Starting phenix.real_space_refine on Thu May 29 15:44:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iar_35316/05_2025/8iar_35316_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iar_35316/05_2025/8iar_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iar_35316/05_2025/8iar_35316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iar_35316/05_2025/8iar_35316.map" model { file = "/net/cci-nas-00/data/ceres_data/8iar_35316/05_2025/8iar_35316_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iar_35316/05_2025/8iar_35316_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 88 Planarities with less than four sites: {'UQ6:plan-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-5': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 47 Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 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: 60 Planarities with less than four sites: {'UQ6:plan-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-5': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 47 Chain: "Ad" Number of atoms: 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: 20.13, per 1000 atoms: 0.62 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: 9.24 Conformation dependent library (CDL) restraints added in 4.4 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: 3.59 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: 11.11 Time building geometry restraints manager: 10.55 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: 42891 2.66 - 5.32: 1594 5.32 - 7.99: 216 7.99 - 10.65: 73 10.65 - 13.31: 20 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 - 31.28: 19189 31.28 - 62.55: 426 62.55 - 93.83: 73 93.83 - 125.10: 5 125.10 - 156.38: 7 Dihedral angle restraints: 19700 sinusoidal: 8167 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=" C11 U10Ac 404 " pdb=" C12 U10Ac 404 " pdb=" C13 U10Ac 404 " pdb=" C14 U10Ac 404 " ideal model delta sinusoidal sigma weight residual 126.68 -76.94 -156.38 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 19697 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=" C12 UQ6AC 406 " 0.315 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C13 UQ6AC 406 " -0.459 2.00e-02 2.50e+03 pdb=" C14 UQ6AC 406 " -0.098 2.00e-02 2.50e+03 pdb=" C15 UQ6AC 406 " 0.186 2.00e-02 2.50e+03 pdb=" C16 UQ6AC 406 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ6Ac 405 " -0.315 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C13 UQ6Ac 405 " 0.459 2.00e-02 2.50e+03 pdb=" C14 UQ6Ac 405 " 0.098 2.00e-02 2.50e+03 pdb=" C15 UQ6Ac 405 " -0.186 2.00e-02 2.50e+03 pdb=" C16 UQ6Ac 405 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 UQ6Ac 405 " -0.268 2.00e-02 2.50e+03 2.25e-01 6.35e+02 pdb=" C18 UQ6Ac 405 " 0.377 2.00e-02 2.50e+03 pdb=" C19 UQ6Ac 405 " 0.082 2.00e-02 2.50e+03 pdb=" C20 UQ6Ac 405 " -0.181 2.00e-02 2.50e+03 pdb=" C21 UQ6Ac 405 " -0.010 2.00e-02 2.50e+03 ... (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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 71.500 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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= 0.601 Angle : 1.194 13.311 44806 Z= 0.758 Chirality : 0.056 0.426 4839 Planarity : 0.010 0.267 5666 Dihedral : 14.425 156.377 12256 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 28.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (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 TRP 0.025 0.002 TRPAC 141 HIS 0.009 0.001 HISAC 196 PHE 0.049 0.002 PHEAC 183 TYR 0.049 0.002 TYRAe 235 ARG 0.007 0.001 ARGAE 250 Details of bonding type rmsd hydrogen bonds : bond 0.18084 ( 1856) hydrogen bonds : angle 7.25985 ( 5328) SS BOND : bond 0.01316 ( 6) SS BOND : angle 4.56294 ( 12) covalent geometry : bond 0.00898 (33031) covalent geometry : angle 1.19159 (44794) Misc. bond : bond 0.09598 ( 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 : 3.979 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: 0.6544 (tp) REVERT: AA 449 PHE cc_start: 0.7923 (m-80) cc_final: 0.7555 (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: 0.8348 (ttt180) REVERT: AD 259 THR cc_start: 0.8148 (m) cc_final: 0.7830 (m) REVERT: AF 108 TRP cc_start: 0.8550 (t-100) cc_final: 0.8350 (t60) REVERT: Aa 468 TYR cc_start: 0.8348 (t80) cc_final: 0.8140 (t80) REVERT: Ab 109 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8024 (mttm) REVERT: Ab 141 THR cc_start: 0.7974 (p) cc_final: 0.7745 (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: 0.9024 (p) REVERT: Ac 59 THR cc_start: 0.8902 (p) cc_final: 0.8664 (p) REVERT: Ac 156 ILE cc_start: 0.8262 (pt) cc_final: 0.8009 (pt) REVERT: Ac 235 MET cc_start: 0.9298 (tmm) cc_final: 0.8962 (ttp) REVERT: Ac 252 ASP cc_start: 0.7593 (t0) cc_final: 0.7001 (t0) REVERT: Ac 312 GLN cc_start: 0.8795 (mt0) cc_final: 0.8398 (mt0) REVERT: Ac 313 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8196 (ttt-90) REVERT: Ad 156 ASP cc_start: 0.8433 (t0) cc_final: 0.7618 (t0) REVERT: Ad 165 PHE cc_start: 0.8128 (p90) cc_final: 0.7791 (p90) REVERT: Ad 296 MET cc_start: 0.8270 (mmt) cc_final: 0.8056 (mmp) REVERT: Ad 309 HIS cc_start: 0.7013 (t70) cc_final: 0.6731 (t-90) REVERT: Ad 322 ARG cc_start: 0.8759 (mmm160) cc_final: 0.8173 (mtp85) REVERT: Ae 191 GLU cc_start: 0.7863 (mp0) cc_final: 0.7620 (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: 0.7863 (mp) REVERT: Aj 8 SER cc_start: 0.6113 (t) cc_final: 0.5611 (p) REVERT: Ak 23 MET cc_start: 0.8558 (tpp) cc_final: 0.8077 (mmp) outliers start: 13 outliers final: 0 residues processed: 1218 average time/residue: 0.5095 time to fit residues: 942.9338 Evaluate side-chains 667 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 666 time to evaluate : 3.553 ------------------------------------------------------------------------------- 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 325 optimal weight: 6.9990 chunk 292 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 156 optimal weight: 0.3980 chunk 302 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 350 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN AA 397 ASN AB 167 GLN AC 206 ASN AC 308 HIS AD 107 HIS AD 309 HIS ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 219 HIS AE 242 HIS AH 53 ASN AI 58 GLN AI 71 ASN AJ 48 ASN AK 16 ASN Aa 87 ASN Aa 160 GLN Aa 181 ASN Aa 207 ASN ** Aa 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 373 GLN ** Aa 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 167 GLN ** Ac 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 90 HIS ** Ad 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 155 GLN Ad 189 ASN Ad 190 ASN ** Ad 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 194 GLN ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 GLN ** Ai 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 16 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089555 restraints weight = 69060.857| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.95 r_work: 0.3158 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.488 33045 Z= 0.172 Angle : 0.708 12.523 44806 Z= 0.355 Chirality : 0.044 0.208 4839 Planarity : 0.005 0.077 5666 Dihedral : 13.109 146.020 4870 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.77 % Allowed : 12.20 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 3916 helix: 1.03 (0.11), residues: 2082 sheet: -0.14 (0.26), residues: 393 loop : -0.33 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPAE 169 HIS 0.013 0.001 HISAe 200 PHE 0.032 0.002 PHEAd 273 TYR 0.021 0.002 TYRAJ 44 ARG 0.010 0.001 ARGAE 170 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 1856) hydrogen bonds : angle 5.04453 ( 5328) SS BOND : bond 0.00617 ( 6) SS BOND : angle 1.34111 ( 12) covalent geometry : bond 0.00371 (33031) covalent geometry : angle 0.70782 (44794) Misc. bond : bond 0.23970 ( 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 825 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 732 time to evaluate : 3.