Starting phenix.real_space_refine on Fri Jun 27 05:55:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibc_35339/06_2025/8ibc_35339_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibc_35339/06_2025/8ibc_35339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibc_35339/06_2025/8ibc_35339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibc_35339/06_2025/8ibc_35339.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibc_35339/06_2025/8ibc_35339_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibc_35339/06_2025/8ibc_35339_neut.cif" } resolution = 3.6 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= 0.055 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 152 5.16 5 C 20185 2.51 5 N 5337 2.21 5 O 5743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31431 Number of models: 1 Model: "" Number of chains: 27 Chain: "AA" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3117 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 15, 'TRANS': 383} Chain breaks: 2 Chain: "AB" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3107 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 10, 'TRANS': 403} Chain breaks: 1 Chain: "AC" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "AD" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1896 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "AE" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "AF" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "AG" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "AH" Number of atoms: 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: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 347 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain breaks: 3 Chain: "AJ" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "AK" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 278 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "Aa" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3131 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 15, 'TRANS': 385} Chain breaks: 2 Chain: "Ab" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3101 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 10, 'TRANS': 402} Chain breaks: 2 Chain: "Ac" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "Ad" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1895 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "Ae" Number of atoms: 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: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "Ah" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "Aj" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "Ak" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "AC" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'3PE': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "Ac" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 214 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 118 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Time building chain proxies: 20.08, per 1000 atoms: 0.64 Number of scatterers: 31431 At special positions: 0 Unit cell: (157.3, 144.1, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 152 16.00 P 8 15.00 O 5743 8.00 N 5337 7.00 C 20185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYSAA 338 " - pdb=" SG CYSAA 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 217 " - pdb=" SG CYSAE 236 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 222 " - pdb=" SG CYSAE 238 " distance=2.00 Simple disulfide: pdb=" SG CYSAH 51 " - pdb=" SG CYSAH 65 " distance=2.04 Simple disulfide: pdb=" SG CYSAa 338 " - pdb=" SG CYSAa 360 " distance=2.04 Simple disulfide: pdb=" SG CYSAe 222 " - pdb=" SG CYSAe 238 " distance=2.10 Simple disulfide: pdb=" SG CYSAh 35 " - pdb=" SG CYSAh 79 " distance=2.03 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.77 Conformation dependent library (CDL) restraints added in 4.3 seconds 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7306 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 16 sheets defined 58.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 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: 3.536A pdb=" N GLUAA 145 " --> pdb=" O PROAA 141 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEUAA 147 " --> pdb=" O VALAA 143 " (cutoff:3.500A) Processing helix chain 'AA' and resid 157 through 176 removed outlier: 3.715A 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 398 Processing helix chain 'AA' and resid 405 through 419 Processing helix chain 'AA' and resid 425 through 435 Processing helix chain 'AA' and resid 437 through 449 Processing helix chain 'AA' and resid 467 through 475 Processing helix chain 'AB' and resid 68 through 72 removed outlier: 3.545A 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: 4.713A pdb=" N SERAB 156 " --> pdb=" O ALAAB 152 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLNAB 157 " --> pdb=" O ALAAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 168 through 182 removed outlier: 3.869A pdb=" N ARGAB 172 " --> pdb=" O ASNAB 168 " (cutoff:3.500A) Processing helix chain 'AB' and resid 201 through 213 Processing helix chain 'AB' and resid 214 through 216 No H-bonds generated for 'chain 'AB' and resid 214 through 216' Processing helix chain 'AB' and resid 226 through 237 removed outlier: 3.596A pdb=" N LEUAB 230 " --> pdb=" O SERAB 226 " (cutoff:3.500A) Processing helix chain 'AB' and resid 280 through 294 removed outlier: 3.828A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 308 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: 3.608A 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: 3.580A pdb=" N THRAC 108 " --> pdb=" O GLYAC 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 105 through 108' Processing helix chain 'AC' and resid 109 through 133 Processing helix chain 'AC' and resid 136 through 152 removed outlier: 3.507A pdb=" N LEUAC 150 " --> pdb=" O ILEAC 146 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SERAC 151 " --> pdb=" O THRAC 147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALAAC 152 " --> pdb=" O ASNAC 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 156 through 166 Processing helix chain 'AC' and resid 171 through 202 removed outlier: 3.553A pdb=" N ARGAC 177 " --> pdb=" O ALAAC 173 " (cutoff:3.500A) Proline residue: AC 186 - end of helix Processing helix chain 'AC' and resid 212 through 215 removed outlier: 4.576A pdb=" N ALAAC 215 " --> pdb=" O ASNAC 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 212 through 215' Processing helix chain 'AC' and resid 224 through 244 removed outlier: 3.500A pdb=" N ASPAC 228 " --> pdb=" O TYRAC 224 " (cutoff:3.500A) Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 284 removed outlier: 4.375A pdb=" N PHEAC 276 " --> pdb=" O TRPAC 272 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALAAC 277 " --> pdb=" O TYRAC 273 " (cutoff:3.500A) Processing helix chain 'AC' and resid 286 through 304 removed outlier: 3.505A pdb=" N ILEAC 298 " --> pdb=" O LEUAC 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAC 301 " --> pdb=" O SERAC 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 305 through 308 removed outlier: 3.963A pdb=" N HISAC 308 " --> pdb=" O PROAC 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 305 through 308' Processing helix chain 'AC' and resid 318 through 341 removed outlier: 3.760A pdb=" N GLYAC 340 " --> pdb=" O THRAC 336 " (cutoff:3.500A) Processing helix chain 'AC' and resid 346 through 364 Processing helix chain 'AC' and resid 364 through 377 Processing helix chain 'AD' and resid 106 through 120 Processing helix chain 'AD' and resid 131 through 136 removed outlier: 3.879A pdb=" N LEUAD 135 " --> pdb=" O ALAAD 131 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VALAD 136 " --> pdb=" O TYRAD 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 131 through 136' Processing helix chain 'AD' and resid 141 through 150 Processing helix chain 'AD' and resid 181 through 189 Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 207 through 216 removed outlier: 3.509A pdb=" N VALAD 211 " --> pdb=" O GLYAD 207 " (cutoff:3.500A) Processing helix chain 'AD' and resid 237 through 241 removed outlier: 4.099A pdb=" N ALAAD 241 " --> pdb=" O PROAD 238 " (cutoff:3.500A) Processing helix chain 'AD' and resid 262 through 279 Processing helix chain 'AD' and resid 281 through 317 Proline residue: AD 301 - end of helix removed outlier: 3.864A pdb=" N VALAD 313 " --> pdb=" O HISAD 309 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEUAD 314 " --> pdb=" O LYSAD 310 " (cutoff:3.500A) Processing helix chain 'AE' and resid 107 through 141 Processing helix chain 'AE' and resid 143 through 148 Processing helix chain 'AE' and resid 155 through 159 Processing helix chain 'AE' and resid 180 through 187 Processing helix chain 'AE' and resid 188 through 191 Processing helix chain 'AE' and resid 201 through 205 Processing helix chain 'AF' and resid 15 through 26 removed outlier: 3.720A pdb=" N GLYAF 26 " --> pdb=" O TYRAF 22 " (cutoff:3.500A) Processing helix chain 'AF' and resid 34 through 38 removed outlier: 3.684A 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: 4.176A pdb=" N TYRAF 94 " --> pdb=" O TYRAF 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUAF 97 " --> pdb=" O PROAF 93 " (cutoff:3.500A) Processing helix chain 'AG' and resid 21 through 24 Processing helix chain 'AG' and resid 29 through 72 removed outlier: 3.850A pdb=" N ILEAG 35 " --> pdb=" O PHEAG 31 " (cutoff:3.500A) Proline residue: AG 36 - end of helix removed outlier: 5.323A pdb=" N LEUAG 47 " --> pdb=" O ARGAG 43 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGAG 48 " --> pdb=" O GLUAG 44 " (cutoff:3.500A) Proline residue: AG 51 - end of helix Processing helix chain 'AH' and resid 26 through 38 Processing helix chain 'AH' and resid 38 through 58 Processing helix chain 'AH' and resid 65 through 88 removed outlier: 4.475A pdb=" N ASPAH 71 " --> pdb=" O GLUAH 67 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHEAH 85 " --> pdb=" O ALAAH 81 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LYSAH 86 " --> pdb=" O HISAH 82 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASNAH 87 " --> pdb=" O LYSAH 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUAH 88 " --> pdb=" O LEUAH 84 " (cutoff:3.500A) Processing helix chain 'AI' and resid 11 through 16 Processing helix chain 'AJ' and resid 17 through 48 removed outlier: 4.351A pdb=" N ARGAJ 34 " --> pdb=" O LEUAJ 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 10 through 37 Proline residue: AK 19 - end of helix Processing helix chain 'Aa' and resid 78 through 82 Processing helix chain 'Aa' and resid 88 through 97 Processing helix chain 'Aa' and resid 106 through 116 removed outlier: 4.177A pdb=" N GLUAa 110 " --> pdb=" O GLYAa 106 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILEAa 116 " --> pdb=" O GLUAa 112 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 139 through 152 Processing helix chain 'Aa' and resid 157 through 176 Processing helix chain 'Aa' and resid 178 through 192 Processing helix chain 'Aa' and resid 204 through 210 Processing helix chain 'Aa' and resid 212 through 224 Processing helix chain 'Aa' and resid 225 through 227 No H-bonds generated for 'chain 'Aa' and resid 225 through 227' Processing helix chain 'Aa' and resid 238 through 249 Processing helix chain 'Aa' and resid 299 through 312 removed outlier: 4.195A pdb=" N THRAa 303 " --> pdb=" O PROAa 299 " (cutoff:3.500A) 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 400 removed outlier: 3.903A pdb=" N VALAa 388 " --> pdb=" O THRAa 384 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 405 through 419 Processing helix chain 'Aa' and resid 425 through 435 Processing helix chain 'Aa' and resid 437 through 449 Processing helix chain 'Aa' and resid 467 through 475 Processing helix chain 'Ab' and resid 68 through 72 removed outlier: 3.543A pdb=" N GLUAb 72 " --> pdb=" O SERAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 78 through 86 Processing helix chain 'Ab' and resid 95 through 106 removed outlier: 4.348A pdb=" N ILEAb 103 " --> pdb=" O ILEAb 99 " (cutoff:3.500A) removed outlier: 3.664A 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: 4.282A pdb=" N GLNAb 157 " --> pdb=" O ALAAb 153 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 168 through 182 removed outlier: 3.870A pdb=" N ARGAb 172 " --> pdb=" O ASNAb 168 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 201 through 213 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: 3.593A pdb=" N LEUAb 230 " --> pdb=" O SERAb 226 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLUAb 235 " --> pdb=" O LYSAb 231 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLNAb 236 " --> pdb=" O GLNAb 232 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHEAb 237 " --> pdb=" O VALAb 233 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 280 through 294 removed outlier: 4.196A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALAAb 285 " --> pdb=" O ALAAb 281 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 307 through 312 Processing helix chain 'Ab' and resid 346 through 363 Processing helix chain 'Ab' and resid 367 through 387 Processing helix chain 'Ab' and resid 388 through 404 Processing helix chain 'Ab' and resid 408 through 419 Processing helix chain 'Ab' and resid 420 through 434 Processing helix chain 'Ac' and resid 9 through 19 Processing helix chain 'Ac' and resid 28 through 31 Processing helix chain 'Ac' and resid 32 through 53 Processing helix chain 'Ac' and resid 61 through 72 Processing helix chain 'Ac' and resid 75 through 104 Processing helix chain 'Ac' and resid 105 through 108 removed outlier: 3.580A pdb=" N THRAc 108 " --> pdb=" O GLYAc 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 105 through 108' Processing helix chain 'Ac' and resid 109 through 133 Processing helix chain 'Ac' and resid 136 through 151 removed outlier: 3.525A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 166 Processing helix chain 'Ac' and resid 171 through 202 removed outlier: 3.553A pdb=" N ARGAc 177 " --> pdb=" O ALAAc 173 " (cutoff:3.500A) Proline residue: Ac 186 - end of helix Processing helix chain 'Ac' and resid 212 through 215 removed outlier: 4.576A 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 241 Processing helix chain 'Ac' and resid 252 through 257 Processing helix chain 'Ac' and resid 271 through 273 No H-bonds generated for 'chain 'Ac' and resid 271 through 273' Processing helix chain 'Ac' and resid 274 through 284 Processing helix chain 'Ac' and resid 286 through 304 removed outlier: 3.505A pdb=" N ILEAc 298 " --> pdb=" O LEUAc 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 308 removed outlier: 3.962A 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 96 through 100 Processing helix chain 'Ad' and resid 108 through 120 removed outlier: 3.541A pdb=" N ARGAd 112 " --> pdb=" O THRAd 108 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 121 through 124 removed outlier: 3.510A pdb=" N CYSAd 124 " --> pdb=" O CYSAd 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 