Starting phenix.real_space_refine on Mon Jul 6 02:55:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iar_35316/07_2026/8iar_35316_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iar_35316/07_2026/8iar_35316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iar_35316/07_2026/8iar_35316_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iar_35316/07_2026/8iar_35316_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iar_35316/07_2026/8iar_35316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iar_35316/07_2026/8iar_35316.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.076 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 17 5.49 5 S 152 5.16 5 C 20733 2.51 5 N 5433 2.21 5 O 5912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32253 Number of models: 1 Model: "" Number of chains: 30 Chain: "AA" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3153 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 15, 'TRANS': 387} Chain breaks: 2 Chain: "AB" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3137 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain: "AC" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "AD" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1912 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 22, 'TRANS': 217} 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 562 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "AI" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 217 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain breaks: 1 Chain: "AJ" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 332 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "AK" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 401 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Aa" Number of atoms: 3225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3225 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 16, 'TRANS': 395} Chain breaks: 1 Chain: "Ab" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3094 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} 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: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1912 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 22, 'TRANS': 217} 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 562 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "Ai" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 207 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 1 Chain: "Aj" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 391 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "Ak" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 401 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "AC" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 195 Unusual residues: {'3PE': 2, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 55 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: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Chain: "Aa" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 82 Chain: "Ac" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PE': 1, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 55 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: "Ae" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "Ag" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'3PE': 1, 'CDL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 102 Time building chain proxies: 6.46, per 1000 atoms: 0.20 Number of scatterers: 32253 At special positions: 0 Unit cell: (155.1, 146.3, 172.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 152 16.00 P 17 15.00 O 5912 8.00 N 5433 7.00 C 20733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYSAA 338 " - pdb=" SG CYSAA 360 " distance=2.03 Simple disulfide: pdb=" SG CYSAE 222 " - pdb=" SG CYSAE 238 " distance=2.05 Simple disulfide: pdb=" SG CYSAH 51 " - pdb=" SG CYSAH 65 " distance=2.03 Simple disulfide: pdb=" SG CYSAa 338 " - pdb=" SG CYSAa 360 " distance=2.03 Simple disulfide: pdb=" SG CYSAe 222 " - pdb=" SG CYSAe 238 " distance=2.05 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7426 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 17 sheets defined 58.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 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 106 through 116 removed outlier: 4.176A pdb=" N GLUAA 110 " --> pdb=" O GLYAA 106 " (cutoff:3.500A) removed outlier: 3.555A 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: 4.196A 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 402 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: 3.663A pdb=" N VALAB 106 " --> pdb=" O GLYAB 102 " (cutoff:3.500A) Processing helix chain 'AB' and resid 129 through 143 Processing helix chain 'AB' and resid 147 through 166 removed outlier: 4.714A pdb=" N SERAB 156 " --> pdb=" O ALAAB 152 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLNAB 157 " --> pdb=" O ALAAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 168 through 182 removed outlier: 3.870A pdb=" N ARGAB 172 " --> pdb=" O ASNAB 168 " (cutoff:3.500A) Processing helix chain 'AB' and resid 201 through 213 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: 3.829A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 307 through 315 Processing helix chain 'AB' and resid 346 through 363 Processing helix chain 'AB' and resid 367 through 387 Processing helix chain 'AB' and resid 388 through 404 Processing helix chain 'AB' and resid 408 through 419 Processing helix chain 'AB' and resid 420 through 434 Processing helix chain 'AC' and resid 9 through 19 removed outlier: 3.509A pdb=" N ILEAC 13 " --> pdb=" O PROAC 9 " (cutoff:3.500A) Processing helix chain 'AC' and resid 28 through 31 Processing helix chain 'AC' and resid 32 through 53 Processing helix chain 'AC' and resid 61 through 72 Processing helix chain 'AC' and resid 75 through 104 Processing helix chain 'AC' and resid 105 through 108 removed outlier: 3.579A pdb=" N THRAC 108 " --> pdb=" O GLYAC 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 105 through 108' Processing helix chain 'AC' and resid 109 through 133 Processing helix chain 'AC' and resid 136 through 152 removed outlier: 3.508A pdb=" N LEUAC 150 " --> pdb=" O ILEAC 146 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SERAC 151 " --> pdb=" O THRAC 147 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALAAC 152 " --> pdb=" O ASNAC 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 156 through 166 Processing helix chain 'AC' and resid 171 through 202 removed outlier: 3.552A pdb=" N ARGAC 177 " --> pdb=" O ALAAC 173 " (cutoff:3.500A) Proline residue: AC 186 - end of helix Processing helix chain 'AC' and resid 212 through 215 removed outlier: 4.575A pdb=" N ALAAC 215 " --> pdb=" O ASNAC 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 212 through 215' Processing helix chain 'AC' and resid 224 through 244 Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 273 No H-bonds generated for 'chain 'AC' and resid 271 through 273' Processing helix chain 'AC' and resid 274 through 284 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: 4.598A pdb=" N LEUAC 301 " --> pdb=" O SERAC 297 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALAAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 305 through 307 No H-bonds generated for 'chain 'AC' and resid 305 through 307' Processing helix chain 'AC' and resid 318 through 341 removed outlier: 3.759A pdb=" N GLYAC 340 " --> pdb=" O THRAC 336 " (cutoff:3.500A) Processing helix chain 'AC' and resid 346 through 364 Processing helix chain 'AC' and resid 364 through 377 Processing helix chain 'AD' and resid 106 through 120 Processing helix chain 'AD' and resid 121 through 124 removed outlier: 3.512A pdb=" N CYSAD 124 " --> pdb=" O CYSAD 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 121 through 124' Processing helix chain 'AD' and resid 131 through 136 Processing helix chain 'AD' and resid 141 through 151 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: 4.097A pdb=" N ALAAD 241 " --> pdb=" O PROAD 238 " (cutoff:3.500A) Processing helix chain 'AD' and resid 262 through 279 Processing helix chain 'AD' and resid 281 through 317 Proline residue: AD 301 - end of helix removed outlier: 3.865A pdb=" N VALAD 313 " --> pdb=" O HISAD 309 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEUAD 314 " --> pdb=" O LYSAD 310 " (cutoff:3.500A) Processing helix chain 'AE' and resid 104 through 140 removed outlier: 4.378A pdb=" N ALAAE 109 " --> pdb=" O GLUAE 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N METAE 140 " --> pdb=" O PHEAE 136 " (cutoff:3.500A) Processing helix chain 'AE' and resid 143 through 148 Processing helix chain 'AE' and resid 155 through 159 Processing helix chain 'AE' and resid 168 through 172 Processing helix chain 'AE' and resid 180 through 190 Processing helix chain 'AE' and resid 200 through 205 Processing helix chain 'AF' and resid 15 through 26 removed outlier: 3.721A pdb=" N GLYAF 26 " --> pdb=" O TYRAF 22 " (cutoff:3.500A) Processing helix chain 'AF' and resid 34 through 38 removed outlier: 3.686A pdb=" N LEUAF 38 " --> pdb=" O ASPAF 35 " (cutoff:3.500A) Processing helix chain 'AF' and resid 41 through 50 Processing helix chain 'AF' and resid 52 through 72 Processing helix chain 'AF' and resid 77 through 81 Processing helix chain 'AF' and resid 90 through 111 removed outlier: 4.178A pdb=" N TYRAF 94 " --> pdb=" O TYRAF 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUAF 97 " --> pdb=" O PROAF 93 " (cutoff:3.500A) Processing helix chain 'AG' and resid 21 through 24 Processing helix chain 'AG' and resid 29 through 72 removed outlier: 3.851A pdb=" N ILEAG 35 " --> pdb=" O PHEAG 31 " (cutoff:3.500A) Proline residue: AG 36 - end of helix removed outlier: 5.323A pdb=" N LEUAG 47 " --> pdb=" O ARGAG 43 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARGAG 48 " --> pdb=" O GLUAG 44 " (cutoff:3.500A) Proline residue: AG 51 - end of helix Processing helix chain 'AH' and resid 26 through 37 removed outlier: 3.627A pdb=" N THRAH 30 " --> pdb=" O ASPAH 26 " (cutoff:3.500A) Processing helix chain 'AH' and resid 38 through 58 Processing helix chain 'AH' and resid 65 through 84 removed outlier: 3.830A pdb=" N LYSAH 83 " --> pdb=" O CYSAH 79 " (cutoff:3.500A) Processing helix chain 'AH' and resid 85 through 88 Processing helix chain 'AJ' and resid 9 through 15 Processing helix chain 'AJ' and resid 17 through 48 removed outlier: 4.295A pdb=" N ARGAJ 34 " --> pdb=" O LEUAJ 30 " (cutoff:3.500A) Processing helix chain 'AK' and resid 7 through 36 Proline residue: AK 19 - end of helix Processing helix chain 'AK' and resid 38 through 43 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: 4.175A 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 311 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 403 Processing helix chain 'Aa' and resid 405 through 419 Processing helix chain 'Aa' and resid 425 through 435 Processing helix chain 'Aa' and resid 437 through 449 Processing helix chain 'Aa' and resid 467 through 475 Processing helix chain 'Ab' and resid 68 through 72 removed outlier: 3.544A pdb=" N GLUAb 72 " --> pdb=" O SERAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 78 through 86 Processing helix chain 'Ab' and resid 95 through 106 removed outlier: 3.663A pdb=" N VALAb 106 " --> pdb=" O GLYAb 102 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 129 through 143 Processing helix chain 'Ab' and resid 147 through 166 removed outlier: 4.713A pdb=" N SERAb 156 " --> pdb=" O ALAAb 152 " (cutoff:3.500A) removed outlier: 4.284A 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: 3.596A pdb=" N LEUAb 230 " --> pdb=" O SERAb 226 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 280 through 294 removed outlier: 3.828A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 307 through 313 removed outlier: 3.613A pdb=" N VALAb 313 " --> pdb=" O LEUAb 309 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 346 through 363 Processing helix chain 'Ab' and resid 367 through 387 Processing helix chain 'Ab' and resid 388 through 404 Processing helix chain 'Ab' and resid 408 through 419 Processing helix chain 'Ab' and resid 420 through 434 