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 123 TYR cc_start: 0.7698 (p90) cc_final: 0.7077 (p90) REVERT: AA 163 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8682 (mtmm) REVERT: AA 179 MET cc_start: 0.7761 (mtm) cc_final: 0.7373 (mtm) REVERT: AA 243 LEU cc_start: 0.8754 (tp) cc_final: 0.8553 (mt) REVERT: AA 385 GLU cc_start: 0.8977 (tt0) cc_final: 0.8721 (tm-30) REVERT: AA 395 LEU cc_start: 0.9156 (tp) cc_final: 0.8904 (tt) REVERT: AB 74 SER cc_start: 0.8765 (m) cc_final: 0.8322 (p) REVERT: AB 119 MET cc_start: 0.8730 (ttm) cc_final: 0.8529 (mtm) REVERT: AB 407 MET cc_start: 0.8790 (mtm) cc_final: 0.8423 (mpp) REVERT: AC 104 TYR cc_start: 0.9138 (m-80) cc_final: 0.8920 (m-80) REVERT: AC 341 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7589 (mm-40) REVERT: AD 119 GLN cc_start: 0.9296 (tp40) cc_final: 0.9093 (mm110) REVERT: AD 144 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7691 (tt0) REVERT: AD 255 TYR cc_start: 0.7174 (m-80) cc_final: 0.6856 (m-80) REVERT: AE 135 GLN cc_start: 0.8735 (mp10) cc_final: 0.8039 (mp10) REVERT: AE 149 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7602 (tpp) REVERT: AE 165 MET cc_start: 0.7657 (tpt) cc_final: 0.7348 (tpp) REVERT: AE 169 TRP cc_start: 0.8421 (t60) cc_final: 0.7784 (t60) REVERT: AE 170 ARG cc_start: 0.8953 (mtm180) cc_final: 0.8587 (mmt180) REVERT: AF 54 ASP cc_start: 0.8570 (p0) cc_final: 0.8330 (p0) REVERT: AF 57 ASN cc_start: 0.8283 (m-40) cc_final: 0.8078 (m-40) REVERT: AF 64 LYS cc_start: 0.8932 (tptm) cc_final: 0.8541 (tptm) REVERT: AG 13 HIS cc_start: 0.8072 (m90) cc_final: 0.7863 (m90) REVERT: AG 72 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.7771 (tpt170) REVERT: AG 77 MET cc_start: 0.8087 (tpt) cc_final: 0.7577 (tpt) REVERT: AH 64 ASP cc_start: 0.8192 (p0) cc_final: 0.7830 (t0) REVERT: AH 71 ASP cc_start: 0.9301 (m-30) cc_final: 0.9003 (m-30) REVERT: AH 73 LEU cc_start: 0.9085 (mp) cc_final: 0.8810 (mt) REVERT: AJ 33 GLU cc_start: 0.8224 (tt0) cc_final: 0.7851 (tt0) REVERT: AJ 37 ASP cc_start: 0.8320 (m-30) cc_final: 0.8077 (m-30) REVERT: AJ 38 GLN cc_start: 0.8266 (tp-100) cc_final: 0.7912 (tm-30) REVERT: Aa 85 LYS cc_start: 0.7973 (pptt) cc_final: 0.7712 (pptt) REVERT: Aa 94 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8755 (tm-30) REVERT: Aa 274 GLU cc_start: 0.7925 (pt0) cc_final: 0.7709 (pt0) REVERT: Aa 463 GLU cc_start: 0.8263 (tt0) cc_final: 0.7995 (pt0) REVERT: Aa 468 TYR cc_start: 0.8741 (t80) cc_final: 0.8448 (t80) REVERT: Ab 77 LEU cc_start: 0.8857 (tp) cc_final: 0.8542 (mt) REVERT: Ab 173 ILE cc_start: 0.8714 (tp) cc_final: 0.8284 (mm) REVERT: Ab 218 MET cc_start: 0.8833 (mtm) cc_final: 0.8415 (mtt) REVERT: Ac 42 MET cc_start: 0.8348 (mtt) cc_final: 0.7765 (tpp) REVERT: Ac 44 GLN cc_start: 0.8032 (mm110) cc_final: 0.7642 (mm-40) REVERT: Ac 51 LEU cc_start: 0.9173 (mm) cc_final: 0.8945 (mm) REVERT: Ac 58 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: Ac 171 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: Ac 238 ILE cc_start: 0.9040 (tt) cc_final: 0.8831 (tp) REVERT: Ac 257 MET cc_start: 0.8797 (mtp) cc_final: 0.8511 (mtp) REVERT: Ac 352 GLN cc_start: 0.8699 (mt0) cc_final: 0.8440 (mt0) REVERT: Ad 159 ASN cc_start: 0.7905 (t0) cc_final: 0.6988 (t0) REVERT: Ad 166 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7152 (mmt) REVERT: Ad 173 ASP cc_start: 0.8697 (t0) cc_final: 0.8253 (t0) REVERT: Ad 181 ASN cc_start: 0.8864 (p0) cc_final: 0.8512 (p0) REVERT: Ad 196 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8274 (t70) REVERT: Ad 228 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7089 (tmt170) REVERT: Ad 273 PHE cc_start: 0.9106 (t80) cc_final: 0.8639 (t80) REVERT: Ae 82 ASP cc_start: 0.8402 (p0) cc_final: 0.8177 (m-30) REVERT: Ae 90 ASP cc_start: 0.9013 (m-30) cc_final: 0.8367 (t0) REVERT: Ae 140 MET cc_start: 0.8317 (mtt) cc_final: 0.8084 (mtt) REVERT: Ae 159 ILE cc_start: 0.8055 (mt) cc_final: 0.7758 (mp) REVERT: Ae 170 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7669 (mtt-85) REVERT: Af 19 LYS cc_start: 0.8800 (mttm) cc_final: 0.8180 (mttm) REVERT: Af 78 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8290 (mtpp) REVERT: Af 92 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8497 (tm-30) REVERT: Ag 78 TYR cc_start: 0.8128 (m-80) cc_final: 0.7810 (m-80) REVERT: Ah 33 GLU cc_start: 0.8670 (mp0) cc_final: 0.8374 (pp20) REVERT: Ai 64 LEU cc_start: 0.8085 (mp) cc_final: 0.7841 (mp) REVERT: Ai 72 VAL cc_start: 0.2969 (OUTLIER) cc_final: 0.2626 (p) REVERT: Ak 10 TYR cc_start: 0.7636 (m-80) cc_final: 0.7389 (m-80) REVERT: Ak 23 MET cc_start: 0.7635 (tpp) cc_final: 0.7335 (mmp) REVERT: Ak 47 TYR cc_start: 0.7403 (t80) cc_final: 0.7033 (t80) outliers start: 93 outliers final: 44 residues processed: 789 average time/residue: 0.4167 time to fit residues: 526.2627 Evaluate side-chains 638 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 587 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 180 GLN Chi-restraints excluded: chain AA residue 249 HIS 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 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 250 THR Chi-restraints excluded: chain AE residue 149 MET 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 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 444 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 186 LEU Chi-restraints excluded: chain Ac residue 58 ASP Chi-restraints excluded: chain Ac residue 171 ASP Chi-restraints excluded: chain Ac residue 273 TYR Chi-restraints excluded: chain Ac residue 336 THR Chi-restraints excluded: chain Ac residue 349 ILE Chi-restraints excluded: chain Ad residue 166 MET 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 80 GLN 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 47 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 313 optimal weight: 4.9990 chunk 331 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 316 optimal weight: 20.0000 chunk 354 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN AB 36 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 107 HIS AE 219 HIS AK 16 ASN Aa 55 ASN Aa 87 ASN Aa 181 ASN Aa 249 HIS Aa 308 ASN Aa 434 GLN ** Ab 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 331 ASN Ad 115 GLN Ad 134 HIS ** Ad 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 309 HIS Ah 82 HIS Ai 58 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082733 restraints weight = 73079.248| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.79 r_work: 0.3087 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.632 33045 Z= 0.310 Angle : 0.769 15.316 44806 Z= 0.381 Chirality : 0.047 0.204 4839 Planarity : 0.005 0.061 5666 Dihedral : 12.682 141.457 4868 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.69 % Allowed : 14.52 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.14), residues: 3916 helix: 1.09 (0.11), residues: 2093 sheet: -0.32 (0.25), residues: 402 loop : -0.19 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPAc 141 HIS 0.018 0.002 HISAC 308 PHE 0.025 0.002 PHEAJ 32 TYR 0.025 0.002 TYRAC 224 ARG 0.007 0.001 ARGAh 32 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 1856) hydrogen bonds : angle 4.96479 ( 5328) SS BOND : bond 0.00703 ( 6) SS BOND : angle 1.03412 ( 12) covalent geometry : bond 0.00716 (33031) covalent geometry : angle 0.76854 (44794) Misc. bond : bond 0.32457 ( 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 734 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 610 time to evaluate : 3.857 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 179 MET cc_start: 0.7897 (mtm) cc_final: 0.7615 (mtm) REVERT: AB 173 ILE cc_start: 0.8630 (tp) cc_final: 0.8338 (tt) REVERT: AB 210 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8259 (mp10) REVERT: AB 390 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: AB 407 MET cc_start: 0.8756 (mtm) cc_final: 0.8492 (mpp) REVERT: AC 21 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8692 (pp) REVERT: AC 58 ASP cc_start: 0.8413 (t0) cc_final: 0.8103 (t70) REVERT: AC 257 MET cc_start: 0.8250 (mtm) cc_final: 0.8038 (ptp) REVERT: AC 341 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7788 (mm-40) REVERT: AD 234 ASN cc_start: 0.8748 (t0) cc_final: 0.8027 (m-40) REVERT: AD 255 TYR cc_start: 0.7780 (m-80) cc_final: 0.7042 (m-80) REVERT: AE 110 ARG cc_start: 0.7610 (mtm180) cc_final: 0.7133 (ptt90) REVERT: AE 175 PHE cc_start: 0.8147 (m-10) cc_final: 0.7940 (m-80) REVERT: AE 209 GLU cc_start: 0.5792 (pm20) cc_final: 0.5559 (pm20) REVERT: AE 256 LEU cc_start: 0.8217 (mt) cc_final: 0.8015 (mm) REVERT: AF 43 ASP cc_start: 0.8878 (m-30) cc_final: 0.8654 (m-30) REVERT: AF 110 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7952 (mttm) REVERT: AG 72 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.7832 (tpt170) REVERT: AH 73 LEU cc_start: 0.9196 (mp) cc_final: 0.8940 (mp) REVERT: AJ 33 GLU cc_start: 0.8348 (tt0) cc_final: 0.7815 (tt0) REVERT: AJ 48 ASN cc_start: 0.7881 (t0) cc_final: 0.7587 (t0) REVERT: AK 16 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6550 (t0) REVERT: Aa 87 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.8802 (t0) REVERT: Aa 94 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8730 (tm-30) REVERT: Aa 463 GLU cc_start: 0.8518 (tt0) cc_final: 0.8254 (tt0) REVERT: Ab 157 GLN cc_start: 0.8910 (tp40) cc_final: 0.8382 (tp-100) REVERT: Ab 173 ILE cc_start: 0.8987 (tp) cc_final: 0.8562 (mm) REVERT: Ab 218 MET cc_start: 0.8912 (mtm) cc_final: 0.8462 (mtt) REVERT: Ab 414 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8665 (tm-30) REVERT: Ac 42 MET cc_start: 0.8432 (mtt) cc_final: 0.8112 (tpp) REVERT: Ac 138 MET cc_start: 0.7500 (tpt) cc_final: 0.7274 (tpt) REVERT: Ac 171 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: Ac 202 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8426 (tm-30) REVERT: Ac 271 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8076 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8867 (mt) cc_final: 0.8608 (mt) REVERT: Ac 352 GLN cc_start: 0.8914 (mt0) cc_final: 0.8635 (mt0) REVERT: Ad 159 ASN cc_start: 0.8657 (t0) cc_final: 0.8368 (t0) REVERT: Ad 166 MET cc_start: 0.7589 (mtt) cc_final: 0.7210 (mmt) REVERT: Ad 181 ASN cc_start: 0.8915 (p0) cc_final: 0.8659 (p0) REVERT: Ad 196 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8335 (t70) REVERT: Ad 249 TYR cc_start: 0.8378 (p90) cc_final: 0.8004 (p90) REVERT: Ad 273 PHE cc_start: 0.9328 (t80) cc_final: 0.8838 (t80) REVERT: Ae 82 ASP cc_start: 0.8245 (p0) cc_final: 0.8003 (m-30) REVERT: Ae 90 ASP cc_start: 0.8880 (m-30) cc_final: 0.8576 (t0) REVERT: Ae 209 GLU cc_start: 0.7580 (pm20) cc_final: 0.6737 (pt0) REVERT: Af 92 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8566 (tm-30) REVERT: Ag 23 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8500 (mt-10) REVERT: Ah 35 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7928 (t) REVERT: Ai 72 VAL cc_start: 0.2603 (OUTLIER) cc_final: 0.2302 (p) REVERT: Aj 14 LEU cc_start: 0.8235 (pt) cc_final: 0.8006 (pt) REVERT: Aj 44 TYR cc_start: 0.9020 (t80) cc_final: 0.8809 (t80) REVERT: Ak 47 TYR cc_start: 0.7830 (t80) cc_final: 0.7250 (t80) outliers start: 124 outliers final: 75 residues processed: 693 average time/residue: 0.4297 time to fit residues: 476.9735 Evaluate side-chains 617 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 532 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 380 CYS 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 115 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 309 LEU Chi-restraints excluded: chain AB residue 390 GLU Chi-restraints excluded: chain AC residue 21 LEU Chi-restraints excluded: chain AC residue 43 VAL Chi-restraints excluded: chain AC residue 92 ILE Chi-restraints excluded: chain AC residue 119 LEU Chi-restraints excluded: chain AC residue 126 THR 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 102 LEU Chi-restraints excluded: chain AD residue 201 VAL Chi-restraints excluded: chain AD residue 266 VAL Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AF residue 20 TRP Chi-restraints excluded: chain AF residue 83 LYS Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 55 VAL Chi-restraints excluded: chain AG residue 59 ILE 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 30 LEU Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 87 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 308 ASN 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 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 390 GLU Chi-restraints excluded: chain Ab residue 414 GLN 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 200 ILE Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ae residue 104 LYS Chi-restraints excluded: chain Ae residue 117 VAL Chi-restraints excluded: chain Ae residue 185 ASP Chi-restraints excluded: chain Ae residue 216 VAL 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 Ah residue 30 THR Chi-restraints excluded: chain Ah residue 35 CYS Chi-restraints excluded: chain Ah residue 38 LEU Chi-restraints excluded: chain Ah residue 40 LYS Chi-restraints excluded: chain Ah residue 82 HIS Chi-restraints excluded: chain Ai residue 64 LEU Chi-restraints excluded: chain Ai residue 72 VAL Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 27 VAL 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 163 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 230 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 236 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 201 HIS AD 107 HIS ** AE 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 46 HIS AJ 48 ASN AK 16 ASN Aa 87 ASN Ab 118 ASN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 37 ASN Ak 16 ASN Ak 49 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085781 restraints weight = 72134.835| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.81 r_work: 0.3139 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.482 33045 Z= 0.148 Angle : 0.627 13.549 44806 Z= 0.310 Chirality : 0.042 0.207 4839 Planarity : 0.004 0.060 5666 Dihedral : 12.223 132.556 4868 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.24 % Allowed : 16.69 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3916 helix: 1.37 (0.11), residues: 2084 sheet: -0.27 (0.25), residues: 397 loop : -0.08 (0.17), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPAE 169 HIS 0.018 0.001 HISAh 82 PHE 0.019 0.001 PHEAC 183 TYR 0.020 0.001 TYRAC 224 ARG 0.011 0.000 ARGAA 442 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 1856) hydrogen bonds : angle 4.68610 ( 5328) SS BOND : bond 0.00443 ( 6) SS BOND : angle 0.87019 ( 12) covalent geometry : bond 0.00346 (33031) covalent geometry : angle 0.62728 (44794) Misc. bond : bond 0.26380 ( 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 718 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 609 time to evaluate : 3.460 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 175 ASN cc_start: 0.8310 (m110) cc_final: 0.8032 (p0) REVERT: AA 179 MET cc_start: 0.7771 (mtm) cc_final: 0.7530 (mtm) REVERT: AB 173 ILE cc_start: 0.8568 (tp) cc_final: 0.8251 (tt) REVERT: AB 210 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: AB 322 ASP cc_start: 0.8430 (t70) cc_final: 0.7939 (t0) REVERT: AB 390 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: AB 407 MET cc_start: 0.8813 (mtm) cc_final: 0.8586 (mpp) REVERT: AC 214 ASP cc_start: 0.9033 (m-30) cc_final: 0.8466 (m-30) REVERT: AC 271 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7773 (mt-10) REVERT: AC 311 LYS cc_start: 0.8569 (mptt) cc_final: 0.8206 (mmtp) REVERT: AC 341 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7814 (mm-40) REVERT: AD 234 ASN cc_start: 0.8844 (t0) cc_final: 0.8052 (m-40) REVERT: AD 255 TYR cc_start: 0.7578 (m-80) cc_final: 0.6980 (m-80) REVERT: AE 169 TRP cc_start: 0.8598 (t60) cc_final: 0.8391 (t60) REVERT: AE 200 HIS cc_start: 0.6940 (t70) cc_final: 0.6446 (t70) REVERT: AE 209 GLU cc_start: 0.5712 (pm20) cc_final: 0.5503 (pm20) REVERT: AF 43 ASP cc_start: 0.8771 (m-30) cc_final: 0.8537 (m-30) REVERT: AF 64 LYS cc_start: 0.9182 (tptm) cc_final: 0.8850 (tptm) REVERT: AF 88 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8472 (mtmm) REVERT: AG 72 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.7801 (tpt170) REVERT: AH 23 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7112 (pm20) REVERT: AH 64 ASP cc_start: 0.8529 (p0) cc_final: 0.8095 (t70) REVERT: AJ 11 TYR cc_start: 0.8146 (t80) cc_final: 0.7909 (t80) REVERT: AJ 33 GLU cc_start: 0.8138 (tt0) cc_final: 0.7651 (tt0) REVERT: AJ 34 ARG cc_start: 0.8358 (tpt170) cc_final: 0.8134 (tpt170) REVERT: AJ 38 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7895 (tm-30) REVERT: AJ 48 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7377 (t0) REVERT: AK 16 ASN cc_start: 0.7112 (OUTLIER) cc_final: 0.6597 (t0) REVERT: AK 34 TRP cc_start: 0.8067 (t60) cc_final: 0.7827 (t60) REVERT: Aa 87 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8933 (t0) REVERT: Aa 94 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8668 (tm-30) REVERT: Aa 129 THR cc_start: 0.9348 (m) cc_final: 0.9077 (p) REVERT: Aa 360 CYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7404 (m) REVERT: Aa 463 GLU cc_start: 0.8417 (tt0) cc_final: 0.8119 (tt0) REVERT: Ab 157 GLN cc_start: 0.8730 (tp40) cc_final: 0.8298 (tp40) REVERT: Ab 173 ILE cc_start: 0.8921 (tp) cc_final: 0.8505 (mm) REVERT: Ab 218 MET cc_start: 0.8849 (mtm) cc_final: 0.8408 (mtt) REVERT: Ab 414 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: Ac 42 MET cc_start: 0.8311 (mtt) cc_final: 0.7983 (tpp) REVERT: Ac 119 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8511 (mp) REVERT: Ac 171 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: Ac 202 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8416 (tm-30) REVERT: Ac 257 MET cc_start: 0.8884 (mtp) cc_final: 0.8604 (mtp) REVERT: Ac 271 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7836 (mt-10) REVERT: Ac 275 LEU cc_start: 0.8611 (mt) cc_final: 0.8306 (mt) REVERT: Ac 352 GLN cc_start: 0.8896 (mt0) cc_final: 0.8560 (mt0) REVERT: Ad 159 ASN cc_start: 0.8720 (t0) cc_final: 0.8460 (t0) REVERT: Ad 181 ASN cc_start: 0.8916 (p0) cc_final: 0.8684 (p0) REVERT: Ad 196 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8355 (t70) REVERT: Ad 273 PHE cc_start: 0.9339 (t80) cc_final: 0.8888 (t80) REVERT: Ad 295 MET cc_start: 0.8879 (mmm) cc_final: 0.8441 (tpt) REVERT: Ae 82 ASP cc_start: 0.8180 (p0) cc_final: 0.7977 (m-30) REVERT: Ae 90 ASP cc_start: 0.8851 (m-30) cc_final: 0.8572 (t0) REVERT: Ae 135 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: Ae 170 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7872 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6412 (tm-30) cc_final: 0.6166 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7550 (pm20) cc_final: 0.6932 (pt0) REVERT: Ae 222 CYS cc_start: 0.5896 (m) cc_final: 0.5527 (p) REVERT: Ae 231 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6006 (t80) REVERT: Ah 35 CYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7892 (t) REVERT: Ah 45 ARG cc_start: 0.8559 (ptp-110) cc_final: 0.8024 (ptp-110) REVERT: Ah 85 PHE cc_start: 0.8672 (m-10) cc_final: 0.8459 (m-80) REVERT: Ai 72 VAL cc_start: 0.2604 (OUTLIER) cc_final: 0.2300 (p) REVERT: Aj 14 LEU cc_start: 0.8220 (pt) cc_final: 0.7997 (pt) REVERT: Aj 16 ARG cc_start: 0.7569 (ttt180) cc_final: 0.7138 (ptm-80) REVERT: Ak 17 TRP cc_start: 0.7971 (m100) cc_final: 0.7042 (m-10) REVERT: Ak 47 TYR cc_start: 0.7840 (t80) cc_final: 0.7172 (t80) outliers start: 109 outliers final: 64 residues processed: 679 average time/residue: 0.4322 time to fit residues: 470.8822 Evaluate side-chains 643 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 565 time to evaluate : 3.531 ------------------------------------------------------------------------------- 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 151 VAL Chi-restraints excluded: chain AA residue 180 GLN 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 106 VAL 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 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 149 LEU Chi-restraints excluded: chain AC residue 160 LEU Chi-restraints excluded: chain AC residue 192 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 AD residue 250 THR Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AF residue 20 TRP Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AH residue 28 LEU 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 48 ASN Chi-restraints excluded: chain AK residue 16 ASN Chi-restraints excluded: chain Aa residue 87 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 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 407 MET Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 110 MET 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 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 Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 185 ASP 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 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 35 CYS Chi-restraints excluded: chain Ah residue 38 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 180 optimal weight: 0.9990 chunk 312 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 378 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 103 ASN AB 36 GLN AB 236 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN AE 200 HIS AJ 48 ASN AK 16 ASN Aa 87 ASN Aa 308 ASN Aa 434 GLN Ab 280 ASN Ac 44 GLN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 82 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.106913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083742 restraints weight = 72442.046| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.78 r_work: 0.3107 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.548 33045 Z= 0.205 Angle : 0.663 19.881 44806 Z= 0.321 Chirality : 0.043 0.217 4839 Planarity : 0.004 0.058 5666 Dihedral : 12.113 130.831 4868 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.57 % Allowed : 17.20 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3916 helix: 1.42 (0.11), residues: 2079 sheet: -0.25 (0.25), residues: 397 loop : -0.05 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAc 141 HIS 0.013 0.001 HISAe 200 PHE 0.014 0.001 PHEAd 273 TYR 0.019 0.002 TYRAC 224 ARG 0.014 0.001 ARGAA 442 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1856) hydrogen bonds : angle 4.66049 ( 5328) SS BOND : bond 0.00295 ( 6) SS BOND : angle 0.72755 ( 12) covalent geometry : bond 0.00486 (33031) covalent geometry : angle 0.66262 (44794) Misc. bond : bond 0.30757 ( 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 705 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 585 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 175 ASN cc_start: 0.8367 (m110) cc_final: 0.7944 (p0) REVERT: AA 179 MET cc_start: 0.7656 (mtm) cc_final: 0.7434 (mtm) REVERT: AA 368 MET cc_start: 0.8484 (mmm) cc_final: 0.7733 (tpt) REVERT: AB 134 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: AB 173 ILE cc_start: 0.8534 (tp) cc_final: 0.8250 (tt) REVERT: AB 322 ASP cc_start: 0.8415 (t70) cc_final: 0.8029 (m-30) REVERT: AB 390 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: AB 407 MET cc_start: 0.8806 (mtm) cc_final: 0.8561 (mpp) REVERT: AC 58 ASP cc_start: 0.8439 (t0) cc_final: 0.8103 (t70) REVERT: AC 214 ASP cc_start: 0.9098 (m-30) cc_final: 0.8457 (m-30) REVERT: AC 311 LYS cc_start: 0.8675 (mptt) cc_final: 0.8322 (mmtp) REVERT: AC 341 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7832 (mm-40) REVERT: AD 227 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8041 (pp) REVERT: AD 234 ASN cc_start: 0.8865 (t0) cc_final: 0.8443 (t0) REVERT: AD 255 TYR cc_start: 0.7526 (m-80) cc_final: 0.6872 (m-80) REVERT: AE 108 GLU cc_start: 0.8153 (mp0) cc_final: 0.7169 (mp0) REVERT: AE 110 ARG cc_start: 0.7777 (mtm180) cc_final: 0.7318 (ptt90) REVERT: AE 169 TRP cc_start: 0.8627 (t60) cc_final: 0.8377 (t60) REVERT: AE 200 HIS cc_start: 0.6848 (t-90) cc_final: 0.6290 (t70) REVERT: AE 248 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7865 (mtm180) REVERT: AF 43 ASP cc_start: 0.8838 (m-30) cc_final: 0.8579 (m-30) REVERT: AF 48 ILE cc_start: 0.9254 (tp) cc_final: 0.9051 (tp) REVERT: AF 64 LYS cc_start: 0.9191 (tptm) cc_final: 0.8928 (tptp) REVERT: AG 72 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.7836 (tpt170) REVERT: AJ 33 GLU cc_start: 0.8156 (tt0) cc_final: 0.7694 (tt0) REVERT: AJ 34 ARG cc_start: 0.8354 (tpt170) cc_final: 0.8110 (tpt170) REVERT: AK 16 ASN cc_start: 0.7113 (OUTLIER) cc_final: 0.6656 (t0) REVERT: AK 34 TRP cc_start: 0.8094 (t60) cc_final: 0.7768 (t60) REVERT: Aa 85 LYS cc_start: 0.8076 (pptt) cc_final: 0.7848 (pptt) REVERT: Aa 87 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.9049 (t0) REVERT: Aa 94 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8708 (tm-30) REVERT: Aa 129 THR cc_start: 0.9344 (m) cc_final: 0.9036 (p) REVERT: Aa 463 GLU cc_start: 0.8544 (tt0) cc_final: 0.8227 (tt0) REVERT: Ab 40 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8379 (t80) REVERT: Ab 157 GLN cc_start: 0.8807 (tp40) cc_final: 0.8406 (tp40) REVERT: Ab 173 ILE cc_start: 