121 through 124' Processing helix chain 'Ad' and resid 131 through 136 removed outlier: 3.866A pdb=" N LEUAd 135 " --> pdb=" O ALAAd 131 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALAd 136 " --> pdb=" O TYRAd 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 131 through 136' Processing helix chain 'Ad' and resid 141 through 152 removed outlier: 3.757A pdb=" N VALAd 152 " --> pdb=" O LEUAd 148 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 181 through 189 Processing helix chain 'Ad' and resid 199 through 204 Processing helix chain 'Ad' and resid 206 through 216 Processing helix chain 'Ad' and resid 237 through 241 removed outlier: 4.099A pdb=" N ALAAd 241 " --> pdb=" O PROAd 238 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 262 through 279 Processing helix chain 'Ad' and resid 281 through 317 Proline residue: Ad 301 - end of helix removed outlier: 3.864A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEUAd 314 " --> pdb=" O LYSAd 310 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 79 through 83 removed outlier: 3.744A pdb=" N VALAe 83 " --> pdb=" O HISAe 80 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 104 through 141 removed outlier: 3.693A pdb=" N GLUAe 108 " --> pdb=" O LYSAe 104 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALAAe 109 " --> pdb=" O GLUAe 105 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 143 through 148 Processing helix chain 'Ae' and resid 168 through 172 Processing helix chain 'Ae' and resid 180 through 190 Processing helix chain 'Ae' and resid 200 through 205 Processing helix chain 'Af' and resid 15 through 26 Processing helix 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 91 through 111 removed outlier: 3.859A pdb=" N GLUAf 97 " --> pdb=" O PROAf 93 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 21 through 24 Processing helix chain 'Ag' and resid 29 through 72 removed outlier: 3.850A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 4.580A pdb=" N LEUAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGAg 48 " --> pdb=" O GLUAg 44 " (cutoff:3.500A) Proline residue: Ag 51 - end of helix Processing helix chain 'Ah' and resid 26 through 38 Processing helix chain 'Ah' and resid 38 through 58 Processing helix chain 'Ah' and resid 65 through 88 removed outlier: 4.533A pdb=" N PHEAh 85 " --> pdb=" O ALAAh 81 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYSAh 86 " --> pdb=" O HISAh 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASNAh 87 " --> pdb=" O LYSAh 83 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 8 through 14 Processing helix chain 'Aj' and resid 17 through 48 removed outlier: 3.530A pdb=" N GLUAj 33 " --> pdb=" O ALAAj 29 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARGAj 34 " --> pdb=" O LEUAj 30 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 8 through 37 Proline residue: Ak 19 - end of helix Processing helix chain 'Ak' and resid 40 through 45 removed outlier: 3.789A pdb=" N TRPAk 44 " --> pdb=" O LEUAk 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VALAk 45 " --> pdb=" O ILEAk 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 40 through 45' Processing sheet with id=AA1, first strand: chain 'AA' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'AA' and resid 342 through 348 Processing sheet with id=AA3, first strand: chain 'AB' and resid 41 through 42 removed outlier: 6.157A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEUAB 110 " --> pdb=" O GLYAI 21 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLYAI 21 " --> pdb=" O LEUAB 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.670A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.327A 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 'AD' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'AE' and resid 164 through 166 Processing sheet with id=AA8, first strand: chain 'AE' and resid 234 through 235 removed outlier: 6.660A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AI' and resid 66 through 69 removed outlier: 6.530A pdb=" N VALAb 48 " --> pdb=" O LEUAb 220 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLYAb 222 " --> pdb=" O VALAb 48 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALAAb 50 " --> pdb=" O GLYAb 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Aa' and resid 49 through 52 Processing sheet with id=AB2, first strand: chain 'Aa' and resid 340 through 348 removed outlier: 3.855A pdb=" N SERAa 340 " --> pdb=" O VALAa 359 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Ab' and resid 256 through 260 removed outlier: 3.538A pdb=" N GLYAb 256 " --> pdb=" O LYSAb 436 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ac' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'Ad' and resid 153 through 156 Processing sheet with id=AB6, first strand: chain 'Ae' and resid 174 through 178 removed outlier: 3.834A pdb=" N VALAe 211 " --> pdb=" O ARGAe 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ae' and resid 225 through 226 1796 hydrogen bonds defined for protein. 5166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.48 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 10125 1.35 - 1.54: 21430 1.54 - 1.73: 370 1.73 - 1.92: 258 1.92 - 2.11: 20 Bond restraints: 32203 Sorted by residual: bond pdb=" N PROAI 63 " pdb=" CD PROAI 63 " ideal model delta sigma weight residual 1.473 1.284 0.189 1.40e-02 5.10e+03 1.83e+02 bond pdb=" N PROAd 182 " pdb=" CD PROAd 182 " ideal model delta sigma weight residual 1.473 1.310 0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" CA7 CDLAa 501 " pdb=" OA8 CDLAa 501 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CB7 CDLAc 406 " pdb=" OB8 CDLAc 406 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" CB7 CDLAg 101 " pdb=" OB8 CDLAg 101 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.14e+02 ... (remaining 32198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 42417 3.25 - 6.50: 1082 6.50 - 9.75: 190 9.75 - 13.00: 23 13.00 - 16.25: 5 Bond angle restraints: 43717 Sorted by residual: angle pdb=" N HISAe 242 " pdb=" CA HISAe 242 " pdb=" C HISAe 242 " ideal model delta sigma weight residual 109.11 125.36 -16.25 1.42e+00 4.96e-01 1.31e+02 angle pdb=" N PROAI 63 " pdb=" CA PROAI 63 " pdb=" CB PROAI 63 " ideal model delta sigma weight residual 103.25 93.84 9.41 8.80e-01 1.29e+00 1.14e+02 angle pdb=" N LEUAA 187 " pdb=" CA LEUAA 187 " pdb=" C LEUAA 187 " ideal model delta sigma weight residual 112.38 100.39 11.99 1.22e+00 6.72e-01 9.66e+01 angle pdb=" N GLUAa 385 " pdb=" CA GLUAa 385 " pdb=" C GLUAa 385 " ideal model delta sigma weight residual 111.36 121.95 -10.59 1.09e+00 8.42e-01 9.44e+01 angle pdb=" CA PROAI 63 " pdb=" N PROAI 63 " pdb=" CD PROAI 63 " ideal model delta sigma weight residual 112.00 124.81 -12.81 1.40e+00 5.10e-01 8.37e+01 ... (remaining 43712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 18819 35.82 - 71.64: 246 71.64 - 107.46: 30 107.46 - 143.29: 3 143.29 - 179.11: 4 Dihedral angle restraints: 19102 sinusoidal: 7755 harmonic: 11347 Sorted by residual: dihedral pdb=" C11 U10AC 404 " pdb=" C8 U10AC 404 " pdb=" C9 U10AC 404 " pdb=" C7 U10AC 404 " ideal model delta sinusoidal sigma weight residual -179.95 -0.84 -179.11 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C12 U10AC 404 " pdb=" C13 U10AC 404 " pdb=" C14 U10AC 404 " pdb=" C16 U10AC 404 " ideal model delta sinusoidal sigma weight residual 178.80 -0.20 179.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2B HEMAC 402 " pdb=" C3B HEMAC 402 " pdb=" CAB HEMAC 402 " pdb=" CBB HEMAC 402 " ideal model delta sinusoidal sigma weight residual -0.00 -78.32 78.32 2 1.00e+01 1.00e-02 4.60e+01 ... (remaining 19099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4135 0.079 - 0.159: 545 0.159 - 0.238: 53 0.238 - 0.318: 10 0.318 - 0.397: 3 Chirality restraints: 4746 Sorted by residual: chirality pdb=" CA SERAe 241 " pdb=" N SERAe 241 " pdb=" C SERAe 241 " pdb=" CB SERAe 241 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYRAe 243 " pdb=" N TYRAe 243 " pdb=" C TYRAe 243 " pdb=" CB TYRAe 243 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA ILEAA 471 " pdb=" N ILEAA 471 " pdb=" C ILEAA 471 " pdb=" CB ILEAA 471 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 4743 not shown) Planarity restraints: 5552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 UQ6Ac 405 " -0.315 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C13 UQ6Ac 405 " 0.459 2.00e-02 2.50e+03 pdb=" C14 UQ6Ac 405 " 0.098 2.00e-02 2.50e+03 pdb=" C15 UQ6Ac 405 " -0.186 2.00e-02 2.50e+03 pdb=" C16 UQ6Ac 405 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ6Ac 405 " -0.268 2.00e-02 2.50e+03 2.25e-01 6.34e+02 pdb=" C18 UQ6Ac 405 " 0.377 2.00e-02 2.50e+03 pdb=" C19 UQ6Ac 405 " 0.082 2.00e-02 2.50e+03 pdb=" C20 UQ6Ac 405 " -0.181 2.00e-02 2.50e+03 pdb=" C21 UQ6Ac 405 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ6Ac 405 " -0.179 2.00e-02 2.50e+03 2.20e-01 6.03e+02 pdb=" C11 UQ6Ac 405 " -0.007 2.00e-02 2.50e+03 pdb=" C7 UQ6Ac 405 " -0.261 2.00e-02 2.50e+03 pdb=" C8 UQ6Ac 405 " 0.368 2.00e-02 2.50e+03 pdb=" C9 UQ6Ac 405 " 0.078 2.00e-02 2.50e+03 ... (remaining 5549 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 694 2.63 - 3.20: 32327 3.20 - 3.77: 53992 3.77 - 4.33: 75541 4.33 - 4.90: 116667 Nonbonded interactions: 279221 Sorted by model distance: nonbonded pdb=" O TYRAC 223 " pdb=" NE1 TRPAD 311 " model vdw 2.063 3.120 nonbonded pdb=" NE2 HISAC 83 " pdb="FE HEMAC 401 " model vdw 2.076 3.080 nonbonded pdb=" NE2 HISAc 83 " pdb="FE HEMAc 401 " model vdw 2.096 3.080 nonbonded pdb=" NH2 ARGAa 58 " pdb=" O LEUAa 417 " model vdw 2.102 3.120 nonbonded pdb=" O GLYAD 100 " pdb=" NZ LYSAD 286 " model vdw 2.125 3.120 ... (remaining 279216 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 44 through 477) selection = (chain 'Aa' and (resid 44 through 255 or resid 267 through 312 or resid 338 thro \ ugh 477)) } ncs_group { reference = (chain 'AB' and (resid 36 through 300 or resid 307 through 312 or resid 316 thro \ ugh 453)) selection = (chain 'Ab' and (resid 36 through 300 or resid 307 through 453)) } ncs_group { reference = chain 'AC' selection = (chain 'Ac' and (resid 8 through 380 or resid 401 through 402 or (resid 403 and \ (name N or name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C3 or name C31 or name C32 \ or name C33 or name C34 or name O11 or name O12 or name O13 or name O14 or name \ O21 or name O22 or name O31 or name O32 or name P )) or resid 404 through 405)) \ } ncs_group { reference = (chain 'AD' and (resid 88 through 324 or resid 401)) selection = (chain 'Ad' and (resid 88 through 324 or resid 401)) } ncs_group { reference = chain 'AE' selection = (chain 'Ae' and (resid 79 through 103 or resid 107 through 274)) } ncs_group { reference = chain 'AF' selection = chain 'Af' } ncs_group { reference = chain 'AG' selection = (chain 'Ag' and resid 4 through 79) } ncs_group { reference = chain 'AH' selection = (chain 'Ah' and resid 25 through 88) } 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 71.590 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.341 32218 Z= 0.607 Angle : 1.253 29.332 43733 Z= 0.805 Chirality : 0.055 0.397 4746 Planarity : 0.009 0.267 5552 Dihedral : 13.400 179.108 11772 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 32.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.12), residues: 3849 helix: -0.76 (0.10), residues: 2032 sheet: -0.50 (0.27), residues: 389 loop : -1.59 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPAc 141 HIS 0.009 0.001 HISAE 219 PHE 0.049 0.002 PHEAc 183 TYR 0.031 0.002 TYRAF 56 ARG 0.007 0.001 ARGAE 250 Details of bonding type rmsd hydrogen bonds : bond 0.18840 ( 1796) hydrogen bonds : angle 7.50291 ( 5166) SS BOND : bond 0.02954 ( 8) SS BOND : angle 8.79038 ( 16) covalent geometry : bond 0.00959 (32203) covalent geometry : angle 1.24196 (43717) Misc. bond : bond 0.17404 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1529 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1523 time to evaluate : 3.497 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: AA 444 ILE cc_start: 0.7871 (mt) cc_final: 0.7583 (mt) REVERT: AB 166 PHE cc_start: 0.7600 (m-10) cc_final: 0.7217 (m-10) REVERT: AB 390 GLU cc_start: 0.8207 (pp20) cc_final: 0.7961 (pm20) REVERT: AC 25 SER cc_start: 0.6790 (p) cc_final: 0.5552 (p) REVERT: AC 53 MET cc_start: 0.7488 (mtt) cc_final: 0.6739 (mtm) REVERT: AC 113 TRP cc_start: 0.7773 (t-100) cc_final: 0.7456 (t-100) REVERT: AC 118 LEU cc_start: 0.8603 (tp) cc_final: 0.8285 (tp) REVERT: AC 309 THR cc_start: 0.6967 (p) cc_final: 0.6640 (t) REVERT: AC 343 VAL cc_start: 0.8695 (t) cc_final: 0.8427 (p) REVERT: AE 91 TYR cc_start: 0.6382 (m-80) cc_final: 0.6060 (m-80) REVERT: AE 135 GLN cc_start: 0.7319 (mt0) cc_final: 0.6990 (mt0) REVERT: AE 167 PHE cc_start: 0.7986 (m-80) cc_final: 0.6980 (m-10) REVERT: AF 57 ASN cc_start: 0.7370 (m-40) cc_final: 0.7050 (m-40) REVERT: AG 17 TYR cc_start: 0.7526 (m-80) cc_final: 0.7206 (m-80) REVERT: AG 54 VAL cc_start: 0.8643 (t) cc_final: 0.8440 (t) REVERT: AI 20 ARG cc_start: 0.6800 (mtm180) cc_final: 0.6394 (mpt180) REVERT: AI 73 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8261 (Cg_endo) REVERT: Aa 149 ASP cc_start: 0.8281 (m-30) cc_final: 0.7995 (m-30) REVERT: Aa 440 MET cc_start: 0.7607 (ptp) cc_final: 0.7395 (ptm) REVERT: Ab 292 LEU cc_start: 0.8259 (tp) cc_final: 0.8034 (tp) REVERT: Ab 382 TYR cc_start: 0.8530 (t80) cc_final: 0.8165 (t80) REVERT: Ac 89 MET cc_start: 0.8377 (tpp) cc_final: 0.7840 (tmm) REVERT: Ac 118 LEU cc_start: 0.8384 (tp) cc_final: 0.8032 (tp) REVERT: Ac 230 LEU cc_start: 0.8792 (tp) cc_final: 0.8384 (tt) REVERT: Ac 343 VAL cc_start: 0.8874 (t) cc_final: 0.8571 (p) REVERT: Ad 104 SER cc_start: 0.8938 (p) cc_final: 0.8685 (t) REVERT: Ad 128 ASP cc_start: 0.8254 (m-30) cc_final: 0.8019 (m-30) REVERT: Ad 154 VAL cc_start: 0.7892 (t) cc_final: 0.7654 (t) REVERT: Ae 243 TYR cc_start: 0.5258 (p90) cc_final: 0.5051 (p90) REVERT: Ae 249 ILE cc_start: 0.7322 (tp) cc_final: 0.6945 (tp) REVERT: Af 68 ASP cc_start: 0.8273 (t70) cc_final: 0.7967 (t0) REVERT: Ag 57 TYR cc_start: 0.8423 (t80) cc_final: 0.7911 (t80) REVERT: Aj 23 LEU cc_start: 0.8905 (tp) cc_final: 0.8275 (tp) REVERT: Ak 23 MET cc_start: 0.7382 (mmt) cc_final: 0.7134 (tpp) REVERT: Ak 42 LEU cc_start: 0.8215 (mt) cc_final: 0.7948 (mp) outliers start: 6 outliers final: 2 residues processed: 1527 average time/residue: 0.4737 time to fit residues: 1115.1413 Evaluate side-chains 876 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 874 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 223 VAL Chi-restraints excluded: chain Aa residue 249 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 345 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 43 GLN AA 103 ASN AA 173 GLN ** AA 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AB 139 ASN AB 167 GLN AB 236 GLN AB 284 ASN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 312 GLN AC 345 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN AD 190 ASN ** AE 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 74 GLN AH 37 GLN AH 78 HIS AH 82 HIS ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 119 HIS Aa 207 ASN Aa 434 GLN Ab 118 ASN ** Ab 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 284 ASN Ab 298 HIS ** Ac 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 148 ASN Ac 331 ASN Ac 341 GLN Ad 90 HIS ** Ad 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 155 GLN Ad 190 ASN ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Ah 82 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.124435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095759 restraints weight = 74939.