) REVERT: Ab 213 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: Ab 338 ILE cc_start: 0.8355 (pt) cc_final: 0.7985 (mm) REVERT: Ab 349 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: Ab 407 MET cc_start: 0.8071 (mmp) cc_final: 0.7863 (tpp) REVERT: Ac 20 ASP cc_start: 0.8589 (m-30) cc_final: 0.8197 (m-30) REVERT: Ac 88 SER cc_start: 0.8923 (m) cc_final: 0.8655 (t) REVERT: Ac 129 MET cc_start: 0.7267 (ptt) cc_final: 0.6968 (ppp) REVERT: Ac 135 TRP cc_start: 0.8664 (t-100) cc_final: 0.8144 (t-100) REVERT: Ac 138 MET cc_start: 0.5987 (tpp) cc_final: 0.4848 (tpp) REVERT: Ac 141 TRP cc_start: 0.8081 (m100) cc_final: 0.7466 (m100) REVERT: Ac 187 PHE cc_start: 0.7703 (m-80) cc_final: 0.7227 (m-80) REVERT: Ac 212 ASN cc_start: 0.8294 (t0) cc_final: 0.7842 (p0) REVERT: Ac 216 ASP cc_start: 0.9015 (t0) cc_final: 0.8472 (t0) REVERT: Ac 217 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8532 (mtmm) REVERT: Ac 233 LEU cc_start: 0.9000 (mm) cc_final: 0.8310 (tt) REVERT: Ac 282 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8494 (ptp90) REVERT: Ad 103 SER cc_start: 0.8867 (m) cc_final: 0.8416 (p) REVERT: Ad 249 TYR cc_start: 0.7187 (p90) cc_final: 0.6963 (p90) REVERT: Ad 288 MET cc_start: 0.8416 (mmt) cc_final: 0.7841 (mmt) REVERT: Ae 131 ASN cc_start: 0.7034 (t0) cc_final: 0.6665 (t0) REVERT: Ae 140 MET cc_start: 0.8990 (mmm) cc_final: 0.8318 (mmm) REVERT: Ae 191 GLU cc_start: 0.7453 (pm20) cc_final: 0.6669 (pm20) REVERT: Ae 244 ASP cc_start: 0.1359 (p0) cc_final: 0.0056 (t70) REVERT: Ae 248 ARG cc_start: 0.3572 (ptt180) cc_final: 0.2606 (ptt180) REVERT: Af 15 ASP cc_start: 0.7714 (t70) cc_final: 0.7313 (p0) REVERT: Af 33 MET cc_start: 0.8695 (mmm) cc_final: 0.8148 (mtp) REVERT: Af 83 LYS cc_start: 0.8687 (mptt) cc_final: 0.8437 (mptt) REVERT: Ag 40 ARG cc_start: 0.8792 (tmm-80) cc_final: 0.8184 (tmm-80) REVERT: Ag 43 ARG cc_start: 0.7659 (ptm160) cc_final: 0.6905 (ttp80) REVERT: Ag 60 TYR cc_start: 0.9161 (t80) cc_final: 0.8778 (t80) REVERT: Ai 67 THR cc_start: 0.8767 (m) cc_final: 0.8450 (p) REVERT: Aj 13 LEU cc_start: 0.7627 (mm) cc_final: 0.7302 (mm) REVERT: Aj 16 ARG cc_start: 0.7228 (ptt-90) cc_final: 0.6846 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8119 (tt0) cc_final: 0.7703 (mm-40) REVERT: Ak 23 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6832 (mtm) outliers start: 125 outliers final: 99 residues processed: 740 average time/residue: 0.4168 time to fit residues: 492.3690 Evaluate side-chains 740 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 633 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 116 ILE Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 139 ASP Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 250 LEU Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 99 ILE Chi-restraints excluded: chain AB residue 113 THR Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AB residue 421 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 115 GLN Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 202 ARG Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 51 LEU Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 104 GLU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 209 VAL Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 349 GLU Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 226 ILE Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 307 LEU Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 366 MET Chi-restraints excluded: chain Ad residue 175 PHE Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 272 THR Chi-restraints excluded: chain Ad residue 300 LEU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ae residue 146 VAL Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 45 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 154 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 330 optimal weight: 0.9980 chunk 333 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS AF 23 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 267 HIS Ad 90 HIS Ah 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.128281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098094 restraints weight = 73767.