0.8969 (tp) cc_final: 0.8579 (mm) REVERT: Ab 218 MET cc_start: 0.8899 (mtm) cc_final: 0.8437 (mtt) REVERT: Ab 390 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8705 (tm-30) REVERT: Ac 21 LEU cc_start: 0.9246 (tt) cc_final: 0.8999 (pt) REVERT: Ac 42 MET cc_start: 0.8354 (mtt) cc_final: 0.8043 (tpp) REVERT: Ac 119 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8377 (mp) REVERT: Ac 171 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: Ac 198 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8516 (tt) REVERT: Ac 202 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8470 (tm-30) REVERT: Ac 257 MET cc_start: 0.8911 (mtp) cc_final: 0.8627 (mtp) REVERT: Ac 275 LEU cc_start: 0.8643 (mt) cc_final: 0.8314 (mt) REVERT: Ac 313 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8614 (ttt-90) REVERT: Ac 352 GLN cc_start: 0.8919 (mt0) cc_final: 0.8545 (mt0) REVERT: Ad 159 ASN cc_start: 0.8785 (t0) cc_final: 0.8578 (t0) REVERT: Ad 166 MET cc_start: 0.8340 (mmm) cc_final: 0.7755 (tpp) REVERT: Ad 181 ASN cc_start: 0.8940 (p0) cc_final: 0.8633 (p0) REVERT: Ad 183 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8346 (mp0) REVERT: Ad 196 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8397 (t70) REVERT: Ad 273 PHE cc_start: 0.9372 (t80) cc_final: 0.8991 (t80) REVERT: Ae 90 ASP cc_start: 0.8954 (m-30) cc_final: 0.8591 (t0) REVERT: Ae 135 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: Ae 170 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7836 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6486 (tm-30) cc_final: 0.6264 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7708 (pm20) cc_final: 0.7168 (pt0) REVERT: Ae 222 CYS cc_start: 0.6176 (m) cc_final: 0.5665 (p) REVERT: Ae 231 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.5998 (t80) REVERT: Ae 272 VAL cc_start: 0.8388 (t) cc_final: 0.8106 (t) REVERT: Ah 35 CYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7835 (t) REVERT: Ah 45 ARG cc_start: 0.8594 (ptp-110) cc_final: 0.8082 (ptp-110) REVERT: Ai 72 VAL cc_start: 0.2608 (OUTLIER) cc_final: 0.2368 (p) REVERT: Aj 13 LEU cc_start: 0.8995 (tp) cc_final: 0.8734 (mt) REVERT: Aj 14 LEU cc_start: 0.8251 (pt) cc_final: 0.7952 (pt) REVERT: Aj 16 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7023 (ptm-80) REVERT: Ak 47 TYR cc_start: 0.7937 (t80) cc_final: 0.7238 (t80) outliers start: 120 outliers final: 81 residues processed: 664 average time/residue: 0.4485 time to fit residues: 482.8865 Evaluate side-chains 649 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 552 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 109 LEU 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 275 ILE 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 134 MET Chi-restraints excluded: chain AB residue 164 VAL Chi-restraints excluded: chain AB residue 309 LEU 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 129 MET Chi-restraints excluded: chain AC residue 149 LEU Chi-restraints excluded: chain AC residue 160 LEU Chi-restraints excluded: chain AC residue 192 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 102 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 AD residue 250 THR Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AE residue 191 GLU Chi-restraints excluded: chain AE residue 270 VAL 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 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 AK residue 16 ASN Chi-restraints excluded: chain Aa residue 87 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 308 ASN 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 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 390 GLU Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ac residue 43 VAL 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 278 SER Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 185 ASP 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 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 35 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 268 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 317 optimal weight: 0.0040 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 210 GLN ** AC 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 48 ASN AK 16 ASN Aa 87 ASN Aa 434 GLN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 200 HIS Ah 82 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.108655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085410 restraints weight = 72037.478| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.79 r_work: 0.3133 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.510 33045 Z= 0.152 Angle : 0.631 17.382 44806 Z= 0.306 Chirality : 0.042 0.264 4839 Planarity : 0.004 0.056 5666 Dihedral : 11.899 130.363 4868 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.69 % Allowed : 18.15 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3916 helix: 1.51 (0.11), residues: 2078 sheet: -0.17 (0.25), residues: 395 loop : -0.04 (0.17), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPAc 141 HIS 0.010 0.001 HISAe 200 PHE 0.016 0.001 PHEAb 237 TYR 0.023 0.001 TYRAC 224 ARG 0.005 0.000 ARGAH 47 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 1856) hydrogen bonds : angle 4.56836 ( 5328) SS BOND : bond 0.00225 ( 6) SS BOND : angle 0.80303 ( 12) covalent geometry : bond 0.00360 (33031) covalent geometry : angle 0.63054 (44794) Misc. bond : bond 0.28711 ( 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 714 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 590 time to evaluate : 3.900 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 49 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: AA 179 MET cc_start: 0.7685 (mtm) cc_final: 0.7474 (mtm) REVERT: AA 368 MET cc_start: 0.8479 (mmm) cc_final: 0.7851 (tpt) REVERT: AB 173 ILE cc_start: 0.8505 (tp) cc_final: 0.8216 (tt) REVERT: AB 322 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: AB 390 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: AB 407 MET cc_start: 0.8816 (mtm) cc_final: 0.8562 (mpp) REVERT: AC 58 ASP cc_start: 0.8391 (t0) cc_final: 0.8057 (t70) REVERT: AC 271 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7943 (mt-10) REVERT: AC 311 LYS cc_start: 0.8713 (mptt) cc_final: 0.8360 (mmtp) REVERT: AC 341 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7804 (mm-40) REVERT: AD 127 MET cc_start: 0.8846 (mmm) cc_final: 0.8598 (mmm) REVERT: AD 140 TYR cc_start: 0.8171 (m-10) cc_final: 0.7898 (m-10) REVERT: AD 227 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7862 (pp) REVERT: AD 234 ASN cc_start: 0.8841 (t0) cc_final: 0.8089 (m-40) REVERT: AD 255 TYR cc_start: 0.7482 (m-80) cc_final: 0.6858 (m-80) REVERT: AE 110 ARG cc_start: 0.7743 (mtm180) cc_final: 0.7288 (ptt90) REVERT: AE 169 TRP cc_start: 0.8654 (t60) cc_final: 0.8385 (t60) REVERT: AE 200 HIS cc_start: 0.6917 (t-90) cc_final: 0.6383 (t70) REVERT: AF 43 ASP cc_start: 0.8893 (m-30) cc_final: 0.8643 (m-30) REVERT: AF 48 ILE cc_start: 0.9224 (tp) cc_final: 0.9023 (tp) REVERT: AF 88 LYS cc_start: 0.8697 (mmmt) cc_final: 0.8481 (mtmm) REVERT: AG 72 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.7778 (tpt170) REVERT: AH 23 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7089 (pm20) REVERT: AH 64 ASP cc_start: 0.7959 (t70) cc_final: 0.7697 (p0) REVERT: AH 77 ASP cc_start: 0.8836 (m-30) cc_final: 0.8595 (m-30) REVERT: AJ 11 TYR cc_start: 0.8301 (t80) cc_final: 0.8101 (t80) REVERT: AJ 33 GLU cc_start: 0.8185 (tt0) cc_final: 0.7755 (tt0) REVERT: AJ 34 ARG cc_start: 0.8269 (tpt170) cc_final: 0.8059 (tpt170) REVERT: AJ 38 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7904 (tm-30) REVERT: AK 16 ASN cc_start: 0.7280 (t0) cc_final: 0.6866 (t0) REVERT: AK 34 TRP cc_start: 0.8024 (t60) cc_final: 0.7746 (t60) REVERT: Aa 85 LYS cc_start: 0.8023 (pptt) cc_final: 0.7816 (pptt) REVERT: Aa 87 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8452 (t0) REVERT: Aa 94 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8726 (tm-30) REVERT: Aa 129 THR cc_start: 0.9369 (m) cc_final: 0.9097 (p) REVERT: Aa 210 ARG cc_start: 0.8452 (tmm-80) cc_final: 0.7997 (ttp80) REVERT: Aa 368 MET cc_start: 0.8180 (tpt) cc_final: 0.7796 (mmm) REVERT: Aa 463 GLU cc_start: 0.8524 (tt0) cc_final: 0.8173 (tt0) REVERT: Ab 40 