Processing helix chain 'Ac' and resid 10 through 18 removed outlier: 4.086A pdb=" N ILEAc 14 " --> pdb=" O LEUAc 10 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 28 through 31 Processing helix chain 'Ac' and resid 32 through 53 Processing helix chain 'Ac' and resid 61 through 72 Processing helix chain 'Ac' and resid 75 through 104 Processing helix chain 'Ac' and resid 105 through 108 removed outlier: 3.579A pdb=" N THRAc 108 " --> pdb=" O GLYAc 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 105 through 108' Processing helix chain 'Ac' and resid 109 through 133 Processing helix chain 'Ac' and resid 136 through 152 removed outlier: 3.509A pdb=" N LEUAc 150 " --> pdb=" O ILEAc 146 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALAAc 152 " --> pdb=" O ASNAc 148 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 166 Processing helix chain 'Ac' and resid 171 through 202 removed outlier: 3.551A pdb=" N ARGAc 177 " --> pdb=" O ALAAc 173 " (cutoff:3.500A) Proline residue: Ac 186 - end of helix Processing helix chain 'Ac' and resid 212 through 215 removed outlier: 4.575A pdb=" N ALAAc 215 " --> pdb=" O ASNAc 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 212 through 215' Processing helix chain 'Ac' and resid 224 through 244 Processing helix chain 'Ac' and resid 246 through 251 removed outlier: 4.085A pdb=" N LEUAc 250 " --> pdb=" O PROAc 247 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 252 through 257 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: 4.600A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 307 No H-bonds generated for 'chain 'Ac' and resid 305 through 307' Processing helix chain 'Ac' and resid 318 through 341 removed outlier: 3.759A pdb=" N GLYAc 340 " --> pdb=" O THRAc 336 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 346 through 364 Processing helix chain 'Ac' and resid 364 through 377 Processing helix chain 'Ad' and resid 106 through 120 Processing helix chain 'Ad' and resid 121 through 124 Processing helix chain 'Ad' and resid 131 through 136 removed outlier: 4.066A pdb=" N LEUAd 135 " --> pdb=" O ALAAd 131 " (cutoff:3.500A) removed outlier: 3.763A 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 206 through 216 Processing helix chain 'Ad' and resid 262 through 279 Processing helix chain 'Ad' and resid 281 through 316 Proline residue: Ad 301 - end of helix removed outlier: 3.865A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEUAd 314 " --> pdb=" O LYSAd 310 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 104 through 140 removed outlier: 4.377A pdb=" N ALAAe 109 " --> pdb=" O GLUAe 105 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N METAe 140 " --> pdb=" O PHEAe 136 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 143 through 148 Processing helix chain 'Ae' and resid 157 through 159 No H-bonds generated for 'chain 'Ae' and resid 157 through 159' Processing helix chain 'Ae' and resid 168 through 172 Processing helix chain 'Ae' and resid 180 through 190 Processing helix chain 'Ae' and resid 200 through 205 Processing helix chain 'Af' and resid 15 through 26 removed outlier: 3.720A pdb=" N GLYAf 26 " --> pdb=" O TYRAf 22 " (cutoff:3.500A) Processing helix chain 'Af' and resid 34 through 38 removed outlier: 3.686A pdb=" N LEUAf 38 " --> pdb=" O ASPAf 35 " (cutoff:3.500A) Processing helix chain 'Af' and resid 41 through 50 Processing helix chain 'Af' and resid 52 through 72 Processing helix chain 'Af' and resid 77 through 81 Processing helix chain 'Af' and resid 90 through 111 removed outlier: 4.177A pdb=" N TYRAf 94 " --> pdb=" O TYRAf 90 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUAf 97 " --> pdb=" O PROAf 93 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 20 through 24 Processing helix chain 'Ag' and resid 29 through 72 removed outlier: 3.849A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 5.323A 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 'Ag' and resid 74 through 79 removed outlier: 4.247A pdb=" N TYRAg 78 " --> pdb=" O ASNAg 74 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLUAg 79 " --> pdb=" O PROAg 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 74 through 79' Processing helix chain 'Ah' and resid 26 through 37 removed outlier: 3.627A pdb=" N THRAh 30 " --> pdb=" O ASPAh 26 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 38 through 58 Processing helix chain 'Ah' and resid 65 through 84 removed outlier: 3.830A pdb=" N LYSAh 83 " --> pdb=" O CYSAh 79 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 85 through 88 Processing helix chain 'Aj' and resid 7 through 15 Processing helix chain 'Aj' and resid 17 through 48 removed outlier: 4.296A pdb=" N ARGAj 34 " --> pdb=" O LEUAj 30 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 7 through 36 Proline residue: Ak 19 - end of helix Processing helix chain 'Ak' and resid 38 through 43 Processing sheet with id=AA1, first strand: chain 'AA' and resid 49 through 52 Processing sheet with id=AA2, 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=AA3, first strand: chain 'AB' and resid 39 through 42 removed outlier: 6.529A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARGAI 77 " --> pdb=" O VALAI 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.892A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLYAB 442 " --> pdb=" O ILEAB 258 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLUAB 260 " --> pdb=" O GLYAB 442 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLYAB 334 " --> pdb=" O SERAB 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AC' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'AD' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'AE' and resid 163 through 165 Processing sheet with id=AA8, first strand: chain 'AE' and resid 225 through 226 removed outlier: 6.659A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Aa' and resid 49 through 52 Processing sheet with id=AB1, 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=AB2, first strand: chain 'Ab' and resid 41 through 42 Processing sheet with id=AB3, first strand: chain 'Ab' and resid 256 through 260 removed outlier: 3.653A pdb=" N GLYAb 256 " --> pdb=" O LYSAb 436 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SERAb 342 " --> pdb=" O VALAb 267 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYRAb 339 " --> pdb=" O SERAb 324 " (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 155 Processing sheet with id=AB6, first strand: chain 'Ae' and resid 152 through 155 removed outlier: 4.036A pdb=" N ILEAe 152 " --> pdb=" O VALAe 273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Ae' and resid 163 through 165 Processing sheet with id=AB8, first strand: chain 'Ae' and resid 225 through 226 removed outlier: 6.660A pdb=" N HISAe 242 " --> pdb=" O ARGAe 250 " (cutoff:3.500A) 1856 hydrogen bonds defined for protein. 5328 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: 4.97 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 10515 1.36 - 1.54: 21712 1.54 - 1.71: 526 1.71 - 1.89: 254 1.89 - 2.06: 24 Bond restraints: 33031 Sorted by residual: bond pdb=" C ASPAi 44 " pdb=" N VALAi 45 " ideal model delta sigma weight residual 1.332 1.516 -0.185 9.20e-03 1.18e+04 4.02e+02 bond pdb=" C ASPAI 44 " pdb=" N VALAI 45 " ideal model delta sigma weight residual 1.332 1.516 -0.184 9.20e-03 1.18e+04 4.02e+02 bond pdb=" C LEUAa 250 " pdb=" N SERAa 251 " ideal model delta sigma weight residual 1.330 1.584 -0.254 1.30e-02 5.92e+03 3.81e+02 bond pdb=" C VALAI 45 " pdb=" N LYSAI 46 " ideal model delta sigma weight residual 1.331 1.532 -0.202 1.29e-02 6.01e+03 2.44e+02 bond pdb=" C GLUAC 271 " pdb=" N TRPAC 272 " ideal model delta sigma weight residual 1.335 1.516 -0.180 1.32e-02 5.74e+03 1.86e+02 ... (remaining 33026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 42888 2.66 - 5.32: 1594 5.32 - 7.99: 219 7.99 - 10.65: 77 10.65 - 13.31: 16 Bond angle restraints: 44794 Sorted by residual: angle pdb=" CA ASPAI 44 " pdb=" C ASPAI 44 " pdb=" N VALAI 45 " ideal model delta sigma weight residual 119.52 106.94 12.58 7.90e-01 1.60e+00 2.54e+02 angle pdb=" CA ASPAi 44 " pdb=" C ASPAi 44 " pdb=" N VALAi 45 " ideal model delta sigma weight residual 119.52 106.96 12.56 7.90e-01 1.60e+00 2.53e+02 angle pdb=" N THRAB 306 " pdb=" CA THRAB 306 " pdb=" C THRAB 306 " ideal model delta sigma weight residual 111.33 123.38 -12.05 1.21e+00 6.83e-01 9.91e+01 angle pdb=" N THRAb 306 " pdb=" CA THRAb 306 " pdb=" C THRAb 306 " ideal model delta sigma weight residual 111.33 123.33 -12.00 1.21e+00 6.83e-01 9.83e+01 angle pdb=" N ASNAB 303 " pdb=" CA ASNAB 303 " pdb=" C ASNAB 303 " ideal model delta sigma weight residual 112.88 100.14 12.74 1.29e+00 6.01e-01 9.76e+01 ... (remaining 44789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.95: 19008 25.95 - 51.91: 638 51.91 - 77.86: 108 77.86 - 103.81: 28 103.81 - 129.76: 2 Dihedral angle restraints: 19784 sinusoidal: 8251 harmonic: 11533 Sorted by residual: 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 -81.00 81.00 2 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" C2B HEMAC 403 " pdb=" C3B HEMAC 403 " pdb=" CAB HEMAC 403 " pdb=" CBB HEMAC 403 " ideal model delta sinusoidal sigma weight residual 0.00 -80.87 80.87 2 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" C2C HEMAc 401 " pdb=" C3C HEMAc 401 " pdb=" CAC HEMAc 401 " pdb=" CBC HEMAc 401 " ideal model delta sinusoidal sigma weight residual 0.00 75.96 -75.96 2 1.00e+01 1.00e-02 4.52e+01 ... (remaining 19781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4259 0.085 - 0.171: 518 0.171 - 0.256: 52 0.256 - 0.341: 9 0.341 - 0.426: 1 Chirality restraints: 4839 Sorted by residual: chirality pdb=" C2 3PEAC 401 " pdb=" C1 3PEAC 401 " pdb=" C3 3PEAC 401 " pdb=" O21 3PEAC 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.10 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA TYRAK 47 " pdb=" N TYRAK 47 " pdb=" C TYRAK 47 " pdb=" CB TYRAK 47 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA TYRAe 91 " pdb=" N TYRAe 91 " pdb=" C TYRAe 91 " pdb=" CB TYRAe 91 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 4836 not shown) Planarity restraints: 5666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10AC 405 " 0.019 2.00e-02 2.50e+03 2.42e-01 1.76e+03 pdb=" C1M U10AC 405 " -0.237 2.00e-02 2.50e+03 pdb=" C2 U10AC 405 " 0.048 2.00e-02 2.50e+03 pdb=" C3 U10AC 405 " -0.051 2.00e-02 2.50e+03 pdb=" C4 U10AC 405 " -0.062 2.00e-02 2.50e+03 pdb=" C5 U10AC 405 " 0.089 2.00e-02 2.50e+03 pdb=" C6 U10AC 405 " -0.089 2.00e-02 2.50e+03 pdb=" C7 U10AC 405 " -0.215 2.00e-02 2.50e+03 pdb=" O2 U10AC 405 " 0.430 2.00e-02 2.50e+03 pdb=" O3 U10AC 405 " -0.163 2.00e-02 2.50e+03 pdb=" O4 U10AC 405 " -0.294 2.00e-02 2.50e+03 pdb=" O5 U10AC 405 " 0.527 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 U10Ac 404 " -0.019 2.00e-02 2.50e+03 2.42e-01 1.75e+03 pdb=" C1M U10Ac 404 " 0.237 2.00e-02 2.50e+03 pdb=" C2 U10Ac 404 " -0.048 2.00e-02 2.50e+03 pdb=" C3 U10Ac 404 " 0.050 2.00e-02 2.50e+03 pdb=" C4 U10Ac 404 " 0.062 2.00e-02 2.50e+03 pdb=" C5 U10Ac 404 " -0.088 2.00e-02 2.50e+03 pdb=" C6 U10Ac 404 " 0.088 2.00e-02 2.50e+03 pdb=" C7 U10Ac 404 " 0.215 2.00e-02 2.50e+03 pdb=" O2 U10Ac 404 " -0.429 2.00e-02 2.50e+03 pdb=" O3 U10Ac 404 " 0.163 2.00e-02 2.50e+03 pdb=" O4 U10Ac 404 " 0.294 2.00e-02 2.50e+03 pdb=" O5 U10Ac 404 " -0.527 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 U10AC 405 " 0.320 2.00e-02 2.50e+03 2.72e-01 9.27e+02 pdb=" C13 U10AC 405 " -0.472 2.00e-02 2.50e+03 pdb=" C14 U10AC 405 " -0.098 2.00e-02 2.50e+03 pdb=" C15 U10AC 405 " 0.073 2.00e-02 2.50e+03 pdb=" C16 U10AC 405 " 0.177 2.00e-02 2.50e+03 ... (remaining 5663 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 232 2.52 - 3.12: 26781 3.12 - 3.71: 53993 3.71 - 4.31: 78273 4.31 - 4.90: 125257 Nonbonded interactions: 284536 Sorted by model distance: nonbonded pdb=" O THRAA 190 " pdb=" OG SERAA 273 " model vdw 1.929 3.040 nonbonded pdb=" N LEUAa 120 " pdb=" O HISAb 298 " model vdw 2.002 3.120 nonbonded pdb=" NH2 ARGAa 58 " pdb=" O LEUAa 417 " model vdw 2.029 3.120 nonbonded pdb=" O TYRAC 223 " pdb=" NE1 TRPAD 311 " model vdw 2.042 3.120 nonbonded pdb=" O SERAC 17 " pdb=" O2 UQ6AC 406 " model vdw 2.055 3.040 ... (remaining 284531 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 311 or resid 337 through 480)) selection = (chain 'Aa' and (resid 44 through 256 or resid 267 through 480)) } ncs_group { reference = (chain 'AB' and (resid 36 through 313 or resid 320 through 453)) selection = chain 'Ab' } ncs_group { reference = (chain 'AC' and (resid 8 through 380 or resid 402)) selection = (chain 'Ac' and (resid 8 through 380 or resid 402)) } ncs_group { reference = chain 'AD' selection = chain 'Ad' } ncs_group { reference = chain 'AE' selection = (chain 'Ae' and resid 79 through 274) } ncs_group { reference = chain 'AF' selection = chain 'Af' } ncs_group { reference = chain 'AG' selection = chain 'Ag' } ncs_group { reference = chain 'AH' selection = chain 'Ah' } ncs_group { reference = (chain 'AI' and (resid 41 through 47 or resid 58 through 78)) selection = chain 'Ai' } ncs_group { reference = chain 'AJ' selection = (chain 'Aj' and resid 8 through 48) } ncs_group { reference = chain 'AK' selection = chain 'Ak' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.140 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.009 0.254 33045 Z= 0.569 Angle : 1.194 13.311 44806 Z= 0.745 Chirality : 0.056 0.426 4839 Planarity : 0.013 0.272 5666 Dihedral : 13.524 129.762 12340 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 28.