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.100303 restraints weight = 40538.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101324 restraints weight = 26896.565| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.426 31150 Z= 0.146 Angle : 0.716 16.067 42266 Z= 0.343 Chirality : 0.043 0.205 4590 Planarity : 0.005 0.065 5364 Dihedral : 9.322 177.356 4406 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.55 % Allowed : 24.20 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.85 (0.14), residues: 3721 helix: 1.26 (0.12), residues: 1997 sheet: 0.01 (0.28), residues: 372 loop : -0.19 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPAa 376 HIS 0.005 0.001 HISAA 357 PHE 0.033 0.001 PHEAc 276 TYR 0.027 0.001 TYRAC 278 ARG 0.013 0.001 ARGAh 47 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1735) hydrogen bonds : angle 4.75426 ( 4980) SS BOND : bond 0.00343 ( 7) SS BOND : angle 1.05544 ( 14) covalent geometry : bond 0.00344 (31137) covalent geometry : angle 0.71619 (42252) Misc. bond : bond 0.26360 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 663 time to evaluate : 3.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 271 THR cc_start: 0.8919 (m) cc_final: 0.8637 (p) REVERT: AB 69 SER cc_start: 0.8823 (p) cc_final: 0.8421 (t) REVERT: AB 77 LEU cc_start: 0.9357 (mt) cc_final: 0.9095 (mp) REVERT: AB 172 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7742 (tpp80) REVERT: AB 415 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7951 (tm-30) REVERT: AC 31 TRP cc_start: 0.8248 (m-90) cc_final: 0.7386 (m-90) REVERT: AC 40 CYS cc_start: 0.8027 (t) cc_final: 0.7667 (t) REVERT: AC 90 PHE cc_start: 0.8455 (t80) cc_final: 0.8006 (t80) REVERT: AC 91 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7759 (t80) REVERT: AC 95 PHE cc_start: 0.7611 (m-80) cc_final: 0.6471 (m-80) REVERT: AC 124 MET cc_start: 0.7087 (ttp) cc_final: 0.5965 (tmm) REVERT: AC 252 ASP cc_start: 0.5209 (t0) cc_final: 0.4903 (t0) REVERT: AC 275 LEU cc_start: 0.8815 (tp) cc_final: 0.8488 (tp) REVERT: AC 278 TYR cc_start: 0.7560 (t80) cc_final: 0.7315 (t80) REVERT: AD 96 TRP cc_start: 0.7106 (m-90) cc_final: 0.6502 (m-90) REVERT: AD 174 TYR cc_start: 0.7788 (m-80) cc_final: 0.7533 (m-80) REVERT: AD 181 ASN cc_start: 0.7636 (t0) cc_final: 0.7129 (t0) REVERT: AD 244 MET cc_start: 0.7182 (tmm) cc_final: 0.6814 (tmm) REVERT: AD 291 LYS cc_start: 0.9044 (tppp) cc_final: 0.8826 (mmmm) REVERT: AD 296 MET cc_start: 0.7062 (mmp) cc_final: 0.5907 (mtt) REVERT: AD 306 MET cc_start: 0.8849 (tpp) cc_final: 0.8567 (tpp) REVERT: AE 92 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7123 (ttm110) REVERT: AF 21 TYR cc_start: 0.8734 (t80) cc_final: 0.7498 (t80) REVERT: AF 92 GLU cc_start: 0.8492 (tp30) cc_final: 0.7905 (tp30) REVERT: AF 101 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8985 (mt-10) REVERT: AG 57 TYR cc_start: 0.8348 (t80) cc_final: 0.8005 (t80) REVERT: AH 82 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7996 (t-170) REVERT: Aa 79 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8050 (t) REVERT: Aa 123 TYR cc_start: 0.8740 (p90) cc_final: 0.8335 (p90) REVERT: Aa 175 ASN cc_start: 0.8300 (t0) cc_final: 0.7917 (p0) REVERT: Aa 201 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9034 (p) REVERT: Aa 209 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7912 (mtm180) REVERT: Ab 159 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8636 (tptt) REVERT: Ab 213 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: Ab 338 ILE cc_start: 0.8397 (pt) cc_final: 0.7854 (mm) REVERT: Ab 349 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: Ac 20 ASP cc_start: 0.8599 (m-30) cc_final: 0.8187 (m-30) REVERT: Ac 53 MET cc_start: 0.5215 (ttt) cc_final: 0.4961 (ttt) REVERT: Ac 88 SER cc_start: 0.8855 (m) cc_final: 0.8587 (t) REVERT: Ac 129 MET cc_start: 0.7266 (ptt) cc_final: 0.6956 (ppp) REVERT: Ac 135 TRP cc_start: 0.8653 (t-100) cc_final: 0.8145 (t-100) REVERT: Ac 138 MET cc_start: 0.5861 (tpp) cc_final: 0.4747 (tpp) REVERT: Ac 141 TRP cc_start: 0.8027 (m100) cc_final: 0.7443 (m100) REVERT: Ac 187 PHE cc_start: 0.7665 (m-80) cc_final: 0.7261 (m-80) REVERT: Ac 212 ASN cc_start: 0.8291 (t0) cc_final: 0.7751 (p0) REVERT: Ac 216 ASP cc_start: 0.9005 (t0) cc_final: 0.8530 (t0) REVERT: Ac 217 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8519 (mtmm) REVERT: Ac 233 LEU cc_start: 0.9021 (mm) cc_final: 0.8305 (tt) REVERT: Ac 282 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8548 (ptp90) REVERT: Ac 372 ILE cc_start: 0.9477 (mm) cc_final: 0.9175 (mt) REVERT: Ac 373 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7609 (mt-10) REVERT: Ad 103 SER cc_start: 0.8839 (m) cc_final: 0.8428 (p) REVERT: Ad 127 MET cc_start: 0.7916 (tpp) cc_final: 0.7654 (tpp) REVERT: Ad 253 LEU cc_start: 0.7820 (tp) cc_final: 0.7409 (pt) REVERT: Ad 288 MET cc_start: 0.8397 (mmt) cc_final: 0.7811 (mmt) REVERT: Ae 131 ASN cc_start: 0.6993 (t0) cc_final: 0.6603 (t0) REVERT: Ae 140 MET cc_start: 0.9021 (mmm) cc_final: 0.8805 (mmm) REVERT: Ae 156 LEU cc_start: 0.4429 (tp) cc_final: 0.4184 (tp) REVERT: Ae 191 GLU cc_start: 0.7310 (pm20) cc_final: 0.6764 (pm20) REVERT: Ae 244 ASP cc_start: 0.1524 (p0) cc_final: 0.0455 (t0) REVERT: Ae 248 ARG cc_start: 0.4374 (ptt180) cc_final: 0.3275 (ptt180) REVERT: Af 33 MET cc_start: 0.8628 (mmm) cc_final: 0.8103 (mtp) REVERT: Af 53 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7945 (tm-30) REVERT: Af 60 MET cc_start: 0.9147 (tpp) cc_final: 0.8760 (tpp) REVERT: Af 83 LYS cc_start: 0.8654 (mptt) cc_final: 0.8334 (mptt) REVERT: Ag 40 ARG cc_start: 0.8694 (tmm-80) cc_final: 0.7948 (tmm-80) REVERT: Ag 43 ARG cc_start: 0.7650 (ptm160) cc_final: 0.6904 (ttp80) REVERT: Ag 60 TYR cc_start: 0.9158 (t80) cc_final: 0.8884 (t80) REVERT: Ah 89 LYS cc_start: 0.8175 (pptt) cc_final: 0.7883 (pptt) REVERT: Ai 67 THR cc_start: 0.8718 (m) cc_final: 0.8379 (p) REVERT: Ai 77 ARG cc_start: 0.7418 (tmm160) cc_final: 0.7207 (tmm160) REVERT: Aj 13 LEU cc_start: 0.7670 (mm) cc_final: 0.7323 (mm) REVERT: Aj 16 ARG cc_start: 0.7228 (ptt-90) cc_final: 0.6842 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8121 (tt0) cc_final: 0.7636 (mm-40) REVERT: Ak 23 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6794 (mtm) outliers start: 113 outliers final: 93 residues processed: 722 average time/residue: 0.4162 time to fit residues: 481.0397 Evaluate side-chains 730 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 628 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 250 LEU Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 40 PHE Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 99 ILE Chi-restraints excluded: chain AB residue 113 THR Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 65 SER Chi-restraints excluded: chain AC residue 78 LEU Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 292 LEU Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AF residue 51 LEU Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 349 GLU Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 419 VAL Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 217 LYS Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 366 MET Chi-restraints excluded: chain Ad residue 175 PHE Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 300 LEU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 19 LEU Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 45 VAL Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 150 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 270 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 219 optimal weight: 0.9980 chunk 355 optimal weight: 4.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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** AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 267 HIS Ad 90 HIS Ah 34 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098723 restraints weight = 74099.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100698 restraints weight = 43259.