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8375 (t80) REVERT: Ab 157 GLN cc_start: 0.8797 (tp40) cc_final: 0.8389 (tp40) REVERT: Ab 173 ILE cc_start: 0.8924 (tp) cc_final: 0.8688 (tp) REVERT: Ab 218 MET cc_start: 0.8865 (mtm) cc_final: 0.8440 (mtt) REVERT: Ab 414 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: Ac 42 MET cc_start: 0.8313 (mtt) cc_final: 0.8038 (tpp) REVERT: Ac 51 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8963 (mm) REVERT: Ac 119 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8512 (mp) REVERT: Ac 171 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: Ac 202 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8617 (tm-30) REVERT: Ac 257 MET cc_start: 0.8907 (mtp) cc_final: 0.8611 (mtp) REVERT: Ac 275 LEU cc_start: 0.8527 (mt) cc_final: 0.8177 (mt) REVERT: Ac 352 GLN cc_start: 0.8826 (mt0) cc_final: 0.8442 (mt0) REVERT: Ad 166 MET cc_start: 0.8359 (mmm) cc_final: 0.7958 (tpp) REVERT: Ad 181 ASN cc_start: 0.8900 (p0) cc_final: 0.8586 (p0) REVERT: Ad 183 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8359 (mp0) REVERT: Ad 196 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8401 (t70) REVERT: Ad 273 PHE cc_start: 0.9373 (t80) cc_final: 0.8972 (t80) REVERT: Ae 90 ASP cc_start: 0.8948 (m-30) cc_final: 0.8612 (t0) REVERT: Ae 135 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8511 (mp10) REVERT: Ae 170 ARG cc_start: 0.8219 (mtp180) cc_final: 0.7851 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6476 (tm-30) cc_final: 0.6234 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7770 (pm20) cc_final: 0.7245 (pt0) REVERT: Ae 222 CYS cc_start: 0.6150 (m) cc_final: 0.5697 (p) REVERT: Ae 231 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6255 (t80) REVERT: Ae 234 TYR cc_start: 0.8377 (m-80) cc_final: 0.8060 (m-80) REVERT: Ag 32 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8405 (p) REVERT: Ah 35 CYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7591 (t) REVERT: Ah 45 ARG cc_start: 0.8586 (ptp-110) cc_final: 0.8080 (ptp-110) REVERT: Ah 64 ASP cc_start: 0.8933 (p0) cc_final: 0.8521 (p0) REVERT: Ai 72 VAL cc_start: 0.2687 (OUTLIER) cc_final: 0.2473 (p) REVERT: Aj 13 LEU cc_start: 0.8991 (tp) cc_final: 0.8695 (mt) REVERT: Aj 14 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8023 (pt) REVERT: Aj 16 ARG cc_start: 0.7850 (ttt180) cc_final: 0.6993 (ptm-80) REVERT: Ak 47 TYR cc_start: 0.7915 (t80) cc_final: 0.7277 (t80) outliers start: 124 outliers final: 76 residues processed: 665 average time/residue: 0.4192 time to fit residues: 451.7695 Evaluate side-chains 642 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 549 time to evaluate : 3.622 ------------------------------------------------------------------------------- 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 268 CYS Chi-restraints excluded: chain AA residue 275 ILE 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 164 VAL Chi-restraints excluded: chain AB residue 199 LYS Chi-restraints excluded: chain AB residue 210 GLN 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 149 LEU Chi-restraints excluded: chain AC residue 160 LEU Chi-restraints excluded: chain AC residue 192 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 102 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 182 LYS Chi-restraints excluded: chain AE residue 270 VAL Chi-restraints excluded: chain AG residue 39 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AH residue 28 LEU 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 87 ASN 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 216 LEU 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 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 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 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 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 185 ASP Chi-restraints excluded: chain Ae residue 231 PHE 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 35 CYS 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 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 Chi-restraints excluded: chain Ak residue 32 LEU 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 146 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 374 optimal weight: 9.9990 chunk 341 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AC 331 ASN AJ 48 ASN Aa 87 ASN Aa 308 ASN Aa 434 GLN Ab 298 HIS Ac 44 GLN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.083356 restraints weight = 72603.964| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.77 r_work: 0.3097 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.562 33045 Z= 0.214 Angle : 0.671 16.396 44806 Z= 0.326 Chirality : 0.044 0.220 4839 Planarity : 0.004 0.058 5666 Dihedral : 11.881 130.805 4868 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.72 % Allowed : 18.66 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3916 helix: 1.45 (0.11), residues: 2082 sheet: -0.19 (0.25), residues: 395 loop : -0.02 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPAc 141 HIS 0.016 0.001 HISAe 200 PHE 0.030 0.002 PHEAC 183 TYR 0.020 0.002 TYRAa 468 ARG 0.005 0.000 ARGAA 442 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1856) hydrogen bonds : angle 4.60559 ( 5328) SS BOND : bond 0.00567 ( 6) SS BOND : angle 0.86568 ( 12) covalent geometry : bond 0.00508 (33031) covalent geometry : angle 0.67070 (44794) Misc. bond : bond 0.30554 ( 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 680 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 555 time to evaluate : 3.817 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: 0.8333 (OUTLIER) cc_final: 0.8047 (pt0) REVERT: AA 179 MET cc_start: 0.7681 (mtm) cc_final: 0.7461 (mtm) REVERT: AB 173 ILE cc_start: 0.8587 (tp) cc_final: 0.8280 (tt) REVERT: AB 210 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: AB 322 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7967 (m-30) REVERT: AC 58 ASP cc_start: 0.8383 (t0) cc_final: 0.8074 (t70) REVERT: AC 271 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7947 (mt-10) REVERT: AC 311 LYS cc_start: 0.8797 (mptt) cc_final: 0.8451 (mmtp) REVERT: AC 341 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7766 (mm-40) REVERT: AD 127 MET cc_start: 0.8834 (mmm) cc_final: 0.8556 (mmm) REVERT: AD 227 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7850 (pp) REVERT: AD 234 ASN cc_start: 0.8857 (t0) cc_final: 0.8060 (m110) REVERT: AD 255 TYR cc_start: 0.7573 (m-80) cc_final: 0.6918 (m-80) REVERT: AE 110 ARG cc_start: 0.7696 (mtm180) cc_final: 0.7230 (ptt90) REVERT: AE 169 TRP cc_start: 0.8678 (t60) cc_final: 0.8391 (t60) REVERT: AE 200 HIS cc_start: 0.7064 (t-90) cc_final: 0.6479 (t70) REVERT: AF 48 ILE cc_start: 0.9250 (tp) cc_final: 0.9050 (tp) REVERT: AF 64 LYS cc_start: 0.9195 (tptm) cc_final: 0.8742 (tptm) REVERT: AF 88 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8449 (mtmm) REVERT: AG 72 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7740 (tpt170) REVERT: AG 74 ASN cc_start: 0.8780 (p0) cc_final: 0.8571 (p0) REVERT: AH 64 ASP cc_start: 0.7846 (t70) cc_final: 0.7481 (p0) REVERT: AH 77 ASP cc_start: 0.8844 (m-30) cc_final: 0.8576 (m-30) REVERT: AJ 11 TYR cc_start: 0.8365 (t80) cc_final: 0.8087 (t80) REVERT: AJ 33 GLU cc_start: 0.8139 (tt0) cc_final: 0.7719 (tt0) REVERT: AK 16 ASN cc_start: 0.7469 (t0) cc_final: 0.7014 (t0) REVERT: AK 34 TRP cc_start: 0.7968 (t60) cc_final: 0.7677 (t60) REVERT: Aa 87 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8476 (t0) REVERT: Aa 94 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8731 (tm-30) REVERT: Aa 129 THR cc_start: 0.9336 (m) cc_final: 0.9026 (p) REVERT: Aa 360 CYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7799 (m) REVERT: Aa 368 MET cc_start: 0.8459 (tpt) cc_final: 0.8241 (mmm) REVERT: Aa 377 MET cc_start: 0.8682 (mmm) cc_final: 0.8329 (mmp) REVERT: Aa 463 GLU cc_start: 0.8531 (tt0) cc_final: 0.8167 (tt0) REVERT: Ab 40 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8350 (t80) REVERT: Ab 157 GLN cc_start: 0.8760 (tp40) cc_final: 0.8371 (tp40) REVERT: Ab 173 ILE cc_start: 0.8954 (tp) cc_final: 0.8568 (mm) REVERT: Ab 218 MET cc_start: 0.8909 (mtm) cc_final: 0.8467 (mtt) REVERT: Ab 390 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8890 