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098968 restraints weight = 36579.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101150 restraints weight = 23737.305| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.579 32218 Z= 0.213 Angle : 0.825 21.459 43733 Z= 0.402 Chirality : 0.048 0.438 4746 Planarity : 0.006 0.093 5552 Dihedral : 11.501 177.695 4532 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.33 % Allowed : 15.22 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.16 (0.13), residues: 3849 helix: 0.75 (0.11), residues: 2031 sheet: 0.03 (0.28), residues: 354 loop : -0.67 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPAC 77 HIS 0.009 0.002 HISAC 201 PHE 0.028 0.002 PHEAc 276 TYR 0.026 0.002 TYRAc 75 ARG 0.013 0.001 ARGAA 278 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 1796) hydrogen bonds : angle 5.37772 ( 5166) SS BOND : bond 0.00728 ( 8) SS BOND : angle 2.17885 ( 16) covalent geometry : bond 0.00467 (32203) covalent geometry : angle 0.82389 (43717) Misc. bond : bond 0.38023 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 918 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 114 GLU cc_start: 0.8505 (tp30) cc_final: 0.7993 (mt-10) REVERT: AA 123 TYR cc_start: 0.7686 (p90) cc_final: 0.7419 (p90) REVERT: AA 240 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8450 (tp-100) REVERT: AA 444 ILE cc_start: 0.8890 (mt) cc_final: 0.8642 (mm) REVERT: AB 155 ARG cc_start: 0.8796 (mtm180) cc_final: 0.8584 (mtt180) REVERT: AB 197 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7257 (ttm) REVERT: AB 235 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: AC 36 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7950 (tp) REVERT: AC 118 LEU cc_start: 0.9202 (tp) cc_final: 0.8932 (tp) REVERT: AC 133 LEU cc_start: 0.8818 (mt) cc_final: 0.8613 (mt) REVERT: AC 159 THR cc_start: 0.8474 (m) cc_final: 0.8242 (p) REVERT: AC 216 ASP cc_start: 0.8449 (t0) cc_final: 0.8056 (t70) REVERT: AC 232 ILE cc_start: 0.9158 (mm) cc_final: 0.8861 (mt) REVERT: AC 242 LEU cc_start: 0.9035 (tp) cc_final: 0.8754 (tp) REVERT: AC 244 LEU cc_start: 0.8968 (mt) cc_final: 0.8539 (mt) REVERT: AD 96 TRP cc_start: 0.7419 (m100) cc_final: 0.6899 (m100) REVERT: AD 164 MET cc_start: 0.7168 (tmm) cc_final: 0.6723 (tmm) REVERT: AD 190 ASN cc_start: 0.8572 (m-40) cc_final: 0.8143 (p0) REVERT: AE 165 MET cc_start: 0.4489 (tpp) cc_final: 0.4261 (tpp) REVERT: AE 167 PHE cc_start: 0.7891 (m-80) cc_final: 0.7113 (m-10) REVERT: AE 170 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8390 (mtm180) REVERT: AE 231 PHE cc_start: 0.7199 (t80) cc_final: 0.6123 (t80) REVERT: AF 33 MET cc_start: 0.7201 (mmt) cc_final: 0.6559 (mmt) REVERT: AF 53 GLU cc_start: 0.7621 (tp30) cc_final: 0.7142 (tp30) REVERT: AF 57 ASN cc_start: 0.8145 (m-40) cc_final: 0.7741 (m-40) REVERT: AF 101 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8147 (mt-10) REVERT: AG 17 TYR cc_start: 0.7971 (m-80) cc_final: 0.7462 (m-80) REVERT: AG 24 GLN cc_start: 0.7768 (pt0) cc_final: 0.7462 (pt0) REVERT: AG 71 LYS cc_start: 0.8068 (tptp) cc_final: 0.7613 (ptmm) REVERT: AG 78 TYR cc_start: 0.7217 (m-80) cc_final: 0.6869 (m-80) REVERT: AH 87 ASN cc_start: 0.8202 (t0) cc_final: 0.7961 (t0) REVERT: AI 73 PRO cc_start: 0.8257 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: AK 24 TRP cc_start: 0.6237 (m100) cc_final: 0.5806 (m100) REVERT: Aa 162 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7143 (tm-30) REVERT: Aa 199 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: Aa 274 GLU cc_start: 0.8551 (pt0) cc_final: 0.8000 (pt0) REVERT: Aa 377 MET cc_start: 0.9472 (tpp) cc_final: 0.9035 (tpp) REVERT: Aa 381 THR cc_start: 0.8940 (m) cc_final: 0.8501 (p) REVERT: Aa 451 ASP cc_start: 0.6859 (t0) cc_final: 0.6615 (t0) REVERT: Aa 475 MET cc_start: 0.8259 (tpp) cc_final: 0.7678 (tpp) REVERT: Aa 477 TRP cc_start: 0.7699 (m-10) cc_final: 0.7425 (m-10) REVERT: Ab 134 MET cc_start: 0.8428 (ptt) cc_final: 0.8042 (ptp) REVERT: Ab 139 ASN cc_start: 0.6988 (m-40) cc_final: 0.6786 (t0) REVERT: Ab 173 ILE cc_start: 0.8414 (tp) cc_final: 0.7721 (tp) REVERT: Ab 199 LYS cc_start: 0.8293 (tttm) cc_final: 0.7944 (tttm) REVERT: Ab 218 MET cc_start: 0.7898 (mtm) cc_final: 0.7638 (mtp) REVERT: Ab 395 GLU cc_start: 0.8400 (tp30) cc_final: 0.7831 (tp30) REVERT: Ac 15 ASN cc_start: 0.8152 (t0) cc_final: 0.7889 (t0) REVERT: Ac 100 ARG cc_start: 0.8809 (tmm-80) cc_final: 0.8503 (tmm-80) REVERT: Ac 165 TRP cc_start: 0.7243 (m-10) cc_final: 0.6766 (m-10) REVERT: Ac 216 ASP cc_start: 0.8609 (t0) cc_final: 0.8138 (t0) REVERT: Ac 271 GLU cc_start: 0.7773 (tt0) cc_final: 0.7191 (tt0) REVERT: Ac 272 TRP cc_start: 0.8479 (p-90) cc_final: 0.8237 (p-90) REVERT: Ac 352 GLN cc_start: 0.8547 (mt0) cc_final: 0.8310 (mt0) REVERT: Ad 119 GLN cc_start: 0.8857 (mt0) cc_final: 0.8557 (tm-30) REVERT: Ad 127 MET cc_start: 0.8082 (ttm) cc_final: 0.7842 (ttm) REVERT: Ad 134 HIS cc_start: 0.8114 (m90) cc_final: 0.7589 (m90) REVERT: Ad 189 ASN cc_start: 0.7453 (m-40) cc_final: 0.7227 (m-40) REVERT: Ae 108 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8079 (mp0) REVERT: Ae 165 MET cc_start: 0.6951 (tpp) cc_final: 0.6705 (mpp) REVERT: Ae 187 GLU cc_start: 0.7813 (mm-30) cc_final: 0.6804 (mm-30) REVERT: Af 33 MET cc_start: 0.8573 (mtm) cc_final: 0.8240 (mtm) REVERT: Af 60 MET cc_start: 0.8994 (tpp) cc_final: 0.7989 (mpp) REVERT: Af 97 GLU cc_start: 0.8233 (tp30) cc_final: 0.8026 (tp30) REVERT: Af 101 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8376 (mt-10) REVERT: Ag 11 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8558 (mt) REVERT: Ag 29 SER cc_start: 0.8817 (m) cc_final: 0.8261 (t) REVERT: Ag 33 LYS cc_start: 0.8859 (mtpp) cc_final: 0.8483 (mtmt) REVERT: Ag 47 LEU cc_start: 0.9116 (mt) cc_final: 0.8664 (tp) REVERT: Ag 57 TYR cc_start: 0.8783 (t80) cc_final: 0.8509 (t80) REVERT: Ag 66 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8150 (tm-30) REVERT: Ag 70 SER cc_start: 0.9348 (t) cc_final: 0.9073 (p) REVERT: Ah 50 LEU cc_start: 0.9250 (mt) cc_final: 0.8913 (mt) REVERT: Ah 66 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7700 (t) REVERT: Aj 23 LEU cc_start: 0.9230 (tp) cc_final: 0.8642 (tp) REVERT: Aj 43 ILE cc_start: 0.8894 (mm) cc_final: 0.8682 (tt) REVERT: Ak 23 MET cc_start: 0.7046 (mmt) cc_final: 0.6541 (tpp) REVERT: Ak 39 ARG cc_start: 0.7268 (tmt-80) cc_final: 0.6625 (ptt-90) outliers start: 143 outliers final: 78 residues processed: 997 average time/residue: 0.5411 time to fit residues: 878.4237 Evaluate side-chains 870 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 786 time to evaluate : 4.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 127 GLU Chi-restraints excluded: chain AA residue 150 ILE Chi-restraints excluded: chain AA residue 183 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 220 LEU Chi-restraints excluded: chain AA residue 252 SER Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 369 VAL Chi-restraints excluded: chain AA residue 388 VAL Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 79 THR Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 128 SER Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 197 MET Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 258 ILE Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 413 LEU Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 36 LEU Chi-restraints excluded: chain AC residue 37 LEU Chi-restraints excluded: chain AC residue 82 MET Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 236 PHE Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AD residue 211 VAL Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AE residue 176 VAL Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 16 SER Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 368 MET Chi-restraints excluded: chain Aa residue 379 LEU Chi-restraints excluded: chain Ab residue 65 VAL Chi-restraints excluded: chain Ab residue 69 SER Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 177 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 451 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 332 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 43 ASP Chi-restraints excluded: chain Af residue 67 LEU Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 56 VAL Chi-restraints excluded: chain Ah residue 66 THR Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 54 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 325 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 369 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 chunk 3 optimal weight: 0.0070 chunk 232 optimal weight: 0.7980 chunk 375 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 207 ASN ** AA 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AB 139 ASN AC 44 GLN AD 115 GLN ** AD 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 80 GLN ** Aa 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN ** Ab 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 68 HIS Ac 331 ASN ** Ah 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 82 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.123341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094570 restraints weight = 75426.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097789 restraints weight = 36659.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099924 restraints weight = 23752.337| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.510 32218 Z= 0.169 Angle : 0.720 19.130 43733 Z= 0.351 Chirality : 0.045 0.368 4746 Planarity : 0.005 0.068 5552 Dihedral : 10.888 172.067 4531 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.21 % Allowed : 18.10 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.62 (0.14), residues: 3849 helix: 1.10 (0.11), residues: 2030 sheet: 0.16 (0.28), residues: 361 loop : -0.39 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPAc 77 HIS 0.021 0.001 HISAH 78 PHE 0.026 0.002 PHEAg 67 TYR 0.020 0.002 TYRAF 84 ARG 0.008 0.001 ARGAh 45 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 1796) hydrogen bonds : angle 5.07020 ( 5166) SS BOND : bond 0.01839 ( 8) SS BOND : angle 3.60704 ( 16) covalent geometry : bond 0.00375 (32203) covalent geometry : angle 0.71703 (43717) Misc. bond : bond 0.32827 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 850 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 114 GLU cc_start: 0.8338 (tp30) cc_final: 0.7779 (mm-30) REVERT: AA 123 TYR cc_start: 0.7764 (p90) cc_final: 0.7463 (p90) REVERT: AA 240 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8352 (tp-100) REVERT: AA 255 ARG cc_start: 0.7022 (mpp-170) cc_final: 0.6709 (mpp-170) REVERT: AA 444 ILE cc_start: 0.8892 (mt) cc_final: 0.8664 (mm) REVERT: AB 104 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8204 (tt0) REVERT: AB 197 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7242 (mtp) REVERT: AB 235 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: AC 26 ASN cc_start: 0.8899 (p0) cc_final: 0.8611 (p0) REVERT: AC 160 LEU cc_start: 0.8777 (tt) cc_final: 0.8521 (tt) REVERT: AC 163 TRP cc_start: 0.8389 (t60) cc_final: 0.7703 (t60) REVERT: AC 201 HIS cc_start: 0.7570 (t-90) cc_final: 0.7356 (t-170) REVERT: AC 216 ASP cc_start: 0.8505 (t0) cc_final: 0.8185 (t0) REVERT: AC 244 LEU cc_start: 0.9015 (mt) cc_final: 0.8598 (mt) REVERT: AC 316 MET cc_start: 0.8344 (ttm) cc_final: 0.7906 (ttm) REVERT: AC 337 TRP cc_start: 0.9039 (t60) cc_final: 0.8572 (t60) REVERT: AD 96 TRP cc_start: 0.7360 (m100) cc_final: 0.6876 (m100) REVERT: AD 164 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6095 (tmm) REVERT: AD 190 ASN cc_start: 0.8555 (m-40) cc_final: 0.8239 (p0) REVERT: AE 165 MET cc_start: 0.5327 (tpp) cc_final: 0.5032 (tpp) REVERT: AE 167 PHE cc_start: 0.7987 (m-80) cc_final: 0.7374 (m-10) REVERT: AE 169 TRP cc_start: 0.5416 (t60) cc_final: 0.4673 (t60) REVERT: AE 170 ARG cc_start: 0.8589 (mtm180) cc_final: 0.7868 (mtp85) REVERT: AF 33 MET cc_start: 0.7381 (mmt) cc_final: 0.6784 (mmt) REVERT: AF 38 LEU cc_start: 0.9011 (mm) cc_final: 0.8772 (mm) REVERT: AF 57 ASN cc_start: 0.8089 (m-40) cc_final: 0.7734 (m-40) REVERT: AF 99 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8326 (pt) REVERT: AF 101 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8420 (mt-10) REVERT: AG 17 TYR cc_start: 0.8038 (m-80) cc_final: 0.7550 (m-80) REVERT: AG 24 GLN cc_start: 0.7715 (pt0) cc_final: 0.7480 (pt0) REVERT: AG 71 LYS cc_start: 0.8033 (tptp) cc_final: 0.7573 (ptmm) REVERT: AG 78 TYR cc_start: 0.7175 (m-80) cc_final: 0.6813 (m-80) REVERT: AH 39 GLU cc_start: 0.8931 (pm20) cc_final: 0.8515 (pp20) REVERT: AI 73 PRO cc_start: 0.8194 (Cg_exo) cc_final: 0.7935 (Cg_endo) REVERT: Aa 162 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7159 (tm-30) REVERT: Aa 229 MET cc_start: 0.7454 (mmt) cc_final: 0.7004 (mmt) REVERT: Aa 381 THR cc_start: 0.8859 (m) cc_final: 0.8619 (p) REVERT: Aa 410 CYS cc_start: 0.8493 (p) cc_final: 0.7923 (p) REVERT: Aa 435 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7788 (tm-30) REVERT: Ab 83 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8539 (tt) REVERT: Ab 173 ILE cc_start: 0.8589 (tp) cc_final: 0.7944 (tp) REVERT: Ab 199 LYS cc_start: 0.8130 (tttm) cc_final: 0.7780 (tttm) REVERT: Ab 395 GLU cc_start: 0.8427 (tp30) cc_final: 0.7845 (tp30) REVERT: Ac 12 LYS cc_start: 0.7719 (tmtt) cc_final: 0.7016 (mptt) REVERT: Ac 20 ASP cc_start: 0.8041 (m-30) cc_final: 0.7759 (m-30) REVERT: Ac 44 GLN cc_start: 0.7877 (mm110) cc_final: 0.7654 (mm-40) REVERT: Ac 100 ARG cc_start: 0.8850 (tmm-80) cc_final: 0.8471 (tmm-80) REVERT: Ac 165 TRP cc_start: 0.7424 (m-10) cc_final: 0.6937 (m-10) REVERT: Ac 216 ASP cc_start: 0.8627 (t0) cc_final: 0.8308 (t0) REVERT: Ac 280 ILE cc_start: 0.9349 (mm) cc_final: 0.9127 (mm) REVERT: Ac 376 MET cc_start: 0.8534 (ttm) cc_final: 0.8266 (ttm) REVERT: Ad 127 MET cc_start: 0.8099 (ttm) cc_final: 0.7794 (ttm) REVERT: Ad 134 HIS cc_start: 0.8082 (m90) cc_final: 0.7608 (m90) REVERT: Ad 164 MET cc_start: 0.8129 (ptp) cc_final: 0.7837 (ppp) REVERT: Ad 189 ASN cc_start: 0.7411 (m-40) cc_final: 0.7086 (m-40) REVERT: Ad 275 ARG cc_start: 0.8004 (tpt-90) cc_final: 0.7482 (tpt170) REVERT: Ae 140 MET cc_start: 0.8129 (mtp) cc_final: 0.7285 (ttm) REVERT: Ae 165 MET cc_start: 0.7001 (tpp) cc_final: 0.6525 (mpp) REVERT: Af 33 MET cc_start: 0.8556 (mtm) cc_final: 0.8031 (mtm) REVERT: Af 60 MET cc_start: 0.9003 (tpp) cc_final: 0.8109 (mpp) REVERT: Af 70 THR cc_start: 0.9163 (m) cc_final: 0.8939 (p) REVERT: Af 96 LYS cc_start: 0.8885 (mttm) cc_final: 0.8607 (mttm) REVERT: Af 103 LYS cc_start: 0.9359 (tppt) cc_final: 0.9144 (mmmm) REVERT: Ag 29 SER cc_start: 0.8887 (m) cc_final: 0.8398 (t) REVERT: Ag 47 LEU cc_start: 0.9086 (mt) cc_final: 0.8712 (tp) REVERT: Ag 57 TYR cc_start: 0.8669 (t80) cc_final: 0.8438 (t80) REVERT: Ag 66 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7806 (tm-30) REVERT: Ag 70 SER cc_start: 0.9345 (t) cc_final: 0.9015 (p) REVERT: Ah 32 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7588 (ttm110) REVERT: Ah 45 ARG cc_start: 0.8212 (tpt90) cc_final: 0.7847 (ptp-170) REVERT: Ah 62 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7255 (mp0) REVERT: Ah 82 HIS cc_start: 0.8431 (m90) cc_final: 0.8105 (m170) REVERT: Aj 20 THR cc_start: 0.7914 (m) cc_final: 0.7626 (p) REVERT: Aj 23 LEU cc_start: 0.9230 (tp) cc_final: 0.8606 (tp) REVERT: Aj 43 ILE cc_start: 0.9016 (mm) cc_final: 0.8801 (tt) REVERT: Aj 53 TRP cc_start: 0.8177 (t-100) cc_final: 0.7375 (t-100) REVERT: Ak 23 MET cc_start: 0.7259 (mmt) cc_final: 0.6613 (tpp) outliers start: 139 outliers final: 78 residues processed: 916 average time/residue: 0.4489 time to fit residues: 664.8275 Evaluate side-chains 834 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 751 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 183 VAL Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 366 ASP Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 69 SER Chi-restraints excluded: chain AB residue 79 THR Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 139 ASN Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 197 MET Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 82 MET Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 159 ASN Chi-restraints excluded: chain AD residue 164 MET Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AH residue 84 LEU Chi-restraints excluded: chain AI residue 16 SER Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 83 LEU Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 194 ASP Chi-restraints excluded: chain Ab residue 343 GLN Chi-restraints excluded: chain Ab residue 451 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 238 ILE Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 364 ILE Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 239 HIS Chi-restraints excluded: chain Af residue 43 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ah residue 52 ASP Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 10 LEU Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 49 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 349 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 126 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 317 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 402 HIS AC 44 GLN AC 196 HIS AC 263 ASN ** AD 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 37 ASN AH 78 HIS Aa 49 GLN Aa 393 ASN Aa 434 GLN Ab 139 ASN ** Ab 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN Ac 352 GLN ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094590 restraints weight = 75339.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097850 restraints weight = 36730.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.100031 restraints weight = 23690.989| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.424 32218 Z= 0.146 Angle : 0.694 17.603 43733 Z= 0.335 Chirality : 0.044 0.339 4746 Planarity : 0.005 0.075 5552 Dihedral : 10.400 168.136 4531 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.36 % Allowed : 19.34 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.80 (0.14), residues: 3849 helix: 1.24 (0.11), residues: 2028 sheet: 0.31 (0.28), residues: 361 loop : -0.32 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRPAC 113 HIS 0.007 0.001 HISAb 227 PHE 0.030 0.001 PHEAJ 32 TYR 0.017 0.001 TYRAg 60 ARG 0.011 0.001 ARGAH 54 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 1796) hydrogen bonds : angle 4.90342 ( 5166) SS BOND : bond 0.00379 ( 8) SS BOND : angle 2.43607 ( 16) covalent geometry : bond 0.00326 (32203) covalent geometry : angle 0.69221 (43717) Misc. bond : bond 0.28598 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 799 time to evaluate : 3.500 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: AA 114 GLU cc_start: 0.8296 (tp30) cc_final: 0.7812 (mm-30) REVERT: AA 240 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8250 (tp-100) REVERT: AA 444 ILE cc_start: 0.8908 (mt) cc_final: 0.8686 (mm) REVERT: AB 197 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7199 (ttm) REVERT: AB 235 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: AB 240 MET cc_start: 0.7342 (pmm) cc_final: 0.6803 (mtt) REVERT: AC 26 ASN cc_start: 0.8896 (p0) cc_final: 0.8586 (p0) REVERT: AC 36 LEU cc_start: 0.8447 (tp) cc_final: 0.8114 (mp) REVERT: AC 163 TRP cc_start: 0.8419 (t60) cc_final: 0.7881 (t60) REVERT: AC 216 ASP cc_start: 0.8489 (t0) cc_final: 0.7927 (t0) REVERT: AC 244 LEU cc_start: 0.9059 (mt) cc_final: 0.8528 (mt) REVERT: AC 316 MET cc_start: 0.8433 (ttm) cc_final: 0.8035 (ttm) REVERT: AC 337 TRP cc_start: 0.9021 (t60) cc_final: 0.8817 (t60) REVERT: AD 96 TRP cc_start: 0.7361 (m100) cc_final: 0.6900 (m100) REVERT: AD 164 MET cc_start: 0.6773 (tmm) cc_final: 0.5575 (tmm) REVERT: AD 166 MET cc_start: 0.7427 (mpp) cc_final: 0.7054 (mpp) REVERT: AD 170 LYS cc_start: 0.8673 (tptt) cc_final: 0.8426 (tptm) REVERT: AD 190 ASN cc_start: 0.8521 (m-40) cc_final: 0.8243 (p0) REVERT: AD 276 TRP cc_start: 0.8450 (t60) cc_final: 0.7903 (t60) REVERT: AE 91 TYR cc_start: 0.8292 (m-80) cc_final: 0.8003 (m-80) REVERT: AE 165 MET cc_start: 0.5415 (tpp) cc_final: 0.5141 (tpp) REVERT: AE 167 PHE cc_start: 0.8072 (m-80) cc_final: 0.7456 (m-10) REVERT: AE 169 TRP cc_start: 0.5439 (t60) cc_final: 0.4797 (t60) REVERT: AE 170 ARG cc_start: 0.8566 (mtm180) cc_final: 0.7895 (mtp85) REVERT: AE 248 ARG cc_start: 0.6942 (mtp85) cc_final: 0.5937 (mmm160) REVERT: AF 33 MET cc_start: 0.7494 (mmt) cc_final: 0.6853 (mmt) REVERT: AF 38 LEU cc_start: 0.9030 (mm) cc_final: 0.8785 (mm) REVERT: AF 57 ASN cc_start: 0.8051 (m-40) cc_final: 0.7737 (m-40) REVERT: AF 99 ILE cc_start: 0.8904 (mm) cc_final: 0.8317 (pt) REVERT: AF 101 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8435 (mt-10) REVERT: AG 17 TYR cc_start: 0.8062 (m-80) cc_final: 0.7622 (m-80) REVERT: AG 24 GLN cc_start: 0.7692 (pt0) cc_final: 0.7345 (pt0) REVERT: AG 44 GLU cc_start: 0.7887 (tt0) cc_final: 0.7663 (mt-10) REVERT: AG 71 LYS cc_start: 0.8014 (tptp) cc_final: 0.7674 (ptmm) REVERT: AG 78 TYR cc_start: 0.7260 (m-10) cc_final: 0.6915 (m-80) REVERT: AH 33 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8794 (mm-30) REVERT: AH 39 GLU cc_start: 0.8969 (pm20) cc_final: 0.8583 (pp20) REVERT: AI 73 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7919 (Cg_endo) REVERT: AK 27 VAL cc_start: 0.7503 (t) cc_final: 0.7287 (t) REVERT: Aa 92 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8120 (t80) REVERT: Aa 162 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7241 (tm-30) REVERT: Aa 172 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8413 (ttt) REVERT: Aa 199 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: Aa 229 MET cc_start: 0.7414 (mmt) cc_final: 0.6854 (mmt) REVERT: Aa 381 THR cc_start: 0.8957 (m) cc_final: 0.8750 (p) REVERT: Aa 435 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7708 (tm-30) REVERT: Aa 475 MET cc_start: 0.8377 (tpp) cc_final: 0.7870 (tpp) REVERT: Ab 82 LEU cc_start: 0.8870 (tp) cc_final: 0.8639 (tp) REVERT: Ab 173 ILE cc_start: 0.8568 (tp) cc_final: 0.8008 (tp) REVERT: Ab 199 LYS cc_start: 0.8145 (tttm) cc_final: 0.7785 (tttm) REVERT: Ab 390 GLU cc_start: 0.8642 (pp20) cc_final: 0.8433 (tp30) REVERT: Ab 395 GLU cc_start: 0.8536 (tp30) cc_final: 0.7959 (tp30) REVERT: Ac 12 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7292 (mptt) REVERT: Ac 20 ASP cc_start: 0.8010 (m-30) cc_final: 0.7672 (m-30) REVERT: Ac 44 GLN cc_start: 0.7881 (mm110) cc_final: 0.7510 (mm-40) REVERT: Ac 138 MET cc_start: 0.7992 (mtt) cc_final: 0.7769 (mtt) REVERT: Ac 146 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6780 (pt) REVERT: Ac 165 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.7006 (m-10) REVERT: Ac 216 ASP cc_start: 0.8680 (t0) cc_final: 0.8389 (t0) REVERT: Ac 249 MET cc_start: 0.7866 (tpt) cc_final: 0.7605 (tpp) REVERT: Ac 373 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: Ad 119 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8441 (tm-30) REVERT: Ad 127 MET cc_start: 0.8156 (ttm) cc_final: 0.7759 (ttm) REVERT: Ad 134 HIS cc_start: 0.8078 (m90) cc_final: 0.7617 (m90) REVERT: Ad 164 MET cc_start: 0.8171 (ptp) cc_final: 0.7765 (ppp) REVERT: Ad 189 ASN cc_start: 0.7430 (m-40) cc_final: 0.7064 (m-40) REVERT: Ad 275 ARG cc_start: 0.7976 (tpt-90) cc_final: 0.7482 (tpt170) REVERT: Ae 140 MET cc_start: 0.8082 (mtp) cc_final: 0.7320 (ttm) REVERT: Ae 165 MET cc_start: 0.7273 (tpp) cc_final: 0.6723 (mpp) REVERT: Ae 185 ASP cc_start: 0.8414 (p0) cc_final: 0.8163 (p0) REVERT: Ae 249 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6579 (pt) REVERT: Af 33 MET cc_start: 0.8526 (mtm) cc_final: 0.7901 (mtm) REVERT: Af 40 GLU cc_start: 0.8477 (mp0) cc_final: 0.8242 (mp0) REVERT: Af 60 MET cc_start: 0.8985 (tpp) cc_final: 0.8026 (mpp) REVERT: Af 70 THR cc_start: 0.9182 (m) cc_final: 0.8955 (p) REVERT: Ag 29 SER cc_start: 0.8868 (m) cc_final: 0.8366 (t) REVERT: Ag 47 LEU cc_start: 0.8933 (mt) cc_final: 0.8681 (tp) REVERT: Ag 57 TYR cc_start: 0.8684 (t80) cc_final: 0.8439 (t80) REVERT: Ag 59 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8666 (mt) REVERT: Ag 66 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8025 (tm-30) REVERT: Ag 67 PHE cc_start: 0.8919 (t80) cc_final: 0.8695 (t80) REVERT: Ah 32 ARG cc_start: 0.7816 (mtt180) cc_final: 0.7262 (ttm110) REVERT: Ah 67 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: Ah 82 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8075 (m170) REVERT: Aj 23 LEU cc_start: 0.9226 (tp) cc_final: 0.8591 (tp) REVERT: Aj 36 PHE cc_start: 0.8928 (t80) cc_final: 0.8678 (t80) REVERT: Aj 43 ILE cc_start: 0.8960 (mm) cc_final: 0.8734 (tt) REVERT: Aj 53 TRP cc_start: 0.8167 (t-100) cc_final: 0.7244 (t-100) REVERT: Ak 23 MET cc_start: 0.7134 (mmt) cc_final: 0.6521 (tpp) REVERT: Ak 39 ARG cc_start: 0.7379 (tpt90) cc_final: 0.6647 (ptt-90) outliers start: 144 outliers final: 88 residues processed: 876 average time/residue: 0.4192 time to fit residues: 602.7792 Evaluate side-chains 824 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 724 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 127 GLU Chi-restraints excluded: chain AA residue 133 ILE Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 366 ASP Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 139 ASN Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 197 MET Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 159 THR Chi-restraints excluded: chain AC residue 170 VAL Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 159 ASN Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AG residue 37 ASN Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain Aa residue 49 GLN Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 92 PHE Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 133 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 172 MET Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 216 LEU Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 115 THR Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 139 ASN Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ab residue 393 LEU Chi-restraints excluded: chain Ab residue 451 ASP Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 146 ILE Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 238 ILE Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ac residue 364 ILE Chi-restraints excluded: chain Ac residue 373 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 239 HIS Chi-restraints excluded: chain Ae residue 249 ILE Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 43 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 82 HIS Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 10 LEU Chi-restraints excluded: chain Aj residue 54 LYS Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 187 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 227 HIS ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 319 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 196 HIS AD 107 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 37 GLN AH 78 HIS AJ 46 HIS Aa 393 ASN Aa 434 GLN ** Ab 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 376 ASN ** Ac 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN Ad 309 HIS ** Ae 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087474 restraints weight = 77137.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090338 restraints weight = 37631.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091880 restraints weight = 24445.330| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.828 32218 Z= 0.376 Angle : 0.904 20.286 43733 Z= 0.440 Chirality : 0.050 0.487 4746 Planarity : 0.006 0.081 5552 Dihedral : 10.607 137.538 4531 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.67 % Allowed : 20.37 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.25 (0.14), residues: 3849 helix: 0.81 (0.11), residues: 2040 sheet: -0.29 (0.27), residues: 394 loop : -0.51 (0.18), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRPAC 113 HIS 0.017 0.002 HISAH 78 PHE 0.031 0.003 PHEAh 70 TYR 0.027 0.003 TYRAB 182 ARG 0.016 0.001 ARGAh 45 Details of bonding type rmsd hydrogen bonds : bond 0.05201 ( 1796) hydrogen bonds : angle 5.41452 ( 5166) SS BOND : bond 0.00416 ( 8) SS BOND : angle 2.25693 ( 16) covalent geometry : bond 0.00851 (32203) covalent geometry : angle 0.90326 (43717) Misc. bond : bond 0.49586 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 709 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 87 ASN cc_start: 0.8492 (t0) cc_final: 0.8260 (t0) REVERT: AA 114 GLU cc_start: 0.8427 (tp30) cc_final: 0.8054 (mm-30) REVERT: AA 131 TYR cc_start: 0.8794 (m-80) cc_final: 0.8327 (m-80) REVERT: AA 240 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8458 (tp-100) REVERT: AA 292 GLU cc_start: 0.8497 (pp20) cc_final: 0.8019 (pp20) REVERT: AB 142 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8630 (p) REVERT: AB 173 ILE cc_start: 0.8267 (tp) cc_final: 0.7914 (tp) REVERT: AB 235 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: AB 260 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7105 (tm-30) REVERT: AC 118 LEU cc_start: 0.9415 (tp) cc_final: 0.9041 (tt) REVERT: AC 163 TRP cc_start: 0.8716 (t60) cc_final: 0.8091 (t60) REVERT: AC 216 ASP cc_start: 0.8636 (t0) cc_final: 0.7993 (t0) REVERT: AC 316 MET cc_start: 0.8988 (ttm) cc_final: 0.8640 (ttm) REVERT: AC 337 TRP cc_start: 0.9144 (t60) cc_final: 0.8784 (t60) REVERT: AD 96 TRP cc_start: 0.7361 (m100) cc_final: 0.7012 (m100) REVERT: AD 118 LYS cc_start: 0.8254 (mtmt) cc_final: 0.8030 (mtmt) REVERT: AD 164 MET cc_start: 0.6788 (tmm) cc_final: 0.6180 (tmm) REVERT: AE 88 PHE cc_start: 0.8094 (m-80) cc_final: 0.7783 (m-10) REVERT: AE 127 TYR cc_start: 0.7252 (t80) cc_final: 0.6474 (t80) REVERT: AE 167 PHE cc_start: 0.8063 (m-80) cc_final: 0.7502 (m-10) REVERT: AE 170 ARG cc_start: 0.8636 (mtm180) cc_final: 0.7839 (ptt90) REVERT: AE 248 ARG cc_start: 0.7238 (mtp85) cc_final: 0.6471 (mtp85) REVERT: AF 33 MET cc_start: 0.7694 (mmt) cc_final: 0.6912 (mmt) REVERT: AG 43 ARG cc_start: 0.8998 (ptp-170) cc_final: 0.8498 (ptt-90) REVERT: AG 71 LYS cc_start: 0.8236 (tptp) cc_final: 0.7823 (ptmm) REVERT: AG 78 TYR cc_start: 0.7205 (m-80) cc_final: 0.6804 (m-80) REVERT: AH 33 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8751 (tm-30) REVERT: AH 48 LEU cc_start: 0.8845 (tt) cc_final: 0.8450 (mp) REVERT: AH 64 ASP cc_start: 0.6052 (m-30) cc_final: 0.5847 (m-30) REVERT: AJ 34 ARG cc_start: 0.6329 (tpp80) cc_final: 0.5871 (tpp-160) REVERT: Aa 76 ASP cc_start: 0.8287 (t0) cc_final: 0.7869 (t0) REVERT: Aa 84 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8548 (pm20) REVERT: Aa 92 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8693 (t80) REVERT: Aa 172 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8464 (ttt) REVERT: Aa 229 MET cc_start: 0.7701 (mmt) cc_final: 0.7315 (mmt) REVERT: Aa 368 MET cc_start: 0.9069 (mmm) cc_final: 0.8638 (tpt) REVERT: Aa 377 MET cc_start: 0.9517 (tpp) cc_final: 0.9298 (mmm) REVERT: Aa 435 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8076 (tm-30) REVERT: Aa 440 MET cc_start: 0.8488 (ptp) cc_final: 0.8117 (ptp) REVERT: Aa 445 CYS cc_start: 0.8515 (m) cc_final: 0.7430 (t) REVERT: Ab 82 LEU cc_start: 0.9124 (tp) cc_final: 0.8845 (tp) REVERT: Ab 159 LYS cc_start: 0.8714 (tppt) cc_final: 0.8094 (tppt) REVERT: Ab 172 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7665 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8985 (tp) cc_final: 0.8588 (tp) REVERT: Ab 199 LYS cc_start: 0.8390 (tttm) cc_final: 0.8009 (tttm) REVERT: Ab 311 GLN cc_start: 0.7754 (mt0) cc_final: 0.7539 (mm-40) REVERT: Ab 395 GLU cc_start: 0.8765 (tp30) cc_final: 0.8044 (tp30) REVERT: Ac 12 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7363 (mptt) REVERT: Ac 20 ASP cc_start: 0.8286 (m-30) cc_final: 0.7947 (m-30) REVERT: Ac 44 GLN cc_start: 0.7972 (mm110) cc_final: 0.7707 (mm-40) REVERT: Ac 118 LEU cc_start: 0.8939 (tp) cc_final: 0.8363 (tt) REVERT: Ac 165 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.7266 (m-10) REVERT: Ac 216 ASP cc_start: 0.8667 (t0) cc_final: 0.8296 (t0) REVERT: Ac 235 MET cc_start: 0.8758 (tmm) cc_final: 0.8544 (tmm) REVERT: Ac 240 MET cc_start: 0.8205 (mmm) cc_final: 0.7999 (mmm) REVERT: Ac 271 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7780 (mt-10) REVERT: Ac 331 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8325 (p0) REVERT: Ac 344 GLU cc_start: 0.8614 (tp30) cc_final: 0.8272 (tp30) REVERT: Ac 358 TYR cc_start: 0.8795 (t80) cc_final: 0.8119 (t80) REVERT: Ac 378 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8425 (mtmm) REVERT: Ad 119 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8423 (tm-30) REVERT: Ad 127 MET cc_start: 0.8178 (ttm) cc_final: 0.7650 (ttm) REVERT: Ad 164 MET cc_start: 0.8418 (ptp) cc_final: 0.7982 (ppp) REVERT: Ad 189 ASN cc_start: 0.7835 (m-40) cc_final: 0.7392 (m-40) REVERT: Ad 218 TYR cc_start: 0.7168 (m-80) cc_final: 0.6911 (m-10) REVERT: Ad 283 ASP cc_start: 0.8816 (p0) cc_final: 0.8406 (p0) REVERT: Ae 140 MET cc_start: 0.8422 (mtp) cc_final: 0.7416 (ttm) REVERT: Ae 165 MET cc_start: 0.7540 (tpp) cc_final: 0.7104 (mpp) REVERT: Ae 187 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7430 (mm-30) REVERT: Ae 249 ILE cc_start: 0.6837 (tp) cc_final: 0.6618 (pt) REVERT: Af 33 MET cc_start: 0.8633 (mtm) cc_final: 0.7963 (mtt) REVERT: Af 60 MET cc_start: 0.8983 (tpp) cc_final: 0.8098 (mpp) REVERT: Af 76 LEU cc_start: 0.9336 (mt) cc_final: 0.9133 (mt) REVERT: Af 83 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7796 (mmmt) REVERT: Af 86 GLU cc_start: 0.8854 (pt0) cc_final: 0.8611 (mp0) REVERT: Af 107 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8546 (tm-30) REVERT: Ag 29 SER cc_start: 0.8918 (m) cc_final: 0.8513 (t) REVERT: Ag 66 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8407 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8861 (mt0) cc_final: 0.8638 (mt0) REVERT: Ah 62 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7466 (mp0) REVERT: Ah 67 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6875 (pm20) REVERT: Aj 17 ARG cc_start: 0.3792 (tpp-160) cc_final: 0.3484 (tpp-160) REVERT: Aj 36 PHE cc_start: 0.9102 (t80) cc_final: 0.8841 (t80) REVERT: Aj 53 TRP cc_start: 0.8393 (t-100) cc_final: 0.7758 (t-100) outliers start: 187 outliers final: 114 residues processed: 818 average time/residue: 0.4235 time to fit residues: 560.4766 Evaluate side-chains 763 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 640 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 220 LEU Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 366 ASP Chi-restraints excluded: chain AA residue 388 VAL Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 55 TYR Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 79 THR Chi-restraints excluded: chain AB residue 121 TYR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 142 THR Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 258 ILE Chi-restraints excluded: chain AB residue 351 ILE Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AB residue 405 SER Chi-restraints excluded: chain AB residue 424 VAL Chi-restraints excluded: chain AB residue 451 ASP Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 161 VAL Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 243 VAL Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 107 HIS Chi-restraints excluded: chain AD residue 165 PHE Chi-restraints excluded: chain AE residue 87 ASP Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AE residue 270 VAL Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 63 ILE Chi-restraints excluded: chain AF residue 69 LEU Chi-restraints excluded: chain AF residue 92 GLU Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AI residue 67 THR Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain Aa residue 57 LEU Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 92 PHE Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 172 MET Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 410 CYS Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 197 MET Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 371 VAL Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ac residue 353 LEU Chi-restraints excluded: chain Ad residue 101 LEU Chi-restraints excluded: chain Ad residue 130 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 49 VAL Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 26 ASP Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ah residue 66 THR Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 10 LEU Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 89 optimal weight: 0.2980 chunk 146 optimal weight: 3.9990 chunk 377 optimal weight: 6.9990 chunk 181 optimal weight: 0.6980 chunk 254 optimal weight: 0.8980 chunk 351 optimal weight: 0.7980 chunk 348 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 361 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 249 HIS AA 402 HIS ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 357 GLN AC 331 ASN AD 107 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 37 ASN AH 78 HIS Aa 55 ASN Aa 223 HIS Aa 393 ASN Ab 139 ASN Ab 236 GLN Ac 207 ASN Ac 331 ASN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 242 HIS ** Ah 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.120574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091932 restraints weight = 75468.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095149 restraints weight = 36220.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097268 restraints weight = 23186.230| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.443 32218 Z= 0.146 Angle : 0.721 15.204 43733 Z= 0.347 Chirality : 0.045 0.494 4746 Planarity : 0.005 0.060 5552 Dihedral : 10.098 125.917 4531 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.79 % Allowed : 22.40 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.70 (0.14), residues: 3849 helix: 1.17 (0.11), residues: 2044 sheet: -0.05 (0.27), residues: 377 loop : -0.31 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRPAC 113 HIS 0.021 0.001 HISAD 107 PHE 0.029 0.002 PHEAg 67 TYR 0.020 0.002 TYRAE 235 ARG 0.013 0.001 ARGAh 45 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 1796) hydrogen bonds : angle 4.89638 ( 5166) SS BOND : bond 0.00567 ( 8) SS BOND : angle 3.06887 ( 16) covalent geometry : bond 0.00332 (32203) covalent geometry : angle 0.71850 (43717) Misc. bond : bond 0.28681 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 738 time to evaluate : 3.628 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: AA 114 GLU cc_start: 0.8374 (tp30) cc_final: 0.8050 (mm-30) REVERT: AA 131 TYR cc_start: 0.8803 (m-80) cc_final: 0.8251 (m-80) REVERT: AA 140 LEU cc_start: 0.7785 (mt) cc_final: 0.7429 (mt) REVERT: AA 179 MET cc_start: 0.6238 (mtm) cc_final: 0.6010 (mtp) REVERT: AA 240 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8477 (tp-100) REVERT: AA 292 GLU cc_start: 0.8446 (pp20) cc_final: 0.8150 (pp20) REVERT: AA 304 LEU cc_start: 0.9134 (mt) cc_final: 0.8920 (mt) REVERT: AA 377 MET cc_start: 0.8361 (tpp) cc_final: 0.7798 (mmm) REVERT: AA 385 GLU cc_start: 0.8959 (pm20) cc_final: 0.8230 (pm20) REVERT: AB 180 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.8194 (p) REVERT: AB 197 MET cc_start: 0.7976 (mtp) cc_final: 0.7492 (ttm) REVERT: AB 235 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: AB 260 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7086 (tm-30) REVERT: AC 163 TRP cc_start: 0.8788 (t60) cc_final: 0.8103 (t60) REVERT: AC 216 ASP cc_start: 0.8474 (t0) cc_final: 0.7990 (t70) REVERT: AC 337 TRP cc_start: 0.9084 (t60) cc_final: 0.8841 (t60) REVERT: AD 96 TRP cc_start: 0.7330 (m100) cc_final: 0.6942 (m100) REVERT: AD 101 LEU cc_start: 0.8494 (tp) cc_final: 0.8062 (mp) REVERT: AD 140 TYR cc_start: 0.7890 (m-10) cc_final: 0.7663 (m-10) REVERT: AD 164 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.5474 (tmm) REVERT: AD 166 MET cc_start: 0.7565 (mpp) cc_final: 0.7090 (mpp) REVERT: AD 170 LYS cc_start: 0.8740 (tptt) cc_final: 0.8524 (tptm) REVERT: AD 212 PHE cc_start: 0.8419 (t80) cc_final: 0.8159 (t80) REVERT: AD 295 MET cc_start: 0.7555 (ptp) cc_final: 0.7203 (ptt) REVERT: AE 88 PHE cc_start: 0.7985 (m-80) cc_final: 0.7689 (m-10) REVERT: AE 165 MET cc_start: 0.5445 (tpp) cc_final: 0.5184 (tpp) REVERT: AE 167 PHE cc_start: 0.8162 (m-80) cc_final: 0.7692 (m-10) REVERT: AE 169 TRP cc_start: 0.6055 (t60) cc_final: 0.5509 (t60) REVERT: AE 248 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6390 (mtp85) REVERT: AF 33 MET cc_start: 0.7661 (mmt) cc_final: 0.6888 (mmt) REVERT: AG 17 TYR cc_start: 0.7986 (m-80) cc_final: 0.7691 (m-80) REVERT: AG 43 ARG cc_start: 0.8899 (ptp-170) cc_final: 0.8437 (ptt-90) REVERT: AG 44 GLU cc_start: 0.8391 (tt0) cc_final: 0.7931 (mt-10) REVERT: AG 71 LYS cc_start: 0.8118 (tptp) cc_final: 0.7738 (ptmm) REVERT: AG 78 TYR cc_start: 0.7141 (m-80) cc_final: 0.6764 (m-80) REVERT: AH 48 LEU cc_start: 0.8858 (tt) cc_final: 0.8336 (mp) REVERT: AH 86 LYS cc_start: 0.8610 (pttp) cc_final: 0.8042 (mmtt) REVERT: AI 77 ARG cc_start: 0.7143 (tmt-80) cc_final: 0.6922 (tmt-80) REVERT: AJ 34 ARG cc_start: 0.6586 (tpp80) cc_final: 0.6137 (tpp-160) REVERT: Aa 76 ASP cc_start: 0.8252 (t0) cc_final: 0.8003 (t0) REVERT: Aa 84 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8688 (pm20) REVERT: Aa 91 TYR cc_start: 0.9023 (t80) cc_final: 0.8277 (t80) REVERT: Aa 92 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8658 (t80) REVERT: Aa 199 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: Aa 346 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8803 (mm) REVERT: Aa 368 MET cc_start: 0.8800 (mmm) cc_final: 0.8427 (tpt) REVERT: Aa 373 GLN cc_start: 0.8859 (tt0) cc_final: 0.8635 (tt0) REVERT: Aa 377 MET cc_start: 0.9448 (tpp) cc_final: 0.9074 (mmm) REVERT: Aa 379 LEU cc_start: 0.8758 (mm) cc_final: 0.8471 (tp) REVERT: Aa 435 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8115 (tm-30) REVERT: Aa 445 CYS cc_start: 0.8393 (m) cc_final: 0.7450 (t) REVERT: Ab 82 LEU cc_start: 0.9087 (tp) cc_final: 0.8753 (tp) REVERT: Ab 172 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7650 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8742 (tp) cc_final: 0.8307 (tp) REVERT: Ab 199 LYS cc_start: 0.8364 (tttm) cc_final: 0.7977 (tttm) REVERT: Ab 387 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7966 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8913 (pp20) cc_final: 0.8330 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8685 (tp30) cc_final: 0.8217 (tp30) REVERT: Ac 12 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7552 (mptt) REVERT: Ac 20 ASP cc_start: 0.8052 (m-30) cc_final: 0.7711 (m-30) REVERT: Ac 121 PHE cc_start: 0.8779 (m-80) cc_final: 0.8398 (m-10) REVERT: Ac 155 TYR cc_start: 0.5466 (t80) cc_final: 0.5033 (t80) REVERT: Ac 165 TRP cc_start: 0.7418 (OUTLIER) cc_final: 0.7181 (m-10) REVERT: Ac 202 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8246 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8719 (t0) cc_final: 0.8439 (t0) REVERT: Ac 271 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7679 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8758 (mt) cc_final: 0.8465 (mt) REVERT: Ac 344 GLU cc_start: 0.8520 (tp30) cc_final: 0.8198 (tp30) REVERT: Ac 358 TYR cc_start: 0.8769 (t80) cc_final: 0.7993 (t80) REVERT: Ac 378 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8297 (mtmm) REVERT: Ad 127 MET cc_start: 0.8256 (ttm) cc_final: 0.7782 (ttm) REVERT: Ad 164 MET cc_start: 0.8324 (ptp) cc_final: 0.7918 (ppp) REVERT: Ad 177 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9005 (mttm) REVERT: Ad 189 ASN cc_start: 0.7669 (m-40) cc_final: 0.7213 (m-40) REVERT: Ad 295 MET cc_start: 0.8335 (mmp) cc_final: 0.7869 (mmp) REVERT: Ae 140 MET cc_start: 0.8332 (mtp) cc_final: 0.7285 (ttm) REVERT: Ae 165 MET cc_start: 0.7612 (tpp) cc_final: 0.7251 (mpp) REVERT: Ae 248 ARG cc_start: 0.7220 (mtm180) cc_final: 0.6258 (mtm180) REVERT: Af 33 MET cc_start: 0.8594 (mtm) cc_final: 0.8032 (mtt) REVERT: Af 60 MET cc_start: 0.8891 (tpp) cc_final: 0.7898 (mpp) REVERT: Af 83 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7666 (mmmt) REVERT: Af 86 GLU cc_start: 0.8806 (pt0) cc_final: 0.8457 (mp0) REVERT: Ag 29 SER cc_start: 0.8908 (m) cc_final: 0.8461 (t) REVERT: Ag 57 TYR cc_start: 0.8752 (t80) cc_final: 0.8211 (t80) REVERT: Ag 60 TYR cc_start: 0.9004 (t80) cc_final: 0.8624 (t80) REVERT: Ag 66 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8350 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8806 (mt0) cc_final: 0.8590 (mt0) REVERT: Ah 67 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: Ah 89 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7168 (mtpt) REVERT: Aj 36 PHE cc_start: 0.8926 (t80) cc_final: 0.8320 (t80) REVERT: Aj 43 ILE cc_start: 0.9081 (tt) cc_final: 0.8865 (tt) REVERT: Ak 23 MET cc_start: 0.7333 (mmt) cc_final: 0.6294 (tpp) REVERT: Ak 39 ARG cc_start: 0.7312 (tpt90) cc_final: 0.6595 (ptp90) outliers start: 125 outliers final: 83 residues processed: 806 average time/residue: 0.4132 time to fit residues: 539.9934 Evaluate side-chains 769 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 675 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 127 GLU Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 249 HIS Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 366 ASP Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 351 ILE Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 107 HIS Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 164 MET Chi-restraints excluded: chain AD residue 244 MET Chi-restraints excluded: chain AD residue 253 LEU Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 69 LEU Chi-restraints excluded: chain AF residue 76 LEU Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AH residue 80 VAL Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 92 PHE Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 139 ASN Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 156 ILE Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 207 ASN Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 333 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Ae residue 239 HIS Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 39 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 298 optimal weight: 0.0670 chunk 132 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 365 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 328 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 107 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 393 ASN Aa 434 GLN Ab 139 ASN Ab 376 ASN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 82 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.119103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090066 restraints weight = 77051.