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102095 restraints weight = 29003.391| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.6945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.384 31150 Z= 0.139 Angle : 0.725 15.277 42266 Z= 0.348 Chirality : 0.043 0.193 4590 Planarity : 0.004 0.056 5364 Dihedral : 9.227 174.796 4406 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.26 % Allowed : 24.61 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 0.83 (0.14), residues: 3721 helix: 1.22 (0.12), residues: 1994 sheet: -0.02 (0.28), residues: 376 loop : -0.16 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAk 38 HIS 0.010 0.001 HISAD 309 PHE 0.042 0.002 PHEAd 114 TYR 0.026 0.001 TYRAC 278 ARG 0.011 0.001 ARGAD 308 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1735) hydrogen bonds : angle 4.74572 ( 4980) SS BOND : bond 0.00332 ( 7) SS BOND : angle 1.03447 ( 14) covalent geometry : bond 0.00326 (31137) covalent geometry : angle 0.72482 (42252) Misc. bond : bond 0.24912 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7442 Ramachandran restraints generated. 3721 Oldfield, 0 Emsley, 3721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 644 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 271 THR cc_start: 0.8910 (m) cc_final: 0.8672 (p) REVERT: AB 69 SER cc_start: 0.8808 (p) cc_final: 0.8401 (t) REVERT: AB 77 LEU cc_start: 0.9350 (mt) cc_final: 0.9091 (mp) REVERT: AB 172 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7730 (tpp80) REVERT: AB 415 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7959 (tm-30) REVERT: AC 31 TRP cc_start: 0.8291 (m-90) cc_final: 0.7381 (m-90) REVERT: AC 37 LEU cc_start: 0.9125 (mt) cc_final: 0.8868 (mm) REVERT: AC 40 CYS cc_start: 0.8078 (t) cc_final: 0.7736 (t) REVERT: AC 90 PHE cc_start: 0.8501 (t80) cc_final: 0.8088 (t80) REVERT: AC 91 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7962 (t80) REVERT: AC 124 MET cc_start: 0.7151 (ttp) cc_final: 0.6891 (ppp) REVERT: AC 225 THR cc_start: 0.8732 (m) cc_final: 0.8446 (m) REVERT: AC 252 ASP cc_start: 0.5193 (t0) cc_final: 0.4901 (t0) REVERT: AC 275 LEU cc_start: 0.8745 (tp) cc_final: 0.8385 (tp) REVERT: AC 313 ARG cc_start: 0.8242 (ttt180) cc_final: 0.8042 (ttt180) REVERT: AD 96 TRP cc_start: 0.7101 (m-90) cc_final: 0.6554 (m-90) REVERT: AD 146 LYS cc_start: 0.9340 (ttpp) cc_final: 0.9021 (pttp) REVERT: AD 174 TYR cc_start: 0.7902 (m-80) cc_final: 0.7629 (m-80) REVERT: AD 181 ASN cc_start: 0.7560 (t0) cc_final: 0.7065 (t0) REVERT: AD 244 MET cc_start: 0.7161 (tmm) cc_final: 0.6846 (tmm) REVERT: AD 291 LYS cc_start: 0.9074 (tppp) cc_final: 0.8849 (mmmm) REVERT: AD 296 MET cc_start: 0.7119 (mmp) cc_final: 0.5979 (mtt) REVERT: AE 89 SER cc_start: 0.8771 (m) cc_final: 0.8451 (p) REVERT: AE 92 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7254 (ttm110) REVERT: AF 21 TYR cc_start: 0.8848 (t80) cc_final: 0.7595 (t80) REVERT: AF 23 ASN cc_start: 0.8688 (m-40) cc_final: 0.8410 (m110) REVERT: AF 92 GLU cc_start: 0.8532 (tp30) cc_final: 0.7938 (tp30) REVERT: AF 101 GLU cc_start: 0.9232 (mt-10) cc_final: 0.9014 (mt-10) REVERT: AG 17 TYR cc_start: 0.8582 (m-80) cc_final: 0.8292 (m-80) REVERT: AG 57 TYR cc_start: 0.8390 (t80) cc_final: 0.8063 (t80) REVERT: AH 82 HIS cc_start: 0.8381 (OUTLIER) cc_final: 0.8012 (t-170) REVERT: Aa 79 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8079 (t) REVERT: Aa 175 ASN cc_start: 0.8329 (t0) cc_final: 0.7927 (p0) REVERT: Aa 201 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9039 (p) REVERT: Aa 344 PHE cc_start: 0.9215 (p90) cc_final: 0.8960 (p90) REVERT: Aa 377 MET cc_start: 0.8117 (mmm) cc_final: 0.7719 (mmm) REVERT: Aa 468 TYR cc_start: 0.8242 (t80) cc_final: 0.7918 (t80) REVERT: Ab 159 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8609 (tptt) REVERT: Ab 213 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: Ab 311 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: Ab 349 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: Ac 20 ASP cc_start: 0.8576 (m-30) cc_final: 0.8200 (m-30) REVERT: Ac 53 MET cc_start: 0.5408 (ttt) cc_final: 0.5098 (ttt) REVERT: Ac 129 MET cc_start: 0.7297 (ptt) cc_final: 0.6965 (ppp) REVERT: Ac 135 TRP cc_start: 0.8641 (t-100) cc_final: 