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.39 % Allowed : 1.90 % Favored : 97.71 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.12), residues: 3916 helix: -0.70 (0.10), residues: 2039 sheet: -0.21 (0.26), residues: 375 loop : -1.23 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAE 250 TYR 0.049 0.002 TYRAe 235 PHE 0.049 0.002 PHEAC 183 TRP 0.025 0.002 TRPAC 141 HIS 0.009 0.001 HISAC 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00877 / 0.56 (33031) covalent geometry : angle 1.19220 / 0.74 (44794) SS BOND : bond 0.01316 / 0.88 ( 6) SS BOND : angle 4.56294 / 2.86 ( 12) hydrogen bonds : bond 0.18084 / 12.38 ( 1856) hydrogen bonds : angle 7.25985 / 5.02 ( 5328) Misc. bond : bond 0.09598 / 6.41 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 1213 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 109 LEU cc_start: 0.6748 (tt) cc_final: 0.6546 (tp) REVERT: AA 449 PHE cc_start: 0.7923 (m-80) cc_final: 0.7574 (m-80) REVERT: AB 74 SER cc_start: 0.8641 (m) cc_final: 0.8389 (p) REVERT: AB 233 VAL cc_start: 0.9592 (m) cc_final: 0.9196 (p) REVERT: AC 313 ARG cc_start: 0.8630 (ttt180) cc_final: 0.8347 (ttt180) REVERT: AD 259 THR cc_start: 0.8148 (m) cc_final: 0.7835 (m) REVERT: AF 108 TRP cc_start: 0.8550 (t-100) cc_final: 0.8349 (t60) REVERT: Aa 468 TYR cc_start: 0.8348 (t80) cc_final: 0.8139 (t80) REVERT: Ab 109 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8022 (mttm) REVERT: Ab 141 THR cc_start: 0.7974 (p) cc_final: 0.7746 (p) REVERT: Ab 173 ILE cc_start: 0.8750 (tp) cc_final: 0.8337 (mm) REVERT: Ab 267 VAL cc_start: 0.9339 (t) cc_final: 0.9022 (p) REVERT: Ac 59 THR cc_start: 0.8902 (p) cc_final: 0.8669 (p) REVERT: Ac 156 ILE cc_start: 0.8263 (pt) cc_final: 0.8017 (pt) REVERT: Ac 235 MET cc_start: 0.9298 (tmm) cc_final: 0.8966 (ttp) REVERT: Ac 252 ASP cc_start: 0.7593 (t0) cc_final: 0.7002 (t0) REVERT: Ac 312 GLN cc_start: 0.8795 (mt0) cc_final: 0.8399 (mt0) REVERT: Ac 313 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8198 (ttt-90) REVERT: Ad 156 ASP cc_start: 0.8433 (t0) cc_final: 0.8198 (t0) REVERT: Ad 165 PHE cc_start: 0.8128 (p90) cc_final: 0.7590 (p90) REVERT: Ad 296 MET cc_start: 0.8270 (mmt) cc_final: 0.8057 (mmp) REVERT: Ad 309 HIS cc_start: 0.7013 (t70) cc_final: 0.6730 (t-90) REVERT: Ad 322 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8175 (mtp85) REVERT: Ae 191 GLU cc_start: 0.7863 (mp0) cc_final: 0.7505 (mp0) REVERT: Ah 25 VAL cc_start: 0.8398 (t) cc_final: 0.8064 (p) REVERT: Ai 64 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7861 (mp) REVERT: Aj 8 SER cc_start: 0.6113 (t) cc_final: 0.5609 (p) REVERT: Ak 23 MET cc_start: 0.8558 (tpp) cc_final: 0.8078 (mmp) outliers start: 13 outliers final: 0 residues processed: 1218 average time/residue: 0.2102 time to fit residues: 392.0981 Evaluate side-chains 664 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ai residue 64 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN AA 397 ASN ** AB 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 206 ASN AC 308 HIS AD 107 HIS AD 119 GLN AD 309 HIS ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 242 HIS AH 53 ASN AI 58 GLN AI 71 ASN AJ 48 ASN AK 16 ASN ** Aa 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 181 ASN Aa 207 ASN Aa 249 HIS ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 90 HIS Ad 189 ASN Ad 190 ASN ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ai 58 GLN Ai 71 ASN Ak 16 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086355 restraints weight = 70058.501| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.95 r_work: 0.3106 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.504 33045 Z= 0.202 Angle : 0.737 13.534 44806 Z= 0.367 Chirality : 0.045 0.201 4839 Planarity : 0.005 0.078 5666 Dihedral : 11.045 118.820 4954 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.83 % Allowed : 12.32 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 3916 helix: 0.95 (0.11), residues: 2085 sheet: -0.16 (0.26), residues: 393 loop : -0.38 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAD 111 TYR 0.021 0.002 TYRAJ 44 PHE 0.034 0.002 PHEAd 273 TRP 0.017 0.002 TRPAE 169 HIS 0.013 0.001 HISAe 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (33031) covalent geometry : angle 0.73689 / 0.37 (44794) SS BOND : bond 0.00280 / 0.18 ( 6) SS BOND : angle 1.47317 / 0.91 ( 12) hydrogen bonds : bond 0.04990 / 3.40 ( 1856) hydrogen bonds : angle 5.09264 / 3.52 ( 5328) Misc. bond : bond 0.26505 / 16.92 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 705 time to evaluate : 1.182 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 123 TYR cc_start: 0.7759 (p90) cc_final: 0.7165 (p90) REVERT: AA 179 MET cc_start: 0.7791 (mtm) cc_final: 0.7393 (mtm) REVERT: AA 243 LEU cc_start: 0.8778 (tp) cc_final: 0.8558 (mt) REVERT: AA 385 GLU cc_start: 0.8966 (tt0) cc_final: 0.8716 (tm-30) REVERT: AA 395 LEU cc_start: 0.9188 (tp) cc_final: 0.8935 (tt) REVERT: AB 74 SER cc_start: 0.8804 (m) cc_final: 0.8315 (p) REVERT: AB 210 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: AB 407 MET cc_start: 0.8851 (mtm) cc_final: 0.8501 (mpp) REVERT: AC 104 TYR cc_start: 0.9210 (m-80) cc_final: 0.9009 (m-80) REVERT: AC 341 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7713 (mm-40) REVERT: AD 144 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7755 (tt0) REVERT: AD 234 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8328 (m110) REVERT: AD 255 TYR cc_start: 0.7245 (m-80) cc_final: 0.6879 (m-80) REVERT: AE 105 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7045 (pm20) REVERT: AE 108 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7772 (mp0) REVERT: AE 135 GLN cc_start: 0.8574 (mp10) cc_final: 0.7804 (mp10) REVERT: AE 169 TRP cc_start: 0.8445 (t60) cc_final: 0.8194 (t60) REVERT: AE 170 ARG cc_start: 0.8919 (mtm180) cc_final: 0.8585 (mtt-85) REVERT: AE 209 GLU cc_start: 0.6384 (pm20) cc_final: 0.6170 (pm20) REVERT: AF 54 ASP cc_start: 0.8580 (p0) cc_final: 0.8347 (p0) REVERT: AF 57 ASN cc_start: 0.8333 (m-40) cc_final: 0.8061 (m-40) REVERT: AF 64 LYS cc_start: 0.9039 (tptm) cc_final: 0.8619 (tptm) REVERT: AF 96 LYS cc_start: 0.9106 (tppt) cc_final: 0.8720 (tppp) REVERT: AG 66 GLU cc_start: 0.8443 (tp30) cc_final: 0.8121 (tm-30) REVERT: AG 72 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.7784 (tpt170) REVERT: AG 77 MET cc_start: 0.8072 (tpt) cc_final: 0.7750 (tpp) REVERT: AG 78 TYR cc_start: 0.8011 (m-80) cc_final: 0.7785 (m-80) REVERT: AH 64 ASP cc_start: 0.8325 (p0) cc_final: 0.7925 (t0) REVERT: AH 73 LEU cc_start: 0.9075 (mp) cc_final: 0.8802 (mp) REVERT: AJ 33 GLU cc_start: 0.8189 (tt0) cc_final: 0.7698 (tt0) REVERT: AJ 38 GLN cc_start: 0.8338 (tp-100) cc_final: 0.7910 (tm-30) REVERT: Aa 94 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8711 (tm-30) REVERT: Aa 274 GLU cc_start: 0.8101 (pt0) cc_final: 0.7886 (pt0) REVERT: Aa 360 CYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7489 (m) REVERT: Aa 463 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7800 (pt0) REVERT: Aa 468 TYR cc_start: 0.8918 (t80) cc_final: 0.8620 (t80) REVERT: Aa 475 MET cc_start: 0.9055 (mmp) cc_final: 0.8635 (mmp) REVERT: Ab 77 LEU cc_start: 0.8973 (tp) cc_final: 0.8613 (mt) REVERT: Ab 157 GLN cc_start: 0.8836 (tp40) cc_final: 0.8228 (tp-100) REVERT: Ab 173 ILE cc_start: 0.8766 (tp) cc_final: 0.8345 (mm) REVERT: Ab 218 MET cc_start: 0.8848 (mtm) cc_final: 0.8286 (mtt) REVERT: Ab 262 ASN cc_start: 0.8472 (p0) cc_final: 0.8255 (p0) REVERT: Ac 42 MET cc_start: 0.8359 (mtt) cc_final: 0.7817 (tpp) REVERT: Ac 44 GLN cc_start: 0.8129 (mm110) cc_final: 0.7732 (mm-40) REVERT: Ac 51 LEU cc_start: 0.9244 (mm) cc_final: 0.9031 (mm) REVERT: Ac 118 LEU cc_start: 0.8865 (tp) cc_final: 0.8642 (tt) REVERT: Ac 171 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: Ac 257 MET cc_start: 0.8828 (mtp) cc_final: 0.8541 (mtp) REVERT: Ac 312 GLN cc_start: 0.9158 (mt0) cc_final: 0.8682 (mt0) REVERT: Ac 352 GLN cc_start: 0.8761 (mt0) cc_final: 0.8508 (mt0) REVERT: Ad 159 ASN cc_start: 0.7945 (t0) cc_final: 0.7153 (t0) REVERT: Ad 166 MET cc_start: 0.7682 (mtt) cc_final: 0.7396 (mmt) REVERT: Ad 173 ASP cc_start: 0.8717 (t0) cc_final: 0.8223 (t0) REVERT: Ad 196 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8236 (t70) REVERT: Ad 199 TYR cc_start: 0.8705 (m-80) cc_final: 0.8444 (m-80) REVERT: Ad 228 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7089 (tmt170) REVERT: Ad 244 MET cc_start: 0.8694 (ttp) cc_final: 0.8157 (ttp) REVERT: Ad 273 PHE cc_start: 0.9111 (t80) cc_final: 0.8616 (t80) REVERT: Ae 82 ASP cc_start: 0.8416 (p0) cc_final: 0.8188 (m-30) REVERT: Ae 90 ASP cc_start: 0.9040 (m-30) cc_final: 0.8433 (t0) REVERT: Ae 159 ILE cc_start: 0.8064 (mt) cc_final: 0.7771 (mp) REVERT: Ae 168 LYS cc_start: 0.8403 (ptmt) cc_final: 0.8138 (mtpp) REVERT: Ae 170 ARG cc_start: 0.8130 (mtp180) cc_final: 0.7650 (mtt-85) REVERT: Ae 250 ARG cc_start: 0.6551 (mmm160) cc_final: 0.6296 (mmm160) REVERT: Af 19 LYS cc_start: 0.8857 (mttm) cc_final: 0.8431 (mttm) REVERT: Af 78 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8356 (mtpp) REVERT: Af 92 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8526 (tm-30) REVERT: Ag 17 TYR cc_start: 0.9150 (m-80) cc_final: 0.8833 (m-80) REVERT: Ag 78 TYR cc_start: 0.8167 (m-80) cc_final: 0.7842 (m-80) REVERT: Ah 33 GLU cc_start: 0.8654 (mp0) cc_final: 0.8352 (pp20) REVERT: Ah 68 GLU cc_start: 0.7736 (mp0) cc_final: 0.7511 (mp0) REVERT: Ai 72 VAL cc_start: 0.2889 (OUTLIER) cc_final: 0.2591 (p) REVERT: Ak 10 TYR cc_start: 0.7524 (m-80) cc_final: 0.7277 (m-80) REVERT: Ak 23 MET cc_start: 0.7623 (tpp) cc_final: 0.7270 (mmt) REVERT: Ak 47 TYR cc_start: 0.7462 (t80) cc_final: 0.7051 (t80) outliers start: 95 outliers final: 47 residues processed: 769 average time/residue: 0.1860 time to fit residues: 230.8161 Evaluate side-chains 624 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 568 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 233 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AC residue 308 HIS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 234 ASN Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AF residue 20 TRP Chi-restraints excluded: chain AG residue 55 VAL Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 67 THR Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 186 LEU Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 273 TYR Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 349 ILE Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 205 HIS Chi-restraints excluded: chain Ad residue 228 ARG Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 216 VAL Chi-restraints excluded: chain Ae residue 271 VAL Chi-restraints excluded: chain Ae residue 273 VAL Chi-restraints excluded: chain Af residue 37 THR Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 38 LEU Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 41 optimal