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.093545 restraints weight = 37688.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094707 restraints weight = 24229.827| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.581 32218 Z= 0.197 Angle : 0.737 15.434 43733 Z= 0.357 Chirality : 0.046 0.478 4746 Planarity : 0.005 0.059 5552 Dihedral : 9.936 128.176 4531 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.46 % Allowed : 22.70 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.71 (0.14), residues: 3849 helix: 1.21 (0.11), residues: 2042 sheet: -0.08 (0.27), residues: 376 loop : -0.34 (0.18), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPAC 113 HIS 0.011 0.001 HISAd 309 PHE 0.026 0.002 PHEAg 67 TYR 0.020 0.002 TYRAF 22 ARG 0.014 0.001 ARGAH 54 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 1796) hydrogen bonds : angle 4.91220 ( 5166) SS BOND : bond 0.00809 ( 8) SS BOND : angle 3.58773 ( 16) covalent geometry : bond 0.00460 (32203) covalent geometry : angle 0.73372 (43717) Misc. bond : bond 0.31832 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 695 time to evaluate : 3.511 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: AA 114 GLU cc_start: 0.8438 (tp30) cc_final: 0.8089 (mm-30) REVERT: AA 131 TYR cc_start: 0.8813 (m-80) cc_final: 0.8172 (m-80) REVERT: AA 140 LEU cc_start: 0.7784 (mt) cc_final: 0.7475 (mt) REVERT: AA 179 MET cc_start: 0.6467 (mtm) cc_final: 0.6220 (mtp) REVERT: AA 240 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8496 (tp-100) REVERT: AA 292 GLU cc_start: 0.8439 (pp20) cc_final: 0.8173 (pp20) REVERT: AA 385 GLU cc_start: 0.8994 (pm20) cc_final: 0.8267 (pm20) REVERT: AB 180 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (p) REVERT: AB 197 MET cc_start: 0.8000 (mtp) cc_final: 0.7515 (ttm) REVERT: AB 235 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: AC 118 LEU cc_start: 0.9377 (tp) cc_final: 0.8980 (tt) REVERT: AC 163 TRP cc_start: 0.8858 (t60) cc_final: 0.8208 (t60) REVERT: AC 216 ASP cc_start: 0.8578 (t0) cc_final: 0.8040 (t70) REVERT: AC 316 MET cc_start: 0.9024 (ttm) cc_final: 0.8358 (ttm) REVERT: AC 337 TRP cc_start: 0.9089 (t60) cc_final: 0.8813 (t60) REVERT: AD 96 TRP cc_start: 0.7309 (m100) cc_final: 0.6920 (m100) REVERT: AD 101 LEU cc_start: 0.8472 (tp) cc_final: 0.8035 (mp) REVERT: AD 140 TYR cc_start: 0.8096 (m-10) cc_final: 0.7884 (m-10) REVERT: AD 164 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.5892 (tmm) REVERT: AD 170 LYS cc_start: 0.8675 (tptt) cc_final: 0.8424 (tptm) REVERT: AD 212 PHE cc_start: 0.8330 (t80) cc_final: 0.8101 (t80) REVERT: AE 88 PHE cc_start: 0.8002 (m-80) cc_final: 0.7699 (m-10) REVERT: AE 115 TYR cc_start: 0.5757 (m-10) cc_final: 0.5433 (m-10) REVERT: AE 167 PHE cc_start: 0.8167 (m-80) cc_final: 0.7691 (m-10) REVERT: AE 170 ARG cc_start: 0.7502 (mtp85) cc_final: 0.7278 (mtp85) REVERT: AE 197 ASP cc_start: 0.4231 (t70) cc_final: 0.3935 (m-30) REVERT: AE 231 PHE cc_start: 0.7138 (t80) cc_final: 0.5781 (t80) REVERT: AE 248 ARG cc_start: 0.7122 (mtp85) cc_final: 0.6366 (mtp85) REVERT: AF 33 MET cc_start: 0.7669 (mmt) cc_final: 0.6900 (mmt) REVERT: AG 17 TYR cc_start: 0.8188 (m-80) cc_final: 0.7823 (m-80) REVERT: AG 22 PHE cc_start: 0.8399 (m-80) cc_final: 0.8144 (m-80) REVERT: AG 43 ARG cc_start: 0.9008 (ptp-170) cc_final: 0.8485 (ptt180) REVERT: AG 44 GLU cc_start: 0.8616 (tt0) cc_final: 0.8117 (mt-10) REVERT: AG 71 LYS cc_start: 0.8185 (tptp) cc_final: 0.7764 (ptmm) REVERT: AG 78 TYR cc_start: 0.7261 (m-80) cc_final: 0.6845 (m-80) REVERT: AH 48 LEU cc_start: 0.8928 (tt) cc_final: 0.8671 (mm) REVERT: Aa 76 ASP cc_start: 0.8250 (t0) cc_final: 0.7964 (t0) REVERT: Aa 79 SER cc_start: 0.7898 (p) cc_final: 0.7694 (t) REVERT: Aa 84 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: Aa 91 TYR cc_start: 0.9079 (t80) cc_final: 0.8364 (t80) REVERT: Aa 172 MET cc_start: 0.8412 (ttt) cc_final: 0.8188 (ttt) REVERT: Aa 197 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9078 (mp) REVERT: Aa 346 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8823 (mm) REVERT: Aa 377 MET cc_start: 0.9484 (tpp) cc_final: 0.9130 (mmm) REVERT: Aa 435 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8175 (tm-30) REVERT: Aa 445 CYS cc_start: 0.8459 (m) cc_final: 0.7372 (t) REVERT: Ab 82 LEU cc_start: 0.9113 (tp) cc_final: 0.8834 (tp) REVERT: Ab 84 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7566 (ttp-110) REVERT: Ab 172 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7713 (mtp85) REVERT: Ab 173 ILE cc_start: 0.8930 (tp) cc_final: 0.8534 (tp) REVERT: Ab 199 LYS cc_start: 0.8393 (tttm) cc_final: 0.7991 (tttm) REVERT: Ab 387 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8019 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8706 (tp30) cc_final: 0.8167 (tp30) REVERT: Ac 12 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7402 (mptt) REVERT: Ac 20 ASP cc_start: 0.8114 (m-30) cc_final: 0.7767 (m-30) REVERT: Ac 118 LEU cc_start: 0.8908 (tp) cc_final: 0.8333 (tt) REVERT: Ac 121 PHE cc_start: 0.8833 (m-80) cc_final: 0.8518 (m-10) REVERT: Ac 165 TRP cc_start: 0.7559 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: Ac 202 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8349 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8765 (t0) cc_final: 0.8489 (t0) REVERT: Ac 260 ASN cc_start: 0.8888 (t0) cc_final: 0.8565 (t0) REVERT: Ac 271 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7756 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8821 (mt) cc_final: 0.8489 (mt) REVERT: Ac 344 GLU cc_start: 0.8576 (tp30) cc_final: 0.8198 (tp30) REVERT: Ac 358 TYR cc_start: 0.8812 (t80) cc_final: 0.7998 (t80) REVERT: Ac 373 GLU cc_start: 0.8128 (tt0) cc_final: 0.7794 (tt0) REVERT: Ac 378 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8357 (mtmm) REVERT: Ad 127 MET cc_start: 0.8144 (ttm) cc_final: 0.7644 (ttm) REVERT: Ad 164 MET cc_start: 0.8397 (ptp) cc_final: 0.7960 (ppp) REVERT: Ad 189 ASN cc_start: 0.7801 (m-40) cc_final: 0.7330 (m-40) REVERT: Ad 251 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8394 (tm-30) REVERT: Ad 273 PHE cc_start: 0.9256 (t80) cc_final: 0.9020 (t80) REVERT: Ad 295 MET cc_start: 0.8307 (mmp) cc_final: 0.7863 (mmp) REVERT: Ae 140 MET cc_start: 0.8428 (mtp) cc_final: 0.7489 (ttm) REVERT: Ae 165 MET cc_start: 0.7726 (tpp) cc_final: 0.7496 (mpp) REVERT: Af 33 MET cc_start: 0.8624 (mtm) cc_final: 0.8054 (mtt) REVERT: Af 46 GLU cc_start: 0.8395 (tp30) cc_final: 0.8056 (tp30) REVERT: Af 60 MET cc_start: 0.8916 (tpp) cc_final: 0.7946 (mpp) REVERT: Af 91 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8921 (tt) REVERT: Ag 29 SER cc_start: 0.8951 (m) cc_final: 0.8500 (t) REVERT: Ag 57 TYR cc_start: 0.8768 (t80) cc_final: 0.8232 (t80) REVERT: Ag 60 TYR cc_start: 0.9047 (t80) cc_final: 0.8586 (t80) REVERT: Ag 66 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8409 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8838 (mt0) cc_final: 0.8591 (mt0) REVERT: Ah 45 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7881 (ptm160) REVERT: Ah 53 ASN cc_start: 0.9223 (m-40) cc_final: 0.8691 (m110) REVERT: Ah 62 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7312 (mp0) REVERT: Ah 66 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7728 (t) REVERT: Ah 67 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: Ak 39 ARG cc_start: 0.7230 (tpt90) cc_final: 0.6585 (ptp-170) outliers start: 147 outliers final: 100 residues processed: 774 average time/residue: 0.4087 time to fit residues: 517.2003 Evaluate side-chains 768 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 656 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 357 HIS Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 351 ILE Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AC residue 27 ILE Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 107 HIS Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 164 MET Chi-restraints excluded: chain AD residue 244 MET Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 54 ASP Chi-restraints excluded: chain AF residue 76 LEU Chi-restraints excluded: chain AF residue 99 ILE Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 68 THR Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 182 VAL Chi-restraints excluded: chain Aa residue 197 LEU Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 250 LEU Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 84 ARG Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 172 ARG Chi-restraints excluded: chain Ab residue 174 ILE Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 333 LEU Chi-restraints excluded: chain Ac residue 335 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 293 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 91 LEU Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 39 LEU Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 66 THR Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 23 LEU Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 37 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 246 optimal weight: 0.4980 chunk 325 optimal weight: 0.0270 chunk 302 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 308 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 276 optimal weight: 0.6980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 107 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 37 ASN AH 78 HIS Aa 247 GLN Aa 393 ASN Aa 434 GLN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 78 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.120981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092196 restraints weight = 74959.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095342 restraints weight = 36350.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097475 restraints weight = 23378.005| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.423 32218 Z= 0.143 Angle : 0.713 15.343 43733 Z= 0.344 Chirality : 0.045 0.492 4746 Planarity : 0.004 0.047 5552 Dihedral : 9.678 128.334 4531 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.64 % Allowed : 23.46 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.83 (0.14), residues: 3849 helix: 1.26 (0.11), residues: 2044 sheet: 0.10 (0.27), residues: 365 loop : -0.25 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPAA 74 HIS 0.012 0.001 HISAD 107 PHE 0.030 0.001 PHEAg 67 TYR 0.025 0.001 TYRAf 21 ARG 0.010 0.001 ARGAH 54 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 1796) hydrogen bonds : angle 4.78350 ( 5166) SS BOND : bond 0.00588 ( 8) SS BOND : angle 2.64861 ( 16) covalent geometry : bond 0.00327 (32203) covalent geometry : angle 0.71174 (43717) Misc. bond : bond 0.25619 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 733 time to evaluate : 3.459 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: AA 114 GLU cc_start: 0.8509 (tp30) cc_final: 0.8090 (mm-30) REVERT: AA 140 LEU cc_start: 0.7738 (mt) cc_final: 0.7418 (mt) REVERT: AA 179 MET cc_start: 0.6522 (mtm) cc_final: 0.6134 (mtp) REVERT: AA 240 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8419 (tp-100) REVERT: AA 292 GLU cc_start: 0.8405 (pp20) cc_final: 0.8161 (pp20) REVERT: AA 385 GLU cc_start: 0.8916 (pm20) cc_final: 0.8189 (pm20) REVERT: AB 180 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8233 (p) REVERT: AB 197 MET cc_start: 0.7937 (mtp) cc_final: 0.7485 (ttm) REVERT: AB 235 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: AC 163 TRP cc_start: 0.8847 (t60) cc_final: 0.8113 (t60) REVERT: AC 216 ASP cc_start: 0.8553 (t0) cc_final: 0.7999 (t70) REVERT: AC 252 ASP cc_start: 0.7207 (m-30) cc_final: 0.6712 (m-30) REVERT: AC 337 TRP cc_start: 0.9087 (t60) cc_final: 0.8807 (t60) REVERT: AD 96 TRP cc_start: 0.7385 (m100) cc_final: 0.6730 (m100) REVERT: AD 101 LEU cc_start: 0.8531 (tp) cc_final: 0.8136 (mp) REVERT: AD 140 TYR cc_start: 0.8021 (m-10) cc_final: 0.7732 (m-10) REVERT: AD 164 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6036 (tmm) REVERT: AD 170 LYS cc_start: 0.8778 (tptt) cc_final: 0.8499 (tptm) REVERT: AD 212 PHE cc_start: 0.8332 (t80) cc_final: 0.7786 (t80) REVERT: AD 265 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7726 (tp40) REVERT: AD 268 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8294 (ttmm) REVERT: AD 309 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.7508 (t70) REVERT: AE 88 PHE cc_start: 0.7878 (m-80) cc_final: 0.7600 (m-10) REVERT: AE 167 PHE cc_start: 0.8125 (m-80) cc_final: 0.7656 (m-10) REVERT: AE 197 ASP cc_start: 0.4112 (t70) cc_final: 0.3845 (m-30) REVERT: AE 231 PHE cc_start: 0.7254 (t80) cc_final: 0.5893 (t80) REVERT: AF 33 MET cc_start: 0.7685 (mmt) cc_final: 0.6918 (mmt) REVERT: AG 17 TYR cc_start: 0.8112 (m-80) cc_final: 0.7808 (m-80) REVERT: AG 71 LYS cc_start: 0.7883 (tptp) cc_final: 0.7631 (ptmm) REVERT: AG 78 TYR cc_start: 0.7345 (m-80) cc_final: 0.6937 (m-80) REVERT: AH 48 LEU cc_start: 0.8953 (tt) cc_final: 0.8700 (mm) REVERT: AJ 34 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6583 (tpp-160) REVERT: AK 24 TRP cc_start: 0.6349 (m100) cc_final: 0.6063 (m100) REVERT: Aa 76 ASP cc_start: 0.8215 (t0) cc_final: 0.7923 (t0) REVERT: Aa 79 SER cc_start: 0.7874 (p) cc_final: 