0.8144 (t-100) REVERT: Ac 138 MET cc_start: 0.5723 (tpp) cc_final: 0.4621 (tpp) REVERT: Ac 141 TRP cc_start: 0.7975 (m100) cc_final: 0.7435 (m100) REVERT: Ac 187 PHE cc_start: 0.7566 (m-80) cc_final: 0.7204 (m-80) REVERT: Ac 212 ASN cc_start: 0.8342 (t0) cc_final: 0.7832 (p0) REVERT: Ac 216 ASP cc_start: 0.8983 (t0) cc_final: 0.8533 (t0) REVERT: Ac 217 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8572 (mtmm) REVERT: Ac 242 LEU cc_start: 0.9329 (tp) cc_final: 0.8801 (tp) REVERT: Ac 282 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8532 (ptp90) REVERT: Ac 373 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7522 (mt-10) REVERT: Ad 103 SER cc_start: 0.8823 (m) cc_final: 0.8438 (p) REVERT: Ad 209 ASP cc_start: 0.8352 (m-30) cc_final: 0.8066 (m-30) REVERT: Ad 253 LEU cc_start: 0.7751 (tp) cc_final: 0.7480 (pt) REVERT: Ad 288 MET cc_start: 0.8402 (mmt) cc_final: 0.7803 (mmt) REVERT: Ae 140 MET cc_start: 0.9033 (mmm) cc_final: 0.8760 (mmm) REVERT: Ae 191 GLU cc_start: 0.7436 (pm20) cc_final: 0.7217 (pm20) REVERT: Ae 244 ASP cc_start: 0.1595 (p0) cc_final: 0.0192 (t0) REVERT: Ae 248 ARG cc_start: 0.4263 (ptt180) cc_final: 0.3160 (ptt180) REVERT: Af 33 MET cc_start: 0.8591 (mmm) cc_final: 0.8094 (mtp) REVERT: Af 53 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7920 (tm-30) REVERT: Af 83 LYS cc_start: 0.8568 (mptt) cc_final: 0.8226 (mptt) REVERT: Ag 40 ARG cc_start: 0.8669 (tmm-80) cc_final: 0.7945 (tmm-80) REVERT: Ag 43 ARG cc_start: 0.7650 (ptm160) cc_final: 0.6923 (ttp80) REVERT: Ag 72 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7192 (mmp80) REVERT: Ah 43 LYS cc_start: 0.8831 (tptt) cc_final: 0.8522 (mtpt) REVERT: Ah 89 LYS cc_start: 0.8243 (pptt) cc_final: 0.8027 (pptt) REVERT: Ai 67 THR cc_start: 0.8681 (m) cc_final: 0.8378 (p) REVERT: Aj 13 LEU cc_start: 0.7746 (mm) cc_final: 0.7426 (mm) REVERT: Aj 16 ARG cc_start: 0.7250 (ptt-90) cc_final: 0.6916 (ptt-90) REVERT: Aj 38 GLN cc_start: 0.8118 (tt0) cc_final: 0.7631 (mm-40) REVERT: Ak 23 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6761 (mtm) outliers start: 104 outliers final: 88 residues processed: 697 average time/residue: 0.4287 time to fit residues: 479.0816 Evaluate side-chains 722 residues out of total 3186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 625 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 120 LEU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 237 VAL Chi-restraints excluded: chain AA residue 250 LEU Chi-restraints excluded: chain AA residue 410 CYS Chi-restraints excluded: chain AA residue 417 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AB residue 36 GLN Chi-restraints excluded: chain AB residue 63 LEU Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 113 THR Chi-restraints excluded: chain AB residue 290 GLN Chi-restraints excluded: chain AB residue 332 ASP Chi-restraints excluded: chain AC residue 35 SER Chi-restraints excluded: chain AC residue 42 MET Chi-restraints excluded: chain AC residue 91 PHE Chi-restraints excluded: chain AC residue 128 PHE Chi-restraints excluded: chain AC residue 138 MET Chi-restraints excluded: chain AC residue 156 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 201 HIS Chi-restraints excluded: chain AC residue 228 ASP Chi-restraints excluded: chain AC residue 307 LEU Chi-restraints excluded: chain AC residue 332 LEU Chi-restraints excluded: chain AC residue 343 VAL Chi-restraints excluded: chain AC residue 364 ILE Chi-restraints excluded: chain AC residue 366 MET Chi-restraints excluded: chain AD residue 148 LEU Chi-restraints excluded: chain AD residue 202 ARG Chi-restraints excluded: chain AD residue 205 HIS Chi-restraints excluded: chain AD residue 248 ILE Chi-restraints excluded: chain AD residue 270 VAL Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 80 HIS Chi-restraints excluded: chain AF residue 51 LEU Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 82 THR Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 42 VAL Chi-restraints excluded: chain AH residue 48 LEU Chi-restraints excluded: chain AH residue 82 