weight: 0.9990 chunk 363 optimal weight: 1.9990 chunk 336 optimal weight: 9.9990 chunk 328 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 356 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 167 GLN ** AB 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 236 GLN AC 308 HIS AD 107 HIS ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 46 HIS AJ 48 ASN AK 16 ASN Aa 55 ASN Aa 95 HIS Aa 434 GLN Ab 118 ASN Ab 167 GLN Ac 331 ASN Ad 134 HIS ** Ad 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 309 HIS ** Ae 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 49 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086945 restraints weight = 72396.010| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.85 r_work: 0.3170 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.505 33045 Z= 0.176 Angle : 0.643 13.208 44806 Z= 0.320 Chirality : 0.043 0.163 4839 Planarity : 0.004 0.060 5666 Dihedral : 10.506 120.311 4952 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.21 % Allowed : 14.19 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3916 helix: 1.30 (0.11), residues: 2096 sheet: -0.12 (0.26), residues: 396 loop : -0.15 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGAA 442 TYR 0.021 0.001 TYRAJ 44 PHE 0.024 0.002 PHEAC 276 TRP 0.017 0.001 TRPAc 141 HIS 0.014 0.001 HISAC 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (33031) covalent geometry : angle 0.64284 / 0.32 (44794) SS BOND : bond 0.00461 / 0.24 ( 6) SS BOND : angle 0.85390 / 0.53 ( 12) hydrogen bonds : bond 0.04342 / 2.94 ( 1856) hydrogen bonds : angle 4.78640 / 3.31 ( 5328) Misc. bond : bond 0.25181 / 15.63 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 629 time to evaluate : 1.219 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 179 MET cc_start: 0.7703 (mtm) cc_final: 0.7407 (mtm) REVERT: AB 74 SER cc_start: 0.8861 (m) cc_final: 0.8380 (p) REVERT: AB 173 ILE cc_start: 0.8536 (tp) cc_final: 0.8221 (tt) REVERT: AB 390 GLU cc_start: 0.8817 (pp20) cc_final: 0.8498 (tt0) REVERT: AB 407 MET cc_start: 0.8665 (mtm) cc_final: 0.8407 (mpp) REVERT: AC 214 ASP cc_start: 0.8954 (m-30) cc_final: 0.8577 (m-30) REVERT: AC 341 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7756 (mm-40) REVERT: AD 255 TYR cc_start: 0.7676 (m-80) cc_final: 0.7082 (m-80) REVERT: AE 169 TRP cc_start: 0.8551 (t60) cc_final: 0.8066 (t60) REVERT: AE 170 ARG cc_start: 0.8926 (mtm180) cc_final: 0.8698 (mmt180) REVERT: AE 256 LEU cc_start: 0.8231 (mt) cc_final: 0.8026 (mm) REVERT: AF 57 ASN cc_start: 0.8308 (m-40) cc_final: 0.8040 (m-40) REVERT: AF 64 LYS cc_start: 0.9198 (tptm) cc_final: 0.8741 (tptm) REVERT: AF 110 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7887 (mttm) REVERT: AG 66 GLU cc_start: 0.8456 (tp30) cc_final: 0.8204 (tm-30) REVERT: AG 72 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.7815 (tpt170) REVERT: AH 23 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7110 (pm20) REVERT: AH 73 LEU cc_start: 0.9186 (mp) cc_final: 0.8935 (mp) REVERT: AJ 33 GLU cc_start: 0.8147 (tt0) cc_final: 0.7790 (tt0) REVERT: AJ 38 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7865 (tm-30) REVERT: AJ 48 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7339 (t0) REVERT: AK 16 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6483 (t0) REVERT: Aa 94 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8687 (tm-30) REVERT: Aa 129 THR cc_start: 0.9315 (m) cc_final: 0.9000 (p) REVERT: Aa 463 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7793 (pt0) REVERT: Ab 77 LEU cc_start: 0.8991 (tp) cc_final: 0.8641 (mt) REVERT: Ab 157 GLN cc_start: 0.8905 (tp40) cc_final: 0.8380 (tp-100) REVERT: Ab 173 ILE cc_start: 0.8892 (tp) cc_final: 0.8426 (mm) REVERT: Ab 218 MET cc_start: 0.8787 (mtm) cc_final: 0.8377 (mtt) REVERT: Ab 414 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8664 (tm-30) REVERT: Ac 42 MET cc_start: 0.8442 (mtt) cc_final: 0.7979 (tpp) REVERT: Ac 118 LEU cc_start: 0.8948 (tp) cc_final: 0.8710 (tt) REVERT: Ac 171 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: Ac 271 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7936 (mt-10) REVERT: Ac 312 GLN cc_start: 0.9162 (mt0) cc_final: 0.8748 (mt0) REVERT: Ac 313 ARG cc_start: 0.9011 (ttt180) cc_final: 0.8610 (ttt-90) REVERT: Ad 159 ASN cc_start: 0.8621 (t0) cc_final: 0.8196 (t0) REVERT: Ad 196 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8403 (t70) REVERT: Ad 199 TYR cc_start: 0.8631 (m-80) cc_final: 0.8375 (m-80) REVERT: Ad 249 TYR cc_start: 0.8198 (p90) cc_final: 0.7814 (p90) REVERT: Ad 273 PHE cc_start: 0.9283 (t80) cc_final: 0.8880 (t80) REVERT: Ae 90 ASP cc_start: 0.8839 (m-30) cc_final: 0.8541 (t0) REVERT: Ae 231 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6475 (t80) REVERT: Ag 23 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8422 (mt-10) REVERT: Ah 45 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.8263 (ptp-110) REVERT: Ah 46 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8783 (mm-30) REVERT: Ah 63 GLU cc_start: 0.7929 (tt0) cc_final: 0.7681 (tt0) REVERT: Ai 72 VAL cc_start: 0.2678 (OUTLIER) cc_final: 0.2382 (p) REVERT: Ak 9 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7926 (ttt-90) REVERT: Ak 17 TRP cc_start: 0.7760 (m100) cc_final: 0.6876 (m-10) REVERT: Ak 47 TYR cc_start: 0.7773 (t80) cc_final: 0.7240 (t80) outliers start: 108 outliers final: 63 residues processed: 702 average time/residue: 0.1812 time to fit residues: 207.1686 Evaluate side-chains 610 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 539 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 149 ASP Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 216 LEU Chi-restraints excluded: chain AA residue 268 CYS Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 406 THR Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 61 ILE Chi-restraints excluded: chain AB residue 115 THR Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AC residue 37 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 126 THR Chi-restraints excluded: chain AC residue 160 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 233 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AE residue 117 VAL Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AF residue 20 TRP Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 67 THR Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AJ residue 48 ASN Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 392 LYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 390 GLU Chi-restraints excluded: chain Ab residue 407 MET Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 172 SER Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 216 VAL Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ag residue 11 ILE Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 55 VAL Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 38 LEU Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 141 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 chunk 380 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 326 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN AJ 48 ASN AK 16 ASN Aa 434 GLN Ab 167 GLN Ac 44 GLN Ac 331 ASN Ad 115 GLN Ad 134 HIS ** Ad 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 16 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.087004 restraints weight = 71251.317| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.85 r_work: 0.3179 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.468 33045 Z= 0.143 Angle : 0.618 13.853 44806 Z= 0.307 Chirality : 0.042 0.202 4839 Planarity : 0.004 0.065 5666 Dihedral : 10.277 120.274 4952 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.03 % Allowed : 16.10 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3916 helix: 1.42 (0.11), residues: 2086 sheet: -0.10 (0.26), residues: 393 loop : -0.06 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGAA 442 TYR 0.023 0.001 TYRAD 140 PHE 0.019 0.001 PHEAh 85 TRP 0.016 0.001 TRPAc 141 HIS 0.005 0.001 HISAC 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (33031) covalent geometry : angle 0.61777 / 0.31 (44794) SS BOND : bond 0.00341 / 0.18 ( 6) SS BOND : angle 0.80103 / 0.51 ( 12) hydrogen bonds : bond 0.04046 / 2.74 ( 1856) hydrogen bonds : angle 4.63243 / 3.21 ( 5328) Misc. bond : bond 0.23460 / 14.28 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 595 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 179 MET cc_start: 0.7847 (mtm) cc_final: 0.7534 (mtm) REVERT: AA 368 MET cc_start: 0.8533 (mmm) cc_final: 0.7643 (tpt) REVERT: AB 74 SER cc_start: 0.8853 (m) cc_final: 0.8379 (p) REVERT: AB 322 ASP cc_start: 0.8469 (t70) cc_final: 0.8019 (t0) REVERT: AB 390 GLU cc_start: 0.8854 (pp20) cc_final: 0.8541 (tt0) REVERT: AB 407 MET cc_start: 0.8793 (mtm) cc_final: 0.8535 (mpp) REVERT: AC 341 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7705 (mm-40) REVERT: AD 166 MET cc_start: 0.8134 (mmt) cc_final: 0.7828 (mmp) REVERT: AD 234 ASN cc_start: 0.8381 (m110) cc_final: 0.7745 (m-40) REVERT: AD 255 TYR cc_start: 0.7535 (m-80) cc_final: 0.6872 (m-80) REVERT: AE 169 TRP cc_start: 0.8589 (t60) cc_final: 0.8291 (t60) REVERT: AE 170 ARG cc_start: 0.8943 (mtm180) cc_final: 0.8527 (mmt90) REVERT: AE 175 PHE cc_start: 0.8012 (m-80) cc_final: 0.7539 (m-80) REVERT: AE 234 TYR cc_start: 0.8224 (m-80) cc_final: 0.7967 (m-80) REVERT: AE 248 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7817 (mtm-85) REVERT: AF 57 ASN cc_start: 0.8285 (m-40) cc_final: 0.8039 (m-40) REVERT: AF 88 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8534 (mtmm) REVERT: AG 66 GLU cc_start: 0.8500 (tp30) cc_final: 0.8148 (tm-30) REVERT: AG 72 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.7782 (tpt170) REVERT: AH 23 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7166 (pm20) REVERT: AH 64 ASP cc_start: 0.8409 (p0) cc_final: 0.8057 (t0) REVERT: AJ 33 GLU cc_start: 0.8204 (tt0) cc_final: 0.7889 (tt0) REVERT: AJ 38 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7863 (tm-30) REVERT: AK 16 ASN cc_start: 0.7258 (t0) cc_final: 0.6856 (t0) REVERT: Aa 85 LYS cc_start: 0.8103 (pptt) cc_final: 0.7896 (pptt) REVERT: Aa 94 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8713 (tm-30) REVERT: Aa 129 THR cc_start: 0.9302 (m) cc_final: 0.8987 (p) REVERT: Aa 463 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: Ab 77 LEU cc_start: 0.8971 (tp) cc_final: 0.8641 (mt) REVERT: Ab 157 GLN cc_start: 0.8871 (tp40) cc_final: 0.8404 (tp40) REVERT: Ab 173 ILE cc_start: 0.8879 (tp) cc_final: 0.8487 (mm) REVERT: Ab 218 MET cc_start: 0.8815 (mtm) cc_final: 0.8424 (mtt) REVERT: Ab 414 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8670 (tm-30) REVERT: Ac 42 MET cc_start: 0.8330 (mtt) cc_final: 0.7859 (tpp) REVERT: Ac 118 LEU cc_start: 0.8959 (tp) cc_final: 0.8713 (tt) REVERT: Ac 171 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: Ac 202 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8460 (tm-30) REVERT: Ac 257 MET cc_start: 0.8838 (mtp) cc_final: 0.8583 (mtp) REVERT: Ac 312 GLN cc_start: 0.9199 (mt0) cc_final: 0.8806 (mt0) REVERT: Ac 313 ARG cc_start: 0.8983 (ttt180) cc_final: 0.8584 (ttt-90) REVERT: Ac 352 GLN cc_start: 0.8863 (mt0) cc_final: 0.8630 (mt0) REVERT: Ad 159 ASN cc_start: 0.8637 (t0) cc_final: 0.8374 (t0) REVERT: Ad 196 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8395 (t70) REVERT: Ad 199 TYR cc_start: 0.8627 (m-80) cc_final: 0.8353 (m-80) REVERT: Ad 227 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7255 (pp) REVERT: Ad 273 PHE cc_start: 0.9306 (t80) cc_final: 0.8811 (t80) REVERT: Ad 295 MET cc_start: 0.8868 (mmm) cc_final: 0.8480 (tpt) REVERT: Ae 82 ASP cc_start: 0.8269 (p0) cc_final: 0.7877 (m-30) REVERT: Ae 90 ASP cc_start: 0.8867 (m-30) cc_final: 0.8522 (t0) REVERT: Ae 170 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7909 (mpt-90) REVERT: Ae 209 GLU cc_start: 0.7287 (pm20) cc_final: 0.6947 (pp20) REVERT: Ae 231 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.6008 (t80) REVERT: Af 60 MET cc_start: 0.8996 (tpp) cc_final: 0.8583 (tpp) REVERT: Ag 23 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8408 (mt-10) REVERT: Ah 45 ARG cc_start: 0.8492 (ptp-110) cc_final: 0.8073 (ptp-110) REVERT: Ai 64 LEU cc_start: 