0.7544 (t) REVERT: Aa 84 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8673 (pm20) REVERT: Aa 91 TYR cc_start: 0.9041 (t80) cc_final: 0.7471 (t80) REVERT: Aa 140 LEU cc_start: 0.8772 (tp) cc_final: 0.8526 (tp) REVERT: Aa 172 MET cc_start: 0.8445 (ttt) cc_final: 0.8211 (ttt) REVERT: Aa 199 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: Aa 292 GLU cc_start: 0.8359 (pp20) cc_final: 0.8158 (tp30) REVERT: Aa 346 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8712 (mm) REVERT: Aa 377 MET cc_start: 0.9460 (tpp) cc_final: 0.9131 (mmm) REVERT: Aa 435 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8116 (tm-30) REVERT: Aa 445 CYS cc_start: 0.8372 (m) cc_final: 0.7372 (t) REVERT: Aa 475 MET cc_start: 0.8779 (tpp) cc_final: 0.8575 (ttm) REVERT: Ab 82 LEU cc_start: 0.9095 (tp) cc_final: 0.8780 (tp) REVERT: Ab 173 ILE cc_start: 0.8699 (tp) cc_final: 0.8325 (tp) REVERT: Ab 199 LYS cc_start: 0.8405 (tttm) cc_final: 0.8030 (tttm) REVERT: Ab 387 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8206 (tm-30) REVERT: Ab 390 GLU cc_start: 0.8923 (pp20) cc_final: 0.8375 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8718 (tp30) cc_final: 0.8320 (tp30) REVERT: Ac 12 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7464 (mptt) REVERT: Ac 121 PHE cc_start: 0.8757 (m-80) cc_final: 0.8398 (m-10) REVERT: Ac 155 TYR cc_start: 0.5585 (t80) cc_final: 0.5195 (t80) REVERT: Ac 165 TRP cc_start: 0.7493 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: Ac 202 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8313 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8718 (t0) cc_final: 0.8472 (t0) REVERT: Ac 260 ASN cc_start: 0.8854 (t0) cc_final: 0.8561 (t0) REVERT: Ac 271 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7688 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8685 (mt) cc_final: 0.8376 (mt) REVERT: Ac 312 GLN cc_start: 0.8708 (mt0) cc_final: 0.8311 (mm-40) REVERT: Ac 344 GLU cc_start: 0.8506 (tp30) cc_final: 0.8155 (tp30) REVERT: Ac 358 TYR cc_start: 0.8692 (t80) cc_final: 0.7911 (t80) REVERT: Ac 373 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: Ad 127 MET cc_start: 0.8254 (ttm) cc_final: 0.7756 (ttm) REVERT: Ad 164 MET cc_start: 0.8347 (ptp) cc_final: 0.7839 (ppp) REVERT: Ad 177 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9003 (mttm) REVERT: Ad 189 ASN cc_start: 0.7788 (m-40) cc_final: 0.7347 (m-40) REVERT: Ad 295 MET cc_start: 0.8308 (mmp) cc_final: 0.7882 (mmp) REVERT: Ae 140 MET cc_start: 0.8414 (mtp) cc_final: 0.7433 (ttm) REVERT: Ae 165 MET cc_start: 0.7768 (tpp) cc_final: 0.7523 (mpp) REVERT: Af 33 MET cc_start: 0.8606 (mtm) cc_final: 0.8058 (mtt) REVERT: Af 60 MET cc_start: 0.8849 (tpp) cc_final: 0.7875 (mpp) REVERT: Af 86 GLU cc_start: 0.8892 (pt0) cc_final: 0.8476 (mp0) REVERT: Af 91 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8884 (tt) REVERT: Ag 29 SER cc_start: 0.8931 (m) cc_final: 0.8468 (t) REVERT: Ag 57 TYR cc_start: 0.8693 (t80) cc_final: 0.8273 (t80) REVERT: Ag 60 TYR cc_start: 0.8984 (t80) cc_final: 0.8559 (t80) REVERT: Ag 66 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8399 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8784 (mt0) cc_final: 0.8528 (mt0) REVERT: Ah 26 ASP cc_start: 0.8326 (m-30) cc_final: 0.7951 (t70) REVERT: Ah 45 ARG cc_start: 0.8112 (ptm160) cc_final: 0.7820 (ptm160) REVERT: Ah 53 ASN cc_start: 0.9177 (m-40) cc_final: 0.8614 (m110) REVERT: Ah 62 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7382 (mp0) REVERT: Ah 66 THR cc_start: 0.7877 (m) cc_final: 0.7595 (t) REVERT: Ah 67 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: Ak 23 MET cc_start: 0.7359 (mmt) cc_final: 0.6271 (tpp) REVERT: Ak 39 ARG cc_start: 0.7283 (tpt90) cc_final: 0.6617 (ptp-170) outliers start: 120 outliers final: 79 residues processed: 795 average time/residue: 0.4186 time to fit residues: 537.1914 Evaluate side-chains 780 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 688 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 351 ILE Chi-restraints excluded: chain AC residue 102 LEU Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 107 HIS Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 164 MET Chi-restraints excluded: chain AD residue 265 GLN Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AD residue 309 HIS Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 69 LEU Chi-restraints excluded: chain AG residue 11 ILE Chi-restraints excluded: chain AG residue 37 ASN Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 77 ASP Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 182 VAL Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 250 LEU Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 333 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ac residue 373 GLU Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 91 LEU Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 39 LEU Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 23 LEU Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 37 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 371 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 107 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 309 HIS AG 37 ASN AH 78 HIS Aa 103 ASN Aa 393 ASN Aa 434 GLN Ac 207 ASN Ac 312 GLN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 309 HIS ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.116948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087807 restraints weight = 76507.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090759 restraints weight = 37646.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092751 restraints weight = 24676.376| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.675 32218 Z= 0.270 Angle : 0.802 16.102 43733 Z= 0.389 Chirality : 0.048 0.461 4746 Planarity : 0.005 0.066 5552 Dihedral : 9.800 133.333 4531 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.85 % Allowed : 23.98 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.59 (0.14), residues: 3849 helix: 1.10 (0.11), residues: 2034 sheet: -0.07 (0.26), residues: 371 loop : -0.38 (0.18), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPAA 74 HIS 0.016 0.002 HISAH 78 PHE 0.032 0.002 PHEAd 273 TYR 0.029 0.002 TYRAf 21 ARG 0.009 0.001 ARGAj 16 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1796) hydrogen bonds : angle 5.02431 ( 5166) SS BOND : bond 0.00624 ( 8) SS BOND : angle 2.40258 ( 16) covalent geometry : bond 0.00630 (32203) covalent geometry : angle 0.80038 (43717) Misc. bond : bond 0.36189 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 684 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 53 LEU cc_start: 0.8785 (mp) cc_final: 0.8570 (mt) REVERT: AA 74 TRP cc_start: 0.8479 (m-10) cc_final: 0.7372 (m-10) REVERT: AA 114 GLU cc_start: 0.8460 (tp30) cc_final: 0.8020 (mm-30) REVERT: AA 131 TYR cc_start: 0.8776 (m-80) cc_final: 0.8239 (m-80) REVERT: AA 240 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8342 (tp-100) REVERT: AA 244 ASP cc_start: 0.8518 (m-30) cc_final: 0.8180 (m-30) REVERT: AA 292 GLU cc_start: 0.8477 (pp20) cc_final: 0.8264 (pp20) REVERT: AA 304 LEU cc_start: 0.9121 (mt) cc_final: 0.8842 (mt) REVERT: AA 385 GLU cc_start: 0.8911 (pm20) cc_final: 0.8218 (pm20) REVERT: AB 180 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8412 (p) REVERT: AB 197 MET cc_start: 0.8045 (mtp) cc_final: 0.7562 (ttm) REVERT: AB 235 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: AC 20 ASP cc_start: 0.8770 (m-30) cc_final: 0.8451 (t70) REVERT: AC 118 LEU cc_start: 0.9411 (tp) cc_final: 0.9055 (tt) REVERT: AC 163 TRP cc_start: 0.8933 (t60) cc_final: 0.7916 (t60) REVERT: AC 183 PHE cc_start: 0.8720 (t80) cc_final: 0.8435 (t80) REVERT: AC 216 ASP cc_start: 0.8624 (t0) cc_final: 0.7931 (t0) REVERT: AC 337 TRP cc_start: 0.9086 (t60) cc_final: 0.8817 (t60) REVERT: AD 96 TRP cc_start: 0.7324 (m100) cc_final: 0.6737 (m100) REVERT: AD 101 LEU cc_start: 0.8556 (tp) cc_final: 0.8141 (mp) REVERT: AD 140 TYR cc_start: 0.8095 (m-10) cc_final: 0.7882 (m-10) REVERT: AD 164 MET cc_start: 0.6809 (tmm) cc_final: 0.6042 (tmm) REVERT: AD 170 LYS cc_start: 0.8832 (tptt) cc_final: 0.8529 (tptm) REVERT: AD 212 PHE cc_start: 0.8443 (t80) cc_final: 0.8134 (t80) REVERT: AD 265 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7632 (tp40) REVERT: AE 167 PHE cc_start: 0.8127 (m-80) cc_final: 0.7702 (m-10) REVERT: AE 170 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6724 (mmm-85) REVERT: AE 197 ASP cc_start: 0.3947 (t70) cc_final: 0.3547 (m-30) REVERT: AE 248 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6492 (mtp85) REVERT: AF 33 MET cc_start: 0.7691 (mmt) cc_final: 0.7164 (mtt) REVERT: AG 17 TYR cc_start: 0.8320 (m-80) cc_final: 0.7969 (m-80) REVERT: AG 23 GLU cc_start: 0.8507 (mp0) cc_final: 0.8244 (mp0) REVERT: AG 43 ARG cc_start: 0.8877 (ptp-170) cc_final: 0.8394 (ptp-170) REVERT: AG 48 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7083 (mpt180) REVERT: AG 78 TYR cc_start: 0.7360 (m-80) cc_final: 0.6952 (m-80) REVERT: AH 48 LEU cc_start: 0.8951 (tt) cc_final: 0.8694 (mm) REVERT: AJ 34 ARG cc_start: 0.6880 (tpp80) cc_final: 0.6188 (tpm170) REVERT: AK 24 TRP cc_start: 0.6396 (m100) cc_final: 0.6124 (m100) REVERT: Aa 76 ASP cc_start: 0.8253 (t0) cc_final: 0.7697 (t0) REVERT: Aa 79 SER cc_start: 0.7923 (p) cc_final: 0.7719 (t) REVERT: Aa 84 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: Aa 292 GLU cc_start: 0.8447 (pp20) cc_final: 0.8208 (tp30) REVERT: Aa 346 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8831 (mm) REVERT: Aa 377 MET cc_start: 0.9495 (tpp) cc_final: 0.9169 (mmm) REVERT: Aa 435 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8251 (tm-30) REVERT: Aa 440 MET cc_start: 0.8604 (ptp) cc_final: 0.8332 (ptp) REVERT: Aa 445 CYS cc_start: 0.8532 (m) cc_final: 0.7416 (t) REVERT: Ab 101 ARG cc_start: 0.7608 (mmt90) cc_final: 0.7375 (tpp-160) REVERT: Ab 159 LYS cc_start: 0.8657 (tppt) cc_final: 0.8063 (tppt) REVERT: Ab 173 ILE cc_start: 0.9005 (tp) cc_final: 0.8631 (tp) REVERT: Ab 199 LYS cc_start: 0.8420 (tttm) cc_final: 0.7986 (tttm) REVERT: Ab 311 GLN cc_start: 0.7631 (mt0) cc_final: 0.7354 (mm-40) REVERT: Ab 384 MET cc_start: 0.8995 (ptm) cc_final: 0.8752 (ptp) REVERT: Ab 395 GLU cc_start: 0.8762 (tp30) cc_final: 0.8156 (tp30) REVERT: Ac 12 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7488 (mptt) REVERT: Ac 118 LEU cc_start: 0.8981 (tp) cc_final: 0.8390 (tt) REVERT: Ac 121 PHE cc_start: 0.8859 (m-80) cc_final: 0.8651 (m-10) REVERT: Ac 138 MET cc_start: 0.8081 (mtt) cc_final: 0.7441 (mtt) REVERT: Ac 155 TYR cc_start: 0.5594 (t80) cc_final: 0.5226 (t80) REVERT: Ac 165 TRP cc_start: 0.7670 (OUTLIER) cc_final: 0.7358 (m-10) REVERT: Ac 202 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8347 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8719 (t0) cc_final: 0.8328 (t0) REVERT: Ac 263 ASN cc_start: 0.8373 (t0) cc_final: 0.8154 (p0) REVERT: Ac 271 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7873 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8822 (mt) cc_final: 0.8483 (mt) REVERT: Ac 312 GLN cc_start: 0.8641 (mt0) cc_final: 0.8383 (mm-40) REVERT: Ac 344 GLU cc_start: 0.8571 (tp30) cc_final: 0.8208 (tp30) REVERT: Ac 358 TYR cc_start: 0.8900 (t80) cc_final: 0.8239 (t80) REVERT: Ac 373 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: Ad 119 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8548 (tm-30) REVERT: Ad 127 MET cc_start: 0.8153 (ttm) cc_final: 0.7539 (ttm) REVERT: Ad 164 MET cc_start: 0.8417 (ptp) cc_final: 0.7883 (ppp) REVERT: Ad 189 ASN cc_start: 0.7769 (m-40) cc_final: 0.7344 (m-40) REVERT: Ad 273 PHE cc_start: 0.9329 (t80) cc_final: 0.9122 (t80) REVERT: Ad 295 MET cc_start: 0.8466 (mmp) cc_final: 0.8140 (mmp) REVERT: Ae 140 MET cc_start: 0.8539 (mtp) cc_final: 0.7457 (ttm) REVERT: Ae 165 MET cc_start: 0.7679 (tpp) cc_final: 0.7479 (mpp) REVERT: Af 33 MET cc_start: 0.8610 (mtm) cc_final: 0.8100 (mtt) REVERT: Af 46 GLU cc_start: 0.8416 (tp30) cc_final: 0.8106 (tp30) REVERT: Af 60 MET cc_start: 0.8932 (tpp) cc_final: 0.7958 (mpp) REVERT: Af 91 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8956 (tt) REVERT: Ag 29 SER cc_start: 0.8993 (m) cc_final: 0.8535 (t) REVERT: Ag 57 TYR cc_start: 0.8809 (t80) cc_final: 0.8329 (t80) REVERT: Ag 66 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8533 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8809 (mt0) cc_final: 0.8547 (mt0) REVERT: Ah 45 ARG cc_start: 0.8300 (ptm160) cc_final: 0.7973 (ptm160) REVERT: Ah 53 ASN cc_start: 0.9206 (m-40) cc_final: 0.8644 (m110) REVERT: Ah 67 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: Aj 53 TRP cc_start: 0.8385 (t-100) cc_final: 0.7631 (t-100) REVERT: Ak 23 MET cc_start: 0.7457 (mmt) cc_final: 0.6411 (tpp) REVERT: Ak 39 ARG cc_start: 0.7338 (tpt90) cc_final: 0.6630 (ptp-170) outliers start: 127 outliers final: 107 residues processed: 748 average time/residue: 0.4263 time to fit residues: 515.4570 Evaluate side-chains 761 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 644 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 310 ILE Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 357 HIS Chi-restraints excluded: chain AA residue 369 VAL Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 441 LEU Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 351 ILE Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AC residue 45 ILE Chi-restraints excluded: chain AC residue 102 LEU Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 188 ILE Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 89 LEU Chi-restraints excluded: chain AD residue 107 HIS Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 265 GLN Chi-restraints excluded: chain AD residue 300 LEU Chi-restraints excluded: chain AE residue 152 ILE Chi-restraints excluded: chain AE residue 170 ARG Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 35 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AF residue 69 LEU Chi-restraints excluded: chain AF residue 92 GLU Chi-restraints excluded: chain AG residue 11 ILE Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain AK residue 23 MET Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 182 VAL Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 250 LEU Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Aa residue 436 VAL Chi-restraints excluded: chain Ab residue 122 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 169 SER Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 53 MET Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 162 GLU Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 257 MET Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 333 LEU Chi-restraints excluded: chain Ac residue 335 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ac residue 373 GLU Chi-restraints excluded: chain Ad residue 104 SER Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 148 LEU Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 91 LEU Chi-restraints excluded: chain Af residue 99 ILE Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 39 LEU Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 23 LEU Chi-restraints excluded: chain Aj residue 47 ILE Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 37 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 120 optimal weight: 0.0470 chunk 274 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 294 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 107 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 37 ASN AH 37 GLN AH 78 HIS Aa 345 ASN Aa 393 ASN Aa 397 ASN Ab 446 HIS Ac 207 ASN Ac 331 ASN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 78 HIS ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.120339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091573 restraints weight = 75003.