HIS Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 79 SER Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 137 SER Chi-restraints excluded: chain Aa residue 183 VAL Chi-restraints excluded: chain Aa residue 190 THR Chi-restraints excluded: chain Aa residue 201 VAL Chi-restraints excluded: chain Aa residue 273 SER Chi-restraints excluded: chain Aa residue 369 VAL Chi-restraints excluded: chain Aa residue 399 LEU Chi-restraints excluded: chain Ab residue 112 VAL Chi-restraints excluded: chain Ab residue 158 LEU Chi-restraints excluded: chain Ab residue 213 PHE Chi-restraints excluded: chain Ab residue 258 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 311 GLN Chi-restraints excluded: chain Ab residue 349 GLU Chi-restraints excluded: chain Ab residue 384 MET Chi-restraints excluded: chain Ab residue 432 VAL Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 57 SER Chi-restraints excluded: chain Ac residue 63 PHE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 94 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 123 VAL Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 188 ILE Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 195 VAL Chi-restraints excluded: chain Ac residue 203 THR Chi-restraints excluded: chain Ac residue 205 SER Chi-restraints excluded: chain Ac residue 241 THR Chi-restraints excluded: chain Ac residue 282 ARG Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 294 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 352 GLN Chi-restraints excluded: chain Ac residue 366 MET Chi-restraints excluded: chain Ad residue 175 PHE Chi-restraints excluded: chain Ad residue 201 VAL Chi-restraints excluded: chain Ad residue 225 VAL Chi-restraints excluded: chain Ad residue 300 LEU Chi-restraints excluded: chain Ae residue 133 VAL Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 54 VAL Chi-restraints excluded: chain Ah residue 25 VAL Chi-restraints excluded: chain Ah residue 55 VAL Chi-restraints excluded: chain Ah residue 79 CYS Chi-restraints excluded: chain Ai residue 68 VAL Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 23 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 297 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 316 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 315 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 95 HIS AB 36 GLN ** AB 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS ** AC 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 282 HIS AD 309 HIS ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 193 GLN ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 311 GLN Ab 365 ASN ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 267 HIS Ad 90 HIS Ae 200 HIS Ah 34 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.125238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.094323 restraints weight = 74807.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095845 restraints weight = 42827.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097781 restraints weight = 28503.479| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.7030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.640 31150 Z= 0.247 Angle : 0.800 17.741 42266 Z= 0.384 Chirality : 0.045 0.220 4590 Planarity : 0.005 0.056 5364 Dihedral : 9.359 175.613 4406 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.64 % Allowed : 24.67 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.69 (0.14), residues: 3721 helix: 1.12 (0.12), residues: 2001 sheet: -0.04 (0.28), residues: 372 loop : -0.27 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPAk 38 HIS 0.024 0.001 HISAD 309 PHE 0.033 0.002 PHEAc 276 TYR 0.021 0.002 TYRAF 56 ARG 0.017 0.001 ARGAD 308 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 1735) hydrogen bonds : angle 4.91462 ( 4980) SS BOND : bond 0.00459 ( 7) SS BOND : angle 1.25454 ( 14) covalent geometry : bond 0.00570 (31137) covalent geometry : angle 0.79962 (42252) Misc. bond : bond 0.36157 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12763.96 seconds wall clock time: 223 minutes 57.76 seconds (13437.76 seconds total)