0.8160 (tp) cc_final: 0.7959 (tp) REVERT: Ai 72 VAL cc_start: 0.2745 (OUTLIER) cc_final: 0.2450 (p) REVERT: Aj 13 LEU cc_start: 0.8903 (tp) cc_final: 0.8699 (mt) REVERT: Ak 17 TRP cc_start: 0.7800 (m100) cc_final: 0.6901 (m-10) REVERT: Ak 47 TYR cc_start: 0.7806 (t80) cc_final: 0.7158 (t80) outliers start: 102 outliers final: 67 residues processed: 660 average time/residue: 0.1806 time to fit residues: 195.6163 Evaluate side-chains 622 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 548 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 109 LEU Chi-restraints excluded: chain AA residue 149 ASP Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 216 LEU Chi-restraints excluded: chain AA residue 268 CYS Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 199 LYS Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AC residue 37 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 160 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 249 MET Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AD residue 102 LEU Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 168 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 186 LEU Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 390 GLU Chi-restraints excluded: chain Ab residue 407 MET Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 150 LEU Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 154 VAL Chi-restraints excluded: chain Ad residue 172 SER Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 216 VAL Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 38 LEU Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ah residue 80 VAL Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 22 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 40 optimal weight: 0.0670 chunk 259 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 103 ASN AA 181 ASN AB 36 GLN ** AB 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 331 ASN AJ 48 ASN Aa 55 ASN Aa 181 ASN Aa 308 ASN Aa 373 GLN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN Ab 280 ASN Ac 44 GLN ** Ac 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082642 restraints weight = 72741.045| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.80 r_work: 0.3085 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.579 33045 Z= 0.259 Angle : 0.714 14.375 44806 Z= 0.352 Chirality : 0.045 0.186 4839 Planarity : 0.005 0.066 5666 Dihedral : 10.500 121.943 4952 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.22 % Allowed : 16.19 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3916 helix: 1.27 (0.11), residues: 2087 sheet: -0.23 (0.25), residues: 399 loop : -0.05 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAe 179 TYR 0.021 0.002 TYRAa 468 PHE 0.029 0.002 PHEAC 183 TRP 0.021 0.002 TRPAK 34 HIS 0.013 0.002 HISAC 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.26 (33031) covalent geometry : angle 0.71352 / 0.35 (44794) SS BOND : bond 0.00573 / 0.29 ( 6) SS BOND : angle 0.78627 / 0.50 ( 12) hydrogen bonds : bond 0.04459 / 3.02 ( 1856) hydrogen bonds : angle 4.74677 / 3.30 ( 5328) Misc. bond : bond 0.31246 / 18.21 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 576 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 179 MET cc_start: 0.7823 (mtm) cc_final: 0.7576 (mtm) REVERT: AA 243 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8269 (mm) REVERT: AB 134 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7778 (mpp) REVERT: AB 173 ILE cc_start: 0.8586 (tp) cc_final: 0.8290 (tt) REVERT: AB 246 LEU cc_start: 0.8667 (pp) cc_final: 0.8289 (mt) REVERT: AB 322 ASP cc_start: 0.8399 (t70) cc_final: 0.7964 (m-30) REVERT: AB 390 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: AC 58 ASP cc_start: 0.8397 (t0) cc_final: 0.8130 (t70) REVERT: AC 89 MET cc_start: 0.8661 (mmm) cc_final: 0.8048 (tmm) REVERT: AC 341 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7771 (mm-40) REVERT: AD 227 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7970 (pp) REVERT: AD 255 TYR cc_start: 0.7585 (m-80) cc_final: 0.6958 (m-80) REVERT: AD 293 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8958 (mm) REVERT: AE 175 PHE cc_start: 0.8059 (m-80) cc_final: 0.7565 (m-80) REVERT: AE 234 TYR cc_start: 0.8266 (m-80) cc_final: 0.8028 (m-80) REVERT: AF 75 ILE cc_start: 0.9365 (pt) cc_final: 0.9066 (mm) REVERT: AG 72 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.7754 (tpt170) REVERT: AJ 33 GLU cc_start: 0.8273 (tt0) cc_final: 0.7910 (tt0) REVERT: AK 16 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6721 (t0) REVERT: Aa 94 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8731 (tm-30) REVERT: Aa 129 THR cc_start: 0.9285 (m) cc_final: 0.8938 (p) REVERT: Aa 360 CYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7753 (m) REVERT: Aa 472 ARG cc_start: 0.8239 (tpt90) cc_final: 0.7923 (tpt90) REVERT: Ab 40 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8289 (t80) REVERT: Ab 157 GLN cc_start: 0.8959 (tp40) cc_final: 0.8516 (tp-100) REVERT: Ab 173 ILE cc_start: 0.8986 (tp) cc_final: 0.8593 (mm) REVERT: Ab 218 MET cc_start: 0.8900 (mtm) cc_final: 0.8440 (mtt) REVERT: Ab 390 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8862 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8712 (tm-30) REVERT: Ac 42 MET cc_start: 0.8407 (mtt) cc_final: 0.8089 (tpp) REVERT: Ac 171 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: Ac 202 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8479 (tm-30) REVERT: Ac 233 LEU cc_start: 0.9099 (tp) cc_final: 0.8772 (tt) REVERT: Ac 313 ARG cc_start: 0.9041 (ttt180) cc_final: 0.8661 (ttt-90) REVERT: Ac 331 ASN cc_start: 0.9052 (p0) cc_final: 0.8717 (p0) REVERT: Ad 154 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8046 (t) REVERT: Ad 159 ASN cc_start: 0.8708 (t0) cc_final: 0.8430 (t0) REVERT: Ad 196 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8437 (t70) REVERT: Ad 273 PHE cc_start: 0.9363 (t80) cc_final: 0.8984 (t80) REVERT: Ae 82 ASP cc_start: 0.8232 (p0) cc_final: 0.8004 (m-30) REVERT: Ae 90 ASP cc_start: 0.8980 (m-30) cc_final: 0.8632 (t0) REVERT: Ae 140 MET cc_start: 0.8867 (mtp) cc_final: 0.8632 (mtp) REVERT: Ae 170 ARG cc_start: 0.8136 (mtp180) cc_final: 0.7862 (mpt-90) REVERT: Ae 179 ARG cc_start: 0.6617 (mpp80) cc_final: 0.6315 (mpp80) REVERT: Ae 209 GLU cc_start: 0.7276 (pm20) cc_final: 0.6962 (pp20) REVERT: Ae 231 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.6014 (t80) REVERT: Af 92 GLU cc_start: 0.8977 (tp30) cc_final: 0.8752 (tp30) REVERT: Ag 23 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8569 (mt-10) REVERT: Ag 37 ASN cc_start: 0.8584 (t0) cc_final: 0.8157 (t0) REVERT: Ah 45 ARG cc_start: 0.8586 (ptp-110) cc_final: 0.8120 (ptp-110) REVERT: Ai 72 VAL cc_start: 0.2755 (OUTLIER) cc_final: 0.2504 (p) REVERT: Aj 13 LEU cc_start: 0.8938 (tp) cc_final: 0.8722 (mt) REVERT: Ak 47 TYR cc_start: 0.7896 (t80) cc_final: 0.7200 (t80) outliers start: 142 outliers final: 90 residues processed: 671 average time/residue: 0.1852 time to fit residues: 202.9281 Evaluate side-chains 636 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 531 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 151 VAL Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 268 CYS Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 61 ILE Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 134 MET Chi-restraints excluded: chain AB residue 138 LEU Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AB residue 390 GLU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 233 LEU Chi-restraints excluded: chain AC residue 249 MET Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AC residue 331 ASN Chi-restraints excluded: chain AD residue 139 CYS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 227 LEU Chi-restraints excluded: chain AD residue 242 ILE Chi-restraints excluded: chain AD residue 250 THR Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 117 VAL Chi-restraints excluded: chain AE residue 174 LEU Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AF residue 20 TRP Chi-restraints excluded: chain AF residue 79 ASP Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AG residue 59 ILE Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 67 THR Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain AK residue 18 ILE Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 168 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 274 GLU Chi-restraints excluded: chain Aa residue 308 ASN Chi-restraints excluded: chain Aa residue 351 THR Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 380 CYS Chi-restraints excluded: chain Aa residue 392 LYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 386 VAL Chi-restraints excluded: chain Ab residue 390 GLU Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 150 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 154 VAL Chi-restraints excluded: chain Ad residue 172 SER Chi-restraints excluded: chain Ad residue 173 ASP Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ad residue 319 LEU Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 192 VAL Chi-restraints excluded: chain Ae residue 216 VAL Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Af residue 37 THR Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 38 LEU Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ah residue 80 VAL Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Ai residue 65 VAL Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Ak residue 16 ASN Chi-restraints excluded: chain Ak residue 18 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 266 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 330 optimal weight: 0.9990 chunk 364 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 210 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 48 ASN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.084683 restraints weight = 72069.965| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.82 r_work: 0.3129 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.472 33045 Z= 0.150 Angle : 0.636 16.472 44806 Z= 0.309 Chirality : 0.043 0.227 4839 Planarity : 0.004 0.060 5666 Dihedral : 10.208 125.017 4952 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.24 % Allowed : 18.42 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.14), residues: 3916 helix: 1.44 (0.11), residues: 2089 sheet: -0.18 (0.25), residues: 397 loop : -0.02 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAH 47 TYR 0.019 0.001 TYRAD 140 PHE 0.043 0.001 PHEAC 183 TRP 0.028 0.001 TRPAK 34 HIS 0.008 0.001 HISAE 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (33031) covalent geometry : angle 0.63593 / 0.31 (44794) SS BOND : bond 0.00744 / 0.59 ( 6) SS BOND : angle 1.00957 / 0.74 ( 12) hydrogen bonds : bond 0.03985 / 2.70 ( 1856) hydrogen bonds : angle 4.55901 / 3.16 ( 5328) Misc. bond : bond 0.27577 / 18.72 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 591 time to evaluate : 1.095 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 49 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: AA 179 MET cc_start: 0.7635 (mtm) cc_final: 0.7385 (mtm) REVERT: AA 243 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8242 (mm) REVERT: AB 173 ILE cc_start: 0.8470 (tp) cc_final: 0.8159 (tt) REVERT: AB 246 LEU cc_start: 0.8660 (pp) cc_final: 0.8262 (mt) REVERT: AB 322 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: AB 390 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8698 (tt0) REVERT: AB 407 MET cc_start: 0.8673 (mpp) cc_final: 0.8442 (mpp) REVERT: AC 58 ASP cc_start: 0.8456 (t0) cc_final: 0.8117 (t70) REVERT: AC 271 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8012 (mt-10) REVERT: AC 341 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7797 (mm-40) REVERT: AD 127 MET cc_start: 0.8848 (mmm) cc_final: 0.8544 (mmm) REVERT: AD 227 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7883 (pp) REVERT: AD 255 TYR cc_start: 0.7447 (m-80) cc_final: 0.6862 (m-80) REVERT: AD 293 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8901 (mm) REVERT: AE 169 TRP cc_start: 0.8628 (t60) cc_final: 0.7995 (t60) REVERT: AE 175 PHE cc_start: 0.8075 (m-80) cc_final: 0.7530 (m-80) REVERT: AE 200 HIS cc_start: 0.6748 (t70) cc_final: 0.6322 (t70) REVERT: AF 110 LYS cc_start: 0.8313 (ttmm) cc_final: 0.8039 (tttm) REVERT: AG 72 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7763 (tpt170) REVERT: AH 23 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7184 (pm20) REVERT: AH 64 ASP cc_start: 0.8165 (t0) cc_final: 0.7746 (p0) REVERT: AJ 33 GLU cc_start: 0.8194 (tt0) cc_final: 0.7788 (tt0) REVERT: AJ 38 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7859 (tm-30) REVERT: AK 16 ASN cc_start: 0.7208 (t0) cc_final: 0.6677 (t0) REVERT: Aa 94 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8745 (tm-30) REVERT: Aa 129 THR cc_start: 0.9362 (m) cc_final: 0.9070 (p) REVERT: Aa 472 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7710 (tpt90) REVERT: Ab 40 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8320 (t80) REVERT: Ab 157 GLN cc_start: 0.8900 (tp40) cc_final: 0.8421 (tp40) REVERT: Ab 173 ILE cc_start: 0.8897 (tp) cc_final: 0.8649 (tp) REVERT: Ab 218 MET cc_start: 0.8837 (mtm) cc_final: 0.8426 (mtt) REVERT: Ab 390 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8829 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: Ac 42 MET cc_start: 0.8329 (mtt) cc_final: 0.8055 (tpp) REVERT: Ac 51 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9036 (mm) REVERT: Ac 119 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8504 (mp) REVERT: Ac 171 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: Ac 198 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8514 (tt) REVERT: Ac 202 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8627 (tm-30) REVERT: Ac 233 LEU cc_start: 0.9069 (tp) cc_final: 0.8778 (tt) REVERT: Ac 275 LEU cc_start: 0.8881 (mt) cc_final: 0.8679 (mt) REVERT: Ad 166 MET cc_start: 0.8516 (mmm) cc_final: 0.8064 (mmm) REVERT: Ad 196 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8452 (t70) REVERT: Ad 273 PHE cc_start: 0.9369 (t80) cc_final: 0.9019 (t80) REVERT: Ae 90 ASP cc_start: 0.9003 (m-30) cc_final: 0.8696 (t0) REVERT: Ae 135 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: Ae 170 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7801 (mpt-90) REVERT: Ae 209 GLU cc_start: 0.7493 (pm20) cc_final: 0.7131 (pp20) REVERT: Ae 222 CYS cc_start: 0.5954 (m) cc_final: 0.5505 (p) REVERT: Ae 231 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.6250 (t80) REVERT: Ae 234 TYR cc_start: 0.8348 (m-80) cc_final: 0.8020 (m-10) REVERT: Ae 259 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7486 (tm-30) REVERT: Af 92 GLU cc_start: 0.8906 (tp30) cc_final: 0.8645 (tp30) REVERT: Ag 32 SER cc_start: 0.8647 (t) cc_final: 0.8446 (p) REVERT: Ag 37 ASN cc_start: 0.8519 (t0) cc_final: 0.8107 (t0) REVERT: Ah 45 ARG cc_start: 0.8543 (ptp-110) cc_final: 0.8088 (ptp-110) REVERT: Ai 72 VAL cc_start: 0.2789 (OUTLIER) cc_final: 0.2538 (p) REVERT: Aj 45 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8305 (mm-30) REVERT: Ak 17 TRP cc_start: 0.7963 (m100) cc_final: 0.7162 (m-10) REVERT: Ak 47 TYR cc_start: 0.7923 (t80) cc_final: 0.7290 (t80) outliers start: 109 outliers final: 66 residues processed: 662 average time/residue: 0.1798 time to fit residues: 195.2167 Evaluate side-chains 618 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 535 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 GLN Chi-restraints excluded: chain AA residue 151 VAL Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 216 LEU Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 268 CYS Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 61 ILE Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 138 LEU Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AB residue 390 GLU Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 249 MET Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AD residue 139 CYS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 227 LEU Chi-restraints excluded: chain AD residue 293 LEU Chi-restraints excluded: chain AE residue 174 LEU Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 28 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 168 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 359 VAL Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 390 GLU Chi-restraints excluded: chain Ab residue 407 MET Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 198 LEU Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ad residue 319 LEU Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 192 VAL Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 80 VAL Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 309 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 379 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 464 GLN AB 36 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 308 ASN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN Ac 44 GLN ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.108497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.085155 restraints weight = 72202.648| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.84 r_work: 0.3137 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.480 33045 Z= 0.146 Angle : 0.627 13.754 44806 Z= 0.307 Chirality : 0.042 0.245 4839 Planarity : 0.004 0.059 5666 Dihedral : 10.041 126.095 4952 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.12 % Allowed : 19.28 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.14), residues: 3916 helix: 1.54 (0.11), residues: 2082 sheet: -0.16 (0.25), residues: 397 loop : 0.04 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAE 170 TYR 0.026 0.001 TYRAF 21 PHE 0.029 0.001 PHEAC 183 TRP 0.031 0.001 TRPAK 34 HIS 0.008 0.001 HISAE 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 (33031) covalent geometry : angle 0.62694 / 0.31 (44794) SS BOND : bond 0.00222 / 0.12 ( 6) SS BOND : angle 0.88458 / 0.58 ( 12) hydrogen bonds : bond 0.03872 / 2.62 ( 1856) hydrogen bonds : angle 4.50266 / 3.12 ( 5328) Misc. bond : bond 0.26682 / 17.08 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 565 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 49 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7973 (pt0) REVERT: AA 179 MET cc_start: 0.7639 (mtm) cc_final: 0.7395 (mtm) REVERT: AA 243 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8253 (mm) REVERT: AB 173 ILE cc_start: 0.8461 (tp) cc_final: 0.8150 (tt) REVERT: AB 210 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: AB 246 LEU cc_start: 0.8663 (pp) cc_final: 0.8275 (mt) REVERT: AB 322 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: AB 390 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: AB 407 MET cc_start: 0.8776 (mpp) cc_final: 0.8501 (mpp) REVERT: AC 20 ASP cc_start: 0.8040 (m-30) cc_final: 0.7576 (m-30) REVERT: AC 58 ASP cc_start: 0.8430 (t0) cc_final: 0.8081 (t70) REVERT: AC 271 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7958 (mt-10) REVERT: AC 341 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7710 (mm-40) REVERT: AD 127 MET cc_start: 0.8845 (mmm) cc_final: 0.8577 (mmm) REVERT: AD 227 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7891 (pp) REVERT: AD 255 TYR cc_start: 0.7426 (m-80) cc_final: 0.6845 (m-80) REVERT: AD 284 HIS cc_start: 0.7904 (t70) cc_final: 0.7460 (t-170) REVERT: AE 170 ARG cc_start: 0.8823 (mmt180) cc_final: 0.8286 (mmt180) REVERT: AE 175 PHE cc_start: 0.7999 (m-80) cc_final: 0.7552 (m-80) REVERT: AE 200 HIS cc_start: 0.6806 (t70) cc_final: 0.6297 (t70) REVERT: AF 110 LYS cc_start: 0.8348 (ttmm) cc_final: 0.8082 (tttm) REVERT: AG 72 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.7754 (tpt170) REVERT: AH 23 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7133 (pm20) REVERT: AH 64 ASP cc_start: 0.8219 (t0) cc_final: 0.7575 (p0) REVERT: AJ 33 GLU cc_start: 0.8170 (tt0) cc_final: 0.7785 (tt0) REVERT: AK 16 ASN cc_start: 0.7100 (t0) cc_final: 0.6591 (t0) REVERT: Aa 94 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8755 (tm-30) REVERT: Aa 129 THR cc_start: 0.9367 (m) cc_final: 0.9060 (p) REVERT: Aa 463 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: Aa 472 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7481 (tpt90) REVERT: Ab 77 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8861 (mt) REVERT: Ab 157 GLN cc_start: 0.8800 (tp40) cc_final: 0.8345 (tp40) REVERT: Ab 173 ILE cc_start: 0.8891 (tp) cc_final: 0.8666 (tp) REVERT: Ab 218 MET cc_start: 0.8837 (mtm) cc_final: 0.8460 (mtt) REVERT: Ab 390 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8847 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8675 (tm-30) REVERT: Ac 42 MET cc_start: 0.8326 (mtt) cc_final: 0.8040 (tpp) REVERT: Ac 85 ASN cc_start: 0.9035 (m-40) cc_final: 0.8779 (m-40) REVERT: Ac 118 LEU cc_start: 0.9096 (tp) cc_final: 0.8865 (tt) REVERT: Ac 119 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8529 (mp) REVERT: Ac 171 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: Ac 198 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8506 (tt) REVERT: Ac 202 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8667 (tm-30) REVERT: Ac 212 ASN cc_start: 0.8905 (t0) cc_final: 0.8695 (t0) REVERT: Ac 233 LEU cc_start: 0.9023 (tp) cc_final: 0.8722 (tt) REVERT: Ac 275 LEU cc_start: 0.8827 (mt) cc_final: 0.8580 (mt) REVERT: Ac 303 LEU cc_start: 0.9265 (tt) cc_final: 0.9031 (tt) REVERT: Ac 352 GLN cc_start: 0.9150 (mt0) cc_final: 0.8427 (mp10) REVERT: Ad 166 MET cc_start: 0.8637 (mmm) cc_final: 0.8009 (mmm) REVERT: Ad 196 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8444 (t70) REVERT: Ad 273 PHE cc_start: 0.9358 (t80) cc_final: 0.8985 (t80) REVERT: Ae 90 ASP cc_start: 0.9038 (m-30) cc_final: 0.8788 (t0) REVERT: Ae 170 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7815 (mpt-90) REVERT: Ae 209 GLU cc_start: 0.7475 (pm20) cc_final: 0.7192 (pp20) REVERT: Ae 222 CYS cc_start: 0.6274 (m) cc_final: 0.5798 (p) REVERT: Ae 231 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6209 (t80) REVERT: Ae 234 TYR cc_start: 0.8301 (m-80) cc_final: 0.7976 (m-10) REVERT: Af 19 LYS cc_start: 0.8890 (mttm) cc_final: 0.8510 (mttm) REVERT: Af 92 GLU cc_start: 0.8914 (tp30) cc_final: 0.8603 (tp30) REVERT: Ag 37 ASN cc_start: 0.8537 (t0) cc_final: 0.8135 (t0) REVERT: Ah 45 ARG cc_start: 0.8554 (ptp-110) cc_final: 0.8086 (ptp-110) REVERT: Ai 72 VAL cc_start: 0.2786 (OUTLIER) cc_final: 0.2544 (p) REVERT: Aj 45 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8318 (mm-30) REVERT: Ak 17 TRP cc_start: 0.7992 (m100) cc_final: 0.7133 (m-10) REVERT: Ak 47 TYR cc_start: 0.7944 (t80) cc_final: 0.7228 (t80) outliers start: 105 outliers final: 68 residues processed: 631 average time/residue: 0.1701 time to fit residues: 177.2705 Evaluate side-chains 622 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 538 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 GLN Chi-restraints excluded: chain AA residue 151 VAL Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 268 CYS Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 61 ILE Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 138 LEU Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AB residue 390 GLU Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 149 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 249 MET Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AD residue 139 CYS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 227 LEU Chi-restraints excluded: chain AE residue 218 THR Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AJ residue 8 SER Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 168 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 308 ASN Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 359 VAL Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 77 LEU Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 390 GLU Chi-restraints excluded: chain Ab residue 407 MET Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 150 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 198 LEU Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ad residue 319 LEU Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 192 VAL Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 38 LEU Chi-restraints excluded: chain Ah residue 80 VAL Chi-restraints excluded: chain Ah residue 82 HIS Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 377 