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094679 restraints weight = 36268.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.096756 restraints weight = 23342.923| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.448 32218 Z= 0.147 Angle : 0.740 15.859 43733 Z= 0.356 Chirality : 0.046 0.476 4746 Planarity : 0.004 0.105 5552 Dihedral : 9.603 131.022 4531 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.46 % Allowed : 24.55 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3849 helix: 1.18 (0.11), residues: 2035 sheet: 0.02 (0.27), residues: 358 loop : -0.29 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPAG 62 HIS 0.011 0.001 HISAD 107 PHE 0.037 0.002 PHEAJ 32 TYR 0.024 0.002 TYRAf 21 ARG 0.018 0.001 ARGAH 54 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 1796) hydrogen bonds : angle 4.82977 ( 5166) SS BOND : bond 0.00590 ( 8) SS BOND : angle 2.19863 ( 16) covalent geometry : bond 0.00340 (32203) covalent geometry : angle 0.73849 (43717) Misc. bond : bond 0.26648 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7698 Ramachandran restraints generated. 3849 Oldfield, 0 Emsley, 3849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 722 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 53 LEU cc_start: 0.8649 (mp) cc_final: 0.8436 (mt) REVERT: AA 74 TRP cc_start: 0.8237 (m-10) cc_final: 0.7376 (m-10) REVERT: AA 114 GLU cc_start: 0.8495 (tp30) cc_final: 0.8182 (mt-10) REVERT: AA 131 TYR cc_start: 0.8719 (m-80) cc_final: 0.8194 (m-80) REVERT: AA 240 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8303 (tp-100) REVERT: AA 244 ASP cc_start: 0.8516 (m-30) cc_final: 0.8208 (m-30) REVERT: AA 274 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7853 (tm-30) REVERT: AA 377 MET cc_start: 0.8349 (mmm) cc_final: 0.7767 (mmm) REVERT: AA 385 GLU cc_start: 0.8865 (pm20) cc_final: 0.8155 (pm20) REVERT: AB 180 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8259 (p) REVERT: AB 197 MET cc_start: 0.7985 (mtp) cc_final: 0.7515 (ttm) REVERT: AB 235 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: AC 118 LEU cc_start: 0.9386 (tp) cc_final: 0.9019 (tt) REVERT: AC 163 TRP cc_start: 0.8888 (t60) cc_final: 0.8203 (t60) REVERT: AC 198 LEU cc_start: 0.8984 (mt) cc_final: 0.8732 (tp) REVERT: AC 216 ASP cc_start: 0.8577 (t0) cc_final: 0.8039 (t70) REVERT: AC 244 LEU cc_start: 0.9031 (mt) cc_final: 0.8642 (mt) REVERT: AC 246 PHE cc_start: 0.8579 (m-80) cc_final: 0.8297 (m-80) REVERT: AC 252 ASP cc_start: 0.7419 (m-30) cc_final: 0.6957 (m-30) REVERT: AC 316 MET cc_start: 0.8896 (ttm) cc_final: 0.8630 (tpp) REVERT: AC 337 TRP cc_start: 0.9044 (t60) cc_final: 0.8768 (t60) REVERT: AD 96 TRP cc_start: 0.7149 (m100) cc_final: 0.6690 (m100) REVERT: AD 101 LEU cc_start: 0.8528 (tp) cc_final: 0.8141 (mp) REVERT: AD 164 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6084 (tmm) REVERT: AD 212 PHE cc_start: 0.8198 (t80) cc_final: 0.7820 (t80) REVERT: AD 265 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7742 (tp40) REVERT: AD 314 LEU cc_start: 0.8813 (mt) cc_final: 0.8501 (mt) REVERT: AE 167 PHE cc_start: 0.8132 (m-80) cc_final: 0.7707 (m-10) REVERT: AE 197 ASP cc_start: 0.4389 (t70) cc_final: 0.4112 (m-30) REVERT: AE 231 PHE cc_start: 0.7182 (t80) cc_final: 0.5837 (t80) REVERT: AF 33 MET cc_start: 0.7695 (mmt) cc_final: 0.7089 (mtt) REVERT: AG 17 TYR cc_start: 0.8143 (m-80) cc_final: 0.7777 (m-80) REVERT: AG 23 GLU cc_start: 0.8476 (mp0) cc_final: 0.8152 (mp0) REVERT: AG 43 ARG cc_start: 0.8902 (ptp-170) cc_final: 0.8434 (ptp-170) REVERT: AG 48 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7078 (mpt180) REVERT: AG 78 TYR cc_start: 0.7303 (m-80) cc_final: 0.6925 (m-80) REVERT: AH 48 LEU cc_start: 0.8912 (tt) cc_final: 0.8687 (mm) REVERT: AJ 34 ARG cc_start: 0.6630 (tpp80) cc_final: 0.6360 (tpp-160) REVERT: AK 24 TRP cc_start: 0.6422 (m100) cc_final: 0.6145 (m100) REVERT: Aa 76 ASP cc_start: 0.8212 (t0) cc_final: 0.7933 (t0) REVERT: Aa 79 SER cc_start: 0.7856 (p) cc_final: 0.7536 (t) REVERT: Aa 84 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8657 (pm20) REVERT: Aa 140 LEU cc_start: 0.8820 (tp) cc_final: 0.8543 (tp) REVERT: Aa 199 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: Aa 274 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: Aa 346 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8744 (mm) REVERT: Aa 368 MET cc_start: 0.8939 (mmm) cc_final: 0.8698 (mmm) REVERT: Aa 377 MET cc_start: 0.9437 (tpp) cc_final: 0.9118 (mmm) REVERT: Aa 435 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8201 (tm-30) REVERT: Aa 440 MET cc_start: 0.8531 (ptp) cc_final: 0.8247 (ptp) REVERT: Aa 445 CYS cc_start: 0.8486 (m) cc_final: 0.7366 (t) REVERT: Ab 82 LEU cc_start: 0.9029 (tp) cc_final: 0.8791 (tp) REVERT: Ab 173 ILE cc_start: 0.8718 (tp) cc_final: 0.8390 (tp) REVERT: Ab 199 LYS cc_start: 0.8383 (tttm) cc_final: 0.8007 (tttm) REVERT: Ab 311 GLN cc_start: 0.7680 (mt0) cc_final: 0.7260 (mm-40) REVERT: Ab 384 MET cc_start: 0.8961 (ptm) cc_final: 0.8636 (ptp) REVERT: Ab 390 GLU cc_start: 0.8901 (pp20) cc_final: 0.8423 (tm-30) REVERT: Ab 395 GLU cc_start: 0.8852 (tp30) cc_final: 0.8484 (tp30) REVERT: Ac 12 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7576 (mptt) REVERT: Ac 121 PHE cc_start: 0.8746 (m-80) cc_final: 0.8461 (m-10) REVERT: Ac 138 MET cc_start: 0.7976 (mtt) cc_final: 0.7507 (mtt) REVERT: Ac 155 TYR cc_start: 0.5565 (t80) cc_final: 0.5249 (t80) REVERT: Ac 165 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.7100 (m-10) REVERT: Ac 202 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8307 (tm-30) REVERT: Ac 216 ASP cc_start: 0.8608 (t0) cc_final: 0.8355 (t0) REVERT: Ac 256 TYR cc_start: 0.8759 (m-80) cc_final: 0.8508 (m-80) REVERT: Ac 271 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7716 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8650 (mt) cc_final: 0.8328 (mt) REVERT: Ac 316 MET cc_start: 0.8909 (tpp) cc_final: 0.8673 (tpp) REVERT: Ac 344 GLU cc_start: 0.8531 (tp30) cc_final: 0.8202 (tp30) REVERT: Ac 358 TYR cc_start: 0.8825 (t80) cc_final: 0.8244 (t80) REVERT: Ad 119 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8461 (tm-30) REVERT: Ad 127 MET cc_start: 0.8290 (ttm) cc_final: 0.7779 (ttm) REVERT: Ad 164 MET cc_start: 0.8359 (ptp) cc_final: 0.7790 (ppp) REVERT: Ad 166 MET cc_start: 0.7545 (mmm) cc_final: 0.6980 (mmm) REVERT: Ad 170 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8609 (mptt) REVERT: Ad 177 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8946 (mttm) REVERT: Ad 189 ASN cc_start: 0.7803 (m-40) cc_final: 0.7378 (m-40) REVERT: Ad 273 PHE cc_start: 0.9240 (t80) cc_final: 0.8984 (t80) REVERT: Ad 295 MET cc_start: 0.8541 (mmp) cc_final: 0.8315 (mmp) REVERT: Ae 140 MET cc_start: 0.8499 (mtp) cc_final: 0.7514 (ttm) REVERT: Ae 165 MET cc_start: 0.7727 (tpp) cc_final: 0.7475 (mpp) REVERT: Af 33 MET cc_start: 0.8631 (mtm) cc_final: 0.8120 (mtt) REVERT: Af 60 MET cc_start: 0.8857 (tpp) cc_final: 0.7871 (mpp) REVERT: Af 91 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8940 (tt) REVERT: Af 106 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8249 (mt-10) REVERT: Ag 29 SER cc_start: 0.8943 (m) cc_final: 0.8529 (t) REVERT: Ag 57 TYR cc_start: 0.8786 (t80) cc_final: 0.8254 (t80) REVERT: Ag 60 TYR cc_start: 0.8824 (t80) cc_final: 0.8540 (t80) REVERT: Ag 66 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8449 (tm-30) REVERT: Ag 69 GLN cc_start: 0.8781 (mt0) cc_final: 0.8536 (mt0) REVERT: Ah 26 ASP cc_start: 0.8293 (m-30) cc_final: 0.8021 (t70) REVERT: Ah 45 ARG cc_start: 0.8272 (ptm160) cc_final: 0.7930 (ptm160) REVERT: Ah 53 ASN cc_start: 0.9186 (m-40) cc_final: 0.8598 (m110) REVERT: Ah 67 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: Ah 78 HIS cc_start: 0.8790 (t70) cc_final: 0.8535 (t-90) REVERT: Aj 53 TRP cc_start: 0.8356 (t-100) cc_final: 0.7534 (t-100) REVERT: Ak 23 MET cc_start: 0.7409 (mmt) cc_final: 0.6745 (tpp) REVERT: Ak 39 ARG cc_start: 0.7353 (tpt90) cc_final: 0.6700 (ptp-170) outliers start: 114 outliers final: 86 residues processed: 778 average time/residue: 0.4384 time to fit residues: 550.6948 Evaluate side-chains 772 residues out of total 3299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 674 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 92 PHE Chi-restraints excluded: chain AA residue 132 LEU Chi-restraints excluded: chain AA residue 146 LEU Chi-restraints excluded: chain AA residue 214 THR Chi-restraints excluded: chain AA residue 300 ASP Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AA residue 462 ILE Chi-restraints excluded: chain AA residue 475 MET Chi-restraints excluded: chain AB residue 58 LEU Chi-restraints excluded: chain AB residue 83 LEU Chi-restraints excluded: chain AB residue 129 ASP Chi-restraints excluded: chain AB residue 180 VAL Chi-restraints excluded: chain AB residue 225 VAL Chi-restraints excluded: chain AB residue 235 GLU Chi-restraints excluded: chain AB residue 351 ILE Chi-restraints excluded: chain AB residue 371 VAL Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 102 LEU Chi-restraints excluded: chain AC residue 107 TYR Chi-restraints excluded: chain AC residue 112 THR Chi-restraints excluded: chain AC residue 133 LEU Chi-restraints excluded: chain AC residue 200 LEU Chi-restraints excluded: chain AC residue 207 ASN Chi-restraints excluded: chain AC residue 250 LEU Chi-restraints excluded: chain AC residue 283 SER Chi-restraints excluded: chain AC residue 297 SER Chi-restraints excluded: chain AD residue 107 HIS Chi-restraints excluded: chain AD residue 141 THR Chi-restraints excluded: chain AD residue 164 MET Chi-restraints excluded: chain AD residue 265 GLN Chi-restraints excluded: chain AE residue 152 ILE Chi-restraints excluded: chain AE residue 192 VAL Chi-restraints excluded: chain AE residue 201 ASP Chi-restraints excluded: chain AE residue 211 VAL Chi-restraints excluded: chain AE residue 216 VAL Chi-restraints excluded: chain AE residue 251 LYS Chi-restraints excluded: chain AE residue 269 ASP Chi-restraints excluded: chain AF residue 37 THR Chi-restraints excluded: chain AG residue 11 ILE Chi-restraints excluded: chain AG residue 37 ASN Chi-restraints excluded: chain AH residue 29 THR Chi-restraints excluded: chain AH residue 78 HIS Chi-restraints excluded: chain AI residue 18 THR Chi-restraints excluded: chain AJ residue 19 SER Chi-restraints excluded: chain AJ residue 23 LEU Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 84 GLU Chi-restraints excluded: chain Aa residue 120 LEU Chi-restraints excluded: chain Aa residue 132 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 182 VAL Chi-restraints excluded: chain Aa residue 199 GLN Chi-restraints excluded: chain Aa residue 249 HIS Chi-restraints excluded: chain Aa residue 250 LEU Chi-restraints excluded: chain Aa residue 274 GLU Chi-restraints excluded: chain Aa residue 310 ILE Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 346 ILE Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 384 THR Chi-restraints excluded: chain Ab residue 137 LEU Chi-restraints excluded: chain Ab residue 309 LEU Chi-restraints excluded: chain Ab residue 377 LYS Chi-restraints excluded: chain Ac residue 39 VAL Chi-restraints excluded: chain Ac residue 66 VAL Chi-restraints excluded: chain Ac residue 69 ILE Chi-restraints excluded: chain Ac residue 92 ILE Chi-restraints excluded: chain Ac residue 126 THR Chi-restraints excluded: chain Ac residue 165 TRP Chi-restraints excluded: chain Ac residue 189 ILE Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 296 LEU Chi-restraints excluded: chain Ac residue 315 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 333 LEU Chi-restraints excluded: chain Ac residue 335 LEU Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 343 VAL Chi-restraints excluded: chain Ad residue 138 VAL Chi-restraints excluded: chain Ad residue 177 LYS Chi-restraints excluded: chain Ad residue 223 THR Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ae residue 105 GLU Chi-restraints excluded: chain Ae residue 125 VAL Chi-restraints excluded: chain Ae residue 143 SER Chi-restraints excluded: chain Ae residue 202 LEU Chi-restraints excluded: chain Af residue 35 ASP Chi-restraints excluded: chain Af residue 91 LEU Chi-restraints excluded: chain Ag residue 18 SER Chi-restraints excluded: chain Ag residue 39 LEU Chi-restraints excluded: chain Ag residue 47 LEU Chi-restraints excluded: chain Ag residue 59 ILE Chi-restraints excluded: chain Ah residue 67 GLU Chi-restraints excluded: chain Ah residue 86 LYS Chi-restraints excluded: chain Ah residue 87 ASN Chi-restraints excluded: chain Aj residue 18 THR Chi-restraints excluded: chain Aj residue 23 LEU Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 164 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 290 optimal weight: 0.0770 chunk 337 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 339 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 269 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 37 ASN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 312 GLN ** Ad 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.120410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.091328 restraints weight = 75243.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094466 restraints weight = 36753.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096567 restraints weight = 23797.003| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.450 32218 Z= 0.201 Angle : 0.849 59.176 43733 Z= 0.447 Chirality : 0.046 0.459 4746 Planarity : 0.005 0.099 5552 Dihedral : 9.599 131.025 4531 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.24 % Allowed : 24.89 % Favored : 71.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.08 % 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: 3849 helix: 1.16 (0.11), residues: 2035 sheet: 0.07 (0.27), residues: 356 loop : -0.30 (0.18), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRPAG 62 HIS 0.136 0.002 HISAD 107 PHE 0.031 0.002 PHEAg 67 TYR 0.020 0.002 TYRAe 263 ARG 0.015 0.000 ARGAH 54 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 1796) hydrogen bonds : angle 4.83348 ( 5166) SS BOND : bond 0.02344 ( 8) SS BOND : angle 3.73586 ( 16) covalent geometry : bond 0.00437 (32203) covalent geometry : angle 0.84567 (43717) Misc. bond : bond 0.26831 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16373.61 seconds wall clock time: 287 minutes 7.68 seconds (17227.68 seconds total)