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 210 GLN ** AB 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 308 ASN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 159 ASN Ad 189 ASN Ad 282 HIS ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 78 HIS ** 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 = 0.3590 r_free = 0.3590 target = 0.104798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.081288 restraints weight = 73228.525| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.79 r_work: 0.3059 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.602 33045 Z= 0.285 Angle : 0.746 16.037 44806 Z= 0.365 Chirality : 0.046 0.217 4839 Planarity : 0.005 0.057 5666 Dihedral : 10.512 128.887 4952 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.75 % Allowed : 18.95 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.14), residues: 3916 helix: 1.30 (0.11), residues: 2083 sheet: -0.25 (0.25), residues: 396 loop : 0.01 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAg 12 TYR 0.024 0.002 TYRAa 468 PHE 0.024 0.002 PHEAC 183 TRP 0.029 0.002 TRPAK 34 HIS 0.013 0.002 HISAC 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.28 (33031) covalent geometry : angle 0.74561 / 0.36 (44794) SS BOND : bond 0.00412 / 0.22 ( 6) SS BOND : angle 1.02931 / 0.67 ( 12) hydrogen bonds : bond 0.04428 / 3.00 ( 1856) hydrogen bonds : angle 4.75647 / 3.31 ( 5328) Misc. bond : bond 0.32748 / 19.85 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 534 time to evaluate : 1.285 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 49 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: AA 243 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8391 (mm) REVERT: AB 173 ILE cc_start: 0.8499 (tp) cc_final: 0.8271 (tt) REVERT: AB 246 LEU cc_start: 0.8684 (pp) cc_final: 0.8329 (mt) REVERT: AB 322 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: AB 390 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8819 (tt0) REVERT: AB 407 MET cc_start: 0.8743 (mpp) cc_final: 0.8474 (mpp) REVERT: AC 20 ASP cc_start: 0.8162 (m-30) cc_final: 0.7566 (m-30) REVERT: AC 58 ASP cc_start: 0.8426 (t0) cc_final: 0.8127 (t70) REVERT: AC 254 ASP cc_start: 0.8118 (p0) cc_final: 0.7863 (p0) REVERT: AD 127 MET cc_start: 0.8822 (mmm) cc_final: 0.8603 (mmm) REVERT: AD 227 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7940 (pp) REVERT: AD 255 TYR cc_start: 0.7446 (m-80) cc_final: 0.6977 (m-80) REVERT: AE 169 TRP cc_start: 0.8632 (t60) cc_final: 0.8366 (t60) REVERT: AE 170 ARG cc_start: 0.8725 (mmt180) cc_final: 0.8037 (mmt180) REVERT: AE 175 PHE cc_start: 0.8037 (m-80) cc_final: 0.7554 (m-80) REVERT: AE 200 HIS cc_start: 0.7050 (t70) cc_final: 0.6530 (t70) REVERT: AG 72 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7773 (tpt170) REVERT: AJ 33 GLU cc_start: 0.8277 (tt0) cc_final: 0.7890 (tt0) REVERT: AK 16 ASN cc_start: 0.7350 (t0) cc_final: 0.6727 (t0) REVERT: Aa 94 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8729 (tm-30) REVERT: Aa 129 THR cc_start: 0.9313 (m) cc_final: 0.8936 (p) REVERT: Ab 40 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8328 (t80) REVERT: Ab 157 GLN cc_start: 0.8894 (tp40) cc_final: 0.8404 (tp40) REVERT: Ab 173 ILE cc_start: 0.8957 (tp) cc_final: 0.8606 (mm) REVERT: Ab 218 MET cc_start: 0.8959 (mtm) cc_final: 0.8589 (mtt) REVERT: Ab 262 ASN cc_start: 0.8747 (p0) cc_final: 0.8326 (p0) REVERT: Ab 390 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8931 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8759 (tm-30) REVERT: Ac 51 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9011 (mm) REVERT: Ac 119 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8421 (mp) REVERT: Ac 171 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: Ac 198 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8700 (tt) REVERT: Ac 202 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8721 (tm-30) REVERT: Ac 233 LEU cc_start: 0.9089 (tp) cc_final: 0.8804 (tt) REVERT: Ac 352 GLN cc_start: 0.9212 (mt0) cc_final: 0.8458 (mp10) REVERT: Ad 166 MET cc_start: 0.8588 (mmm) cc_final: 0.8188 (mmm) REVERT: Ad 183 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8127 (tp30) REVERT: Ad 196 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8420 (t70) REVERT: Ad 296 MET cc_start: 0.8737 (tpp) cc_final: 0.8312 (mpp) REVERT: Ae 90 ASP cc_start: 0.9065 (m-30) cc_final: 0.8792 (t0) REVERT: Ae 135 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: Ae 170 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7805 (mpt-90) REVERT: Ae 209 GLU cc_start: 0.7489 (pm20) cc_final: 0.6850 (pt0) REVERT: Ae 231 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.6634 (t80) REVERT: Ae 234 TYR cc_start: 0.8395 (m-80) cc_final: 0.8091 (m-10) REVERT: Af 42 GLU cc_start: 0.8744 (tp30) cc_final: 0.8543 (tp30) REVERT: Af 60 MET cc_start: 0.9108 (tpp) cc_final: 0.8822 (tpp) REVERT: Af 92 GLU cc_start: 0.8945 (tp30) cc_final: 0.8538 (tp30) REVERT: Ag 37 ASN cc_start: 0.8757 (t0) cc_final: 0.8304 (t0) REVERT: Ah 45 ARG cc_start: 0.8606 (ptp-110) cc_final: 0.8136 (ptp-110) REVERT: Ai 72 VAL cc_start: 0.2762 (OUTLIER) cc_final: 0.2542 (p) REVERT: Aj 45 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8363 (mm-30) REVERT: Ak 47 TYR cc_start: 0.8014 (t80) cc_final: 0.7328 (t80) outliers start: 126 outliers final: 85 residues processed: 621 average time/residue: 0.1996 time to fit residues: 202.2532 Evaluate side-chains 613 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 512 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 GLN Chi-restraints excluded: chain AA residue 151 VAL Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 216 LEU Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 268 CYS Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 61 ILE Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 113 THR Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 138 LEU Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AB residue 390 GLU Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 233 LEU Chi-restraints excluded: chain AC residue 249 MET Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AD residue 139 CYS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 227 LEU Chi-restraints excluded: chain AD residue 242 ILE Chi-restraints excluded: chain AE residue 218 THR Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AJ residue 8 SER Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 168 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 359 VAL Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 392 LYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 386 VAL Chi-restraints excluded: chain Ab residue 390 GLU Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 150 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 198 LEU Chi-restraints excluded: chain Ac residue 243 VAL Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ad residue 172 SER Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 234 ASN Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 192 VAL Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ae residue 242 HIS Chi-restraints excluded: chain Ag residue 32 SER Chi-restraints excluded: chain Ag residue 42 THR Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ah residue 80 VAL Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 27 VAL Chi-restraints excluded: chain Ak residue 16 ASN Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 117 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 354 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 106 optimal weight: 0.0000 chunk 236 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AA 464 GLN AB 36 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN Ac 68 HIS ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085243 restraints weight = 72081.423| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.81 r_work: 0.3138 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.477 33045 Z= 0.136 Angle : 0.650 13.673 44806 Z= 0.317 Chirality : 0.042 0.200 4839 Planarity : 0.004 0.058 5666 Dihedral : 10.114 128.272 4952 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.62 % Allowed : 20.53 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.14), residues: 3916 helix: 1.53 (0.11), residues: 2081 sheet: -0.23 (0.25), residues: 394 loop : 0.04 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAC 282 TYR 0.021 0.001 TYRAF 21 PHE 0.025 0.001 PHEAC 183 TRP 0.024 0.001 TRPAK 34 HIS 0.012 0.001 HISAE 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (33031) covalent geometry : angle 0.64950 / 0.32 (44794) SS BOND : bond 0.00183 / 0.11 ( 6) SS BOND : angle 1.04640 / 0.68 ( 12) hydrogen bonds : bond 0.03855 / 2.61 ( 1856) hydrogen bonds : angle 4.53023 / 3.14 ( 5328) Misc. bond : bond 0.26858 / 17.36 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 579 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 49 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7916 (pt0) REVERT: AA 243 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8317 (mm) REVERT: AB 173 ILE cc_start: 0.8428 (tp) cc_final: 0.8129 (tt) REVERT: AB 210 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: AB 246 LEU cc_start: 0.8653 (pp) cc_final: 0.8264 (mt) REVERT: AB 322 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: AB 390 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8750 (tt0) REVERT: AB 399 GLN cc_start: 0.8431 (mt0) cc_final: 0.8159 (mt0) REVERT: AC 58 ASP cc_start: 0.8486 (t0) cc_final: 0.8110 (t70) REVERT: AC 341 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7698 (mm-40) REVERT: AD 127 MET cc_start: 0.8766 (mmm) cc_final: 0.8558 (mmm) REVERT: AD 142 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7989 (tm-30) REVERT: AD 227 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7884 (pp) REVERT: AD 255 TYR cc_start: 0.7266 (m-80) cc_final: 0.6879 (m-80) REVERT: AD 284 HIS cc_start: 0.7970 (t70) cc_final: 0.7626 (t70) REVERT: AE 170 ARG cc_start: 0.8663 (mmt180) cc_final: 0.8038 (mmt180) REVERT: AE 175 PHE cc_start: 0.8042 (m-80) cc_final: 0.7535 (m-80) REVERT: AE 183 GLU cc_start: 0.7350 (tp30) cc_final: 0.7145 (tp30) REVERT: AE 200 HIS cc_start: 0.6824 (t70) cc_final: 0.6084 (t70) REVERT: AF 48 ILE cc_start: 0.9269 (tp) cc_final: 0.9045 (tp) REVERT: AG 72 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.7749 (tpt170) REVERT: AH 23 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7152 (pm20) REVERT: AH 64 ASP cc_start: 0.8468 (t0) cc_final: 0.7554 (p0) REVERT: AJ 32 PHE cc_start: 0.8543 (t80) cc_final: 0.8334 (t80) REVERT: AJ 33 GLU cc_start: 0.8128 (tt0) cc_final: 0.7749 (tt0) REVERT: AK 16 ASN cc_start: 0.7259 (t0) cc_final: 0.6738 (t0) REVERT: Aa 94 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8740 (tm-30) REVERT: Aa 129 THR cc_start: 0.9327 (m) cc_final: 0.9001 (p) REVERT: Ab 40 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8378 (t80) REVERT: Ab 157 GLN cc_start: 0.8760 (tp40) cc_final: 0.8293 (tp40) REVERT: Ab 173 ILE cc_start: 0.8840 (tp) cc_final: 0.8631 (tp) REVERT: Ab 218 MET cc_start: 0.8839 (mtm) cc_final: 0.8584 (mtt) REVERT: Ab 414 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8700 (tm-30) REVERT: Ac 42 MET cc_start: 0.8846 (tpp) cc_final: 0.8630 (tpp) REVERT: Ac 51 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8972 (mm) REVERT: Ac 85 ASN cc_start: 0.9110 (m-40) cc_final: 0.8894 (m-40) REVERT: Ac 119 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8512 (mp) REVERT: Ac 138 MET cc_start: 0.7673 (tpt) cc_final: 0.7422 (tpt) REVERT: Ac 171 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: Ac 198 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8486 (tt) REVERT: Ac 244 LEU cc_start: 0.9241 (tp) cc_final: 0.9035 (tp) REVERT: Ac 275 LEU cc_start: 0.8757 (mt) cc_final: 0.8511 (mt) REVERT: Ac 303 LEU cc_start: 0.9225 (tt) cc_final: 0.8972 (tt) REVERT: Ac 344 GLU cc_start: 0.8284 (tp30) cc_final: 0.8014 (tp30) REVERT: Ac 352 GLN cc_start: 0.9175 (mt0) cc_final: 0.8434 (mp10) REVERT: Ad 166 MET cc_start: 0.8724 (mmm) cc_final: 0.8269 (mmm) REVERT: Ad 183 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8075 (tp30) REVERT: Ad 196 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8235 (t70) REVERT: Ae 90 ASP cc_start: 0.9013 (m-30) cc_final: 0.8787 (t0) REVERT: Ae 135 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: Ae 174 LEU cc_start: 0.8299 (tp) cc_final: 0.7798 (tt) REVERT: Ae 209 GLU cc_start: 0.7675 (pm20) cc_final: 0.7394 (pp20) REVERT: Ae 231 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.6796 (t80) REVERT: Ae 234 TYR cc_start: 0.8472 (m-80) cc_final: 0.8198 (m-10) REVERT: Af 88 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8569 (pttp) REVERT: Af 92 GLU cc_start: 0.8930 (tp30) cc_final: 0.8503 (tp30) REVERT: Ag 37 ASN cc_start: 0.8598 (t0) cc_final: 0.8233 (t0) REVERT: Ah 45 ARG cc_start: 0.8575 (ptp-110) cc_final: 0.8086 (ptp-110) REVERT: Aj 45 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8469 (mm-30) REVERT: Ak 17 TRP cc_start: 0.8084 (m100) cc_final: 0.7156 (m-10) REVERT: Ak 47 TYR cc_start: 0.7967 (t80) cc_final: 0.7218 (t80) outliers start: 88 outliers final: 62 residues processed: 635 average time/residue: 0.2044 time to fit residues: 212.9413 Evaluate side-chains 624 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 547 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 GLN Chi-restraints excluded: chain AA residue 151 VAL Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 338 CYS Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 124 GLU Chi-restraints excluded: chain AB residue 138 LEU Chi-restraints excluded: chain AB residue 160 ILE Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AB residue 390 GLU Chi-restraints excluded: chain AC residue 51 LEU Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AC residue 284 ILE Chi-restraints excluded: chain AD residue 139 CYS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 227 LEU Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AE residue 218 THR Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AJ residue 8 SER Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 168 ILE Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 359 VAL Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 43 VAL Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 119 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 198 LEU Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 234 ASN Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 80 VAL Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Ak residue 16 ASN Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 264 optimal weight: 6.9990 chunk 320 optimal weight: 0.0170 chunk 61 optimal weight: 8.9990 chunk 155 optimal weight: 0.0570 chunk 272 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 284 optimal weight: 0.6980 chunk 173 optimal weight: 0.8980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 402 HIS AB 36 GLN AB 236 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 155 GLN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 200 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.110325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087236 restraints weight = 72019.129| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.83 r_work: 0.3175 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.472 33045 Z= 0.128 Angle : 0.648 14.228 44806 Z= 0.314 Chirality : 0.042 0.190 4839 Planarity : 0.004 0.058 5666 Dihedral : 9.872 128.345 4952 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.17 % Allowed : 21.45 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.14), residues: 3916 helix: 1.58 (0.11), residues: 2094 sheet: -0.12 (0.25), residues: 395 loop : 0.10 (0.18), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAh 47 TYR 0.024 0.001 TYRAf 22 PHE 0.026 0.001 PHEAc 183 TRP 0.032 0.001 TRPAK 34 HIS 0.012 0.001 HISAE 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (33031) covalent geometry : angle 0.64803 / 0.31 (44794) SS BOND : bond 0.00376 / 0.24 ( 6) SS BOND : angle 0.91421 / 0.58 ( 12) hydrogen bonds : bond 0.03659 / 2.48 ( 1856) hydrogen bonds : angle 4.40856 / 3.05 ( 5328) Misc. bond : bond 0.25772 / 16.90 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7832 Ramachandran restraints generated. 3916 Oldfield, 0 Emsley, 3916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 592 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 49 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: AA 243 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8312 (mm) REVERT: AB 246 LEU cc_start: 0.8664 (pp) cc_final: 0.8205 (mt) REVERT: AB 322 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7792 (m-30) REVERT: AC 53 MET cc_start: 0.9203 (ttm) cc_final: 0.8999 (ttm) REVERT: AC 271 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7984 (mt-10) REVERT: AC 341 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7633 (mm-40) REVERT: AC 344 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7406 (tm-30) REVERT: AD 127 MET cc_start: 0.8733 (mmm) cc_final: 0.8482 (mmm) REVERT: AD 142 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7959 (tm-30) REVERT: AD 227 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7917 (pp) REVERT: AD 255 TYR cc_start: 0.7485 (m-80) cc_final: 0.7186 (m-80) REVERT: AD 263 MET cc_start: 0.8242 (tpp) cc_final: 0.7835 (tpt) REVERT: AD 284 HIS cc_start: 0.7877 (t70) cc_final: 0.7546 (t70) REVERT: AE 108 GLU cc_start: 0.8195 (mp0) cc_final: 0.7397 (mp0) REVERT: AE 170 ARG cc_start: 0.8637 (mmt180) cc_final: 0.8230 (mmt180) REVERT: AE 175 PHE cc_start: 0.7903 (m-80) cc_final: 0.7452 (m-80) REVERT: AE 200 HIS cc_start: 0.6616 (t70) cc_final: 0.6189 (t70) REVERT: AF 70 THR cc_start: 0.9088 (m) cc_final: 0.8843 (p) REVERT: AG 72 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7756 (tpt170) REVERT: AH 23 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7272 (pm20) REVERT: AH 71 ASP cc_start: 0.9127 (m-30) cc_final: 0.8848 (t0) REVERT: AJ 11 TYR cc_start: 0.8190 (t80) cc_final: 0.7809 (t80) REVERT: AJ 33 GLU cc_start: 0.8085 (tt0) cc_final: 0.7475 (tt0) REVERT: AK 16 ASN cc_start: 0.7220 (t0) cc_final: 0.6718 (t0) REVERT: Aa 94 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8691 (tm-30) REVERT: Aa 129 THR cc_start: 0.9301 (m) cc_final: 0.8923 (p) REVERT: Aa 368 MET cc_start: 0.8338 (mmm) cc_final: 0.8067 (tpp) REVERT: Aa 377 MET cc_start: 0.8663 (mmm) cc_final: 0.8310 (mmp) REVERT: Aa 450 TYR cc_start: 0.8673 (t80) cc_final: 0.8328 (t80) REVERT: Ab 40 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8430 (t80) REVERT: Ab 157 GLN cc_start: 0.8709 (tp40) cc_final: 0.8274 (tp40) REVERT: Ab 173 ILE cc_start: 0.8822 (tp) cc_final: 0.8591 (tp) REVERT: Ab 414 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8684 (tm-30) REVERT: Ac 51 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8868 (mm) REVERT: Ac 85 ASN cc_start: 0.9082 (m-40) cc_final: 0.8845 (m-40) REVERT: Ac 118 LEU cc_start: 0.9055 (tp) cc_final: 0.8826 (tt) REVERT: Ac 138 MET cc_start: 0.7700 (tpt) cc_final: 0.7295 (tpt) REVERT: Ac 171 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: Ac 212 ASN cc_start: 0.8692 (t0) cc_final: 0.8365 (t0) REVERT: Ac 240 MET cc_start: 0.7390 (mmm) cc_final: 0.7101 (mmt) REVERT: Ac 275 LEU cc_start: 0.8712 (mt) cc_final: 0.8466 (mt) REVERT: Ac 352 GLN cc_start: 0.9173 (mt0) cc_final: 0.8395 (mp10) REVERT: Ac 376 MET cc_start: 0.8895 (mmm) cc_final: 0.8604 (mmm) REVERT: Ad 166 MET cc_start: 0.8757 (mmm) cc_final: 0.8427 (mmm) REVERT: Ad 183 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8103 (tp30) REVERT: Ad 196 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8444 (t70) REVERT: Ae 90 ASP cc_start: 0.8965 (m-30) cc_final: 0.8741 (t0) REVERT: Ae 135 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: Ae 209 GLU cc_start: 0.7693 (pm20) cc_final: 0.7193 (pt0) REVERT: Ae 231 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.6789 (t80) REVERT: Ae 234 TYR cc_start: 0.8519 (m-80) cc_final: 0.8260 (m-10) REVERT: Af 40 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8522 (mt-10) REVERT: Af 88 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8676 (pttp) REVERT: Af 92 GLU cc_start: 0.8890 (tp30) cc_final: 0.8483 (tp30) REVERT: Ag 37 ASN cc_start: 0.8571 (t0) cc_final: 0.8217 (t0) REVERT: Ag 66 GLU cc_start: 0.8677 (tp30) cc_final: 0.8432 (tp30) REVERT: Ah 45 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.8163 (ptp-110) REVERT: Ai 46 LYS cc_start: 0.5041 (OUTLIER) cc_final: 0.3610 (pttp) REVERT: Aj 32 PHE cc_start: 0.9056 (t80) cc_final: 0.8694 (t80) REVERT: Ak 17 TRP cc_start: 0.8091 (m100) cc_final: 0.7095 (m-10) REVERT: Ak 47 TYR cc_start: 0.7991 (t80) cc_final: 0.7288 (t80) outliers start: 73 outliers final: 48 residues processed: 636 average time/residue: 0.2052 time to fit residues: 214.5297 Evaluate side-chains 615 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 555 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 49 GLN Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 243 LEU Chi-restraints excluded: chain AA residue 303 THR Chi-restraints excluded: chain AA residue 354 LEU Chi-restraints excluded: chain AA residue 384 THR Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 65 VAL Chi-restraints excluded: chain AB residue 138 LEU Chi-restraints excluded: chain AB residue 160 ILE Chi-restraints excluded: chain AB residue 244 LEU Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 111 GLU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 225 THR Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AD residue 139 CYS Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 227 LEU Chi-restraints excluded: chain AE residue 218 THR Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 58 LEU Chi-restraints excluded: chain AH residue 33 GLU Chi-restraints excluded: chain AH residue 87 ASN Chi-restraints excluded: chain AI residue 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AJ residue 8 SER Chi-restraints excluded: chain Aa residue 96 LEU Chi-restraints excluded: chain Aa residue 109 LEU Chi-restraints excluded: chain Aa residue 171 GLU Chi-restraints excluded: chain Aa residue 262 VAL Chi-restraints excluded: chain Aa residue 338 CYS Chi-restraints excluded: chain Aa residue 354 LEU Chi-restraints excluded: chain Aa residue 359 VAL Chi-restraints excluded: chain Aa residue 360 CYS Chi-restraints excluded: chain Aa residue 463 GLU Chi-restraints excluded: chain Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 299 ILE Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 51 LEU Chi-restraints excluded: chain Ac residue 170 VAL Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ad residue 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 231 PHE Chi-restraints excluded: chain Ag residue 58 LEU Chi-restraints excluded: chain Ah residue 30 THR Chi-restraints excluded: chain Ah residue 82 HIS Chi-restraints excluded: chain Ai residue 46 LYS Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 371 optimal weight: 0.9990 chunk 302 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 308 ASN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 434 GLN ** Ad 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.110505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087436 restraints weight = 72133.878| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.82 r_work: 0.3178 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.460 33045 Z= 0.131 Angle : 0.658 14.535 44806 Z= 0.318 Chirality : 0.042 0.206 4839 Planarity : 0.004 0.061 5666 Dihedral : 9.732 128.681 4952 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.05 % Allowed : 21.72 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.14), residues: 3916 helix: 1.57 (0.11), residues: 2094 sheet: -0.13 (0.25), residues: 388 loop : 0.12 (0.18), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAg 72 TYR 0.030 0.001 TYRAF 21 PHE 0.022 0.001 PHEAc 183 TRP 0.034 0.001 TRPAE 169 HIS 0.011 0.001 HISAE 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (33031) covalent geometry : angle 0.65660 / 0.32 (44794) SS BOND : bond 0.00580 / 0.29 ( 6) SS BOND : angle 2.45406 / 1.53 ( 12) hydrogen bonds : bond 0.03660 / 2.47 ( 1856) hydrogen bonds : angle 4.41033 / 3.05 ( 5328) Misc. bond : bond 0.25580 / 16.80 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7467.05 seconds wall clock time: 129 minutes 23.70 seconds (7763.70 seconds total)