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8688 (tm-30) REVERT: Ac 42 MET cc_start: 0.8377 (mtt) cc_final: 0.8098 (tpp) REVERT: Ac 51 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9002 (mm) REVERT: Ac 119 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8442 (mp) REVERT: Ac 171 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: Ac 198 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8591 (tt) REVERT: Ac 202 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8710 (tm-30) REVERT: Ac 252 ASP cc_start: 0.7363 (t0) cc_final: 0.7142 (t0) REVERT: Ac 275 LEU cc_start: 0.8686 (mt) cc_final: 0.8322 (mt) REVERT: Ac 352 GLN cc_start: 0.8866 (mt0) cc_final: 0.8458 (mt0) REVERT: Ad 181 ASN cc_start: 0.8939 (p0) cc_final: 0.8690 (p0) REVERT: Ad 196 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8428 (t70) REVERT: Ae 81 THR cc_start: 0.9101 (p) cc_final: 0.8887 (p) REVERT: Ae 90 ASP cc_start: 0.9069 (m-30) cc_final: 0.8821 (t0) REVERT: Ae 135 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: Ae 170 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7860 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6587 (tm-30) cc_final: 0.6350 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7724 (pm20) cc_final: 0.7217 (pt0) REVERT: Ae 222 CYS cc_start: 0.6259 (m) cc_final: 0.5834 (p) REVERT: Ae 231 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.6362 (t80) REVERT: Ae 234 TYR cc_start: 0.8386 (m-80) cc_final: 0.8096 (m-10) REVERT: Af 19 LYS cc_start: 0.8952 (mttm) cc_final: 0.8712 (mttm) REVERT: Ah 35 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7528 (t) REVERT: Ah 45 ARG cc_start: 0.8579 (ptp-110) cc_final: 0.8322 (ptm160) REVERT: Ai 72 VAL cc_start: 0.2950 (OUTLIER) cc_final: 0.2725 (p) REVERT: Aj 13 LEU cc_start: 0.8968 (tp) cc_final: 0.8686 (mt) REVERT: Aj 14 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8054 (pt) REVERT: Aj 16 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7227 (ptm-80) REVERT: Aj 30 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8416 (tt) REVERT: Ak 47 TYR cc_start: 0.7964 (t80) cc_final: 0.7246 (t80) outliers start: 125 outliers final: 82 residues processed: 635 average time/residue: 0.4124 time to fit residues: 423.9046 Evaluate side-chains 643 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 541 time to evaluate : 3.409 ------------------------------------------------------------------------------- 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 268 CYS Chi-restraints excluded: chain AA residue 275 ILE 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 384 THR 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 199 LYS Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AB residue 322 ASP 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 129 MET Chi-restraints excluded: chain AC residue 149 LEU Chi-restraints excluded: chain AC residue 192 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 AE residue 161 GLU Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AE residue 270 VAL 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 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 AJ residue 8 SER Chi-restraints excluded: chain Aa residue 87 ASN 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 308 ASN 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 Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 113 THR Chi-restraints excluded: chain Ab residue 132 ILE Chi-restraints excluded: chain Ab residue 160 ILE Chi-restraints excluded: chain Ab residue 223 LEU Chi-restraints excluded: chain Ab residue 299 ILE 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 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 196 ASP Chi-restraints excluded: chain Ad residue 227 LEU Chi-restraints excluded: chain Ad residue 278 SER Chi-restraints excluded: chain Ad residue 286 LYS Chi-restraints excluded: chain Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 185 ASP Chi-restraints excluded: chain Ae residue 231 PHE 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 35 CYS 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 Aj residue 30 LEU Chi-restraints excluded: chain Ak residue 16 ASN Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 32 LEU Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 169 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 384 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 210 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 87 ASN Aa 308 ASN Aa 434 GLN Ac 331 ASN Ad 159 ASN Ad 282 HIS Ah 82 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.107372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.084049 restraints weight = 72451.696| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.79 r_work: 0.3109 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.539 33045 Z= 0.179 Angle : 0.648 14.871 44806 Z= 0.317 Chirality : 0.043 0.217 4839 Planarity : 0.004 0.057 5666 Dihedral : 11.771 131.558 4868 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.66 % Allowed : 18.98 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3916 helix: 1.48 (0.11), residues: 2082 sheet: -0.22 (0.25), residues: 397 loop : 0.00 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAc 141 HIS 0.009 0.001 HISAE 178 PHE 0.022 0.001 PHEAC 183 TYR 0.017 0.001 TYRAa 468 ARG 0.004 0.000 ARGAA 442 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1856) hydrogen bonds : angle 4.56782 ( 5328) SS BOND : bond 0.00421 ( 6) SS BOND : angle 0.94836 ( 12) covalent geometry : bond 0.00427 (33031) covalent geometry : angle 0.64793 (44794) Misc. bond : bond 0.29133 ( 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 676 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 553 time to evaluate : 4.039 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: AA 49 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: AA 179 MET cc_start: 0.7673 (mtm) cc_final: 0.7460 (mtm) REVERT: AA 368 MET cc_start: 0.8540 (mmm) cc_final: 0.8232 (tpt) REVERT: AB 173 ILE cc_start: 0.8530 (tp) cc_final: 0.8235 (tt) REVERT: AB 322 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7920 (m-30) REVERT: AC 58 ASP cc_start: 0.8480 (t0) cc_final: 0.8171 (t70) REVERT: AC 271 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7947 (mt-10) REVERT: AC 311 LYS cc_start: 0.8867 (mptt) cc_final: 0.8528 (mmtp) REVERT: AC 341 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7799 (mm-40) REVERT: AC 372 ILE cc_start: 0.9493 (mt) cc_final: 0.9218 (mt) REVERT: AC 376 MET cc_start: 0.8951 (mmm) cc_final: 0.8744 (mpp) REVERT: AD 127 MET cc_start: 0.8791 (mmm) cc_final: 0.8558 (mmm) REVERT: AD 142 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8071 (tm-30) REVERT: AD 227 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7823 (pp) REVERT: AD 234 ASN cc_start: 0.8837 (t0) cc_final: 0.8007 (m110) REVERT: AD 255 TYR cc_start: 0.7480 (m-80) cc_final: 0.6882 (m-80) REVERT: AD 284 HIS cc_start: 0.7992 (t70) cc_final: 0.7540 (t-170) REVERT: AE 110 ARG cc_start: 0.7545 (mtm180) cc_final: 0.7128 (ptt90) REVERT: AE 169 TRP cc_start: 0.8717 (t60) cc_final: 0.8444 (t60) REVERT: AE 170 ARG cc_start: 0.8738 (mtm180) cc_final: 0.8515 (mtt-85) REVERT: AE 200 HIS cc_start: 0.7010 (t-90) cc_final: 0.6354 (t70) REVERT: AF 36 ASP cc_start: 0.8371 (m-30) cc_final: 0.8074 (m-30) REVERT: AG 72 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7776 (tpt170) REVERT: AH 23 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7096 (pm20) REVERT: AH 77 ASP cc_start: 0.8848 (m-30) cc_final: 0.8607 (m-30) REVERT: AJ 11 TYR cc_start: 0.8320 (t80) cc_final: 0.8047 (t80) REVERT: AJ 33 GLU cc_start: 0.8213 (tt0) cc_final: 0.7607 (tt0) REVERT: AK 16 ASN cc_start: 0.7439 (t0) cc_final: 0.6978 (t0) REVERT: Aa 87 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8563 (t0) REVERT: Aa 94 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8729 (tm-30) REVERT: Aa 129 THR cc_start: 0.9429 (m) cc_final: 0.9133 (p) REVERT: Aa 360 CYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7816 (m) REVERT: Aa 377 MET cc_start: 0.8764 (mmm) cc_final: 0.8527 (mmp) REVERT: Aa 463 GLU cc_start: 0.8488 (tt0) cc_final: 0.8112 (tt0) REVERT: Ab 40 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8360 (t80) REVERT: Ab 157 GLN cc_start: 0.8760 (tp40) cc_final: 0.8391 (tp40) REVERT: Ab 173 ILE cc_start: 0.8916 (tp) cc_final: 0.8707 (tp) REVERT: Ab 218 MET cc_start: 0.8921 (mtm) cc_final: 0.8460 (mtt) REVERT: Ab 390 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8894 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8682 (tm-30) REVERT: Ab 453 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8454 (tt) REVERT: Ac 42 MET cc_start: 0.8350 (mtt) cc_final: 0.8097 (tpp) REVERT: Ac 51 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8974 (mm) REVERT: Ac 119 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8423 (mp) REVERT: Ac 138 MET cc_start: 0.7705 (tpt) cc_final: 0.7488 (tpt) REVERT: Ac 171 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: Ac 198 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (tt) REVERT: Ac 275 LEU cc_start: 0.8668 (mt) cc_final: 0.8297 (mt) REVERT: Ac 332 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8936 (tt) REVERT: Ac 352 GLN cc_start: 0.8882 (mt0) cc_final: 0.8439 (mt0) REVERT: Ad 181 ASN cc_start: 0.8960 (p0) cc_final: 0.8695 (p0) REVERT: Ad 196 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8435 (t70) REVERT: Ae 90 ASP cc_start: 0.9031 (m-30) cc_final: 0.8762 (t0) REVERT: Ae 135 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8486 (mp10) REVERT: Ae 140 MET cc_start: 0.8301 (mtp) cc_final: 0.8093 (mtp) REVERT: Ae 170 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7801 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6602 (tm-30) cc_final: 0.6372 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7704 (pm20) cc_final: 0.7211 (pt0) REVERT: Ae 231 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.6402 (t80) REVERT: Ae 234 TYR cc_start: 0.8377 (m-80) cc_final: 0.8102 (m-10) REVERT: Ah 35 CYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7482 (t) REVERT: Ah 45 ARG cc_start: 0.8578 (ptp-110) cc_final: 0.8079 (ptp-110) REVERT: Aj 13 LEU cc_start: 0.8879 (tp) cc_final: 0.8655 (mt) REVERT: Aj 14 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8053 (pt) REVERT: Aj 16 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7237 (ptm-80) REVERT: Aj 30 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8484 (tt) REVERT: Ak 47 TYR cc_start: 0.7966 (t80) cc_final: 0.7246 (t80) outliers start: 123 outliers final: 82 residues processed: 631 average time/residue: 0.4287 time to fit residues: 442.2600 Evaluate side-chains 634 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 532 time to evaluate : 3.592 ------------------------------------------------------------------------------- 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 268 CYS Chi-restraints excluded: chain AA residue 275 ILE 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 384 THR 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 164 VAL Chi-restraints excluded: chain AB residue 210 GLN Chi-restraints excluded: chain AB residue 278 ILE Chi-restraints excluded: chain AB residue 309 LEU Chi-restraints excluded: chain AB residue 322 ASP 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 129 MET Chi-restraints excluded: chain AC residue 149 LEU Chi-restraints excluded: chain AC residue 192 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 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 122 THR Chi-restraints excluded: chain AE residue 161 GLU Chi-restraints excluded: chain AE residue 174 LEU Chi-restraints excluded: chain AE residue 270 VAL 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 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain Aa residue 87 ASN 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 354 LEU Chi-restraints excluded: chain Aa residue 359 VAL Chi-restraints excluded: chain Aa residue 360 CYS 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 390 GLU Chi-restraints excluded: chain Ab residue 407 MET Chi-restraints excluded: chain Ab residue 414 GLN Chi-restraints excluded: chain Ab residue 453 LEU 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 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 332 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 Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 185 ASP Chi-restraints excluded: chain Ae residue 192 VAL Chi-restraints excluded: chain Ae residue 231 PHE 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 35 CYS 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 Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 30 LEU 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 242 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 328 optimal weight: 0.0470 chunk 105 optimal weight: 20.0000 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 236 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 87 ASN Aa 434 GLN Ac 68 HIS Ac 331 ASN Ah 82 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084996 restraints weight = 72340.066| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.78 r_work: 0.3131 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.522 33045 Z= 0.149 Angle : 0.642 14.781 44806 Z= 0.313 Chirality : 0.042 0.205 4839 Planarity : 0.004 0.078 5666 Dihedral : 11.627 131.410 4868 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.18 % Allowed : 19.55 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3916 helix: 1.52 (0.11), residues: 2080 sheet: -0.20 (0.25), residues: 397 loop : 0.02 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPAK 34 HIS 0.011 0.001 HISAh 82 PHE 0.031 0.001 PHEAb 237 TYR 0.021 0.001 TYRAC 224 ARG 0.005 0.000 ARGAC 282 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 1856) hydrogen bonds : angle 4.51425 ( 5328) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.84929 ( 12) covalent geometry : bond 0.00352 (33031) covalent geometry : angle 0.64204 (44794) Misc. bond : bond 0.28995 ( 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 676 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 569 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 49 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: AA 174 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8426 (tm-30) REVERT: AA 179 MET cc_start: 0.7632 (mtm) cc_final: 0.7412 (mtm) REVERT: AA 368 MET cc_start: 0.8502 (mmm) cc_final: 0.8203 (tpt) REVERT: AB 173 ILE cc_start: 0.8480 (tp) cc_final: 0.8198 (tt) REVERT: AB 322 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: AC 100 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.8069 (tmm-80) REVERT: AC 271 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7914 (mt-10) REVERT: AC 311 LYS cc_start: 0.8859 (mptt) cc_final: 0.8514 (mmtp) REVERT: AC 341 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7761 (mm-40) REVERT: AD 127 MET cc_start: 0.8774 (mmm) cc_final: 0.8568 (mmm) REVERT: AD 142 GLU cc_start: 0.8257 (tm-30) cc_final: 0.8053 (tm-30) REVERT: AD 227 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7803 (pp) REVERT: AD 234 ASN cc_start: 0.8812 (t0) cc_final: 0.8005 (m110) REVERT: AD 255 TYR cc_start: 0.7473 (m-80) cc_final: 0.6943 (m-80) REVERT: AD 284 HIS cc_start: 0.7936 (t70) cc_final: 0.7500 (t-170) REVERT: AE 110 ARG cc_start: 0.7487 (mtm180) cc_final: 0.7049 (ptt90) REVERT: AE 169 TRP cc_start: 0.8645 (t60) cc_final: 0.8333 (t60) REVERT: AE 170 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8502 (mtt-85) REVERT: AE 175 PHE cc_start: 0.8032 (m-80) cc_final: 0.7650 (m-80) REVERT: AE 200 HIS cc_start: 0.6843 (t-90) cc_final: 0.6248 (t70) REVERT: AF 36 ASP cc_start: 0.8373 (m-30) cc_final: 0.8071 (m-30) REVERT: AF 110 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8007 (mmtt) REVERT: AG 72 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7770 (tpt170) REVERT: AH 23 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7154 (pm20) REVERT: AH 73 LEU cc_start: 0.9057 (mp) cc_final: 0.8751 (mt) REVERT: AH 77 ASP cc_start: 0.8855 (m-30) cc_final: 0.8632 (m-30) REVERT: AJ 33 GLU cc_start: 0.8102 (tt0) cc_final: 0.7486 (tt0) REVERT: AK 16 ASN cc_start: 0.7405 (t0) cc_final: 0.6953 (t0) REVERT: Aa 87 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8451 (t0) REVERT: Aa 94 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8727 (tm-30) REVERT: Aa 129 THR cc_start: 0.9373 (m) cc_final: 0.9072 (p) REVERT: Aa 377 MET cc_start: 0.8676 (mmm) cc_final: 0.8385 (mmp) REVERT: Aa 450 TYR cc_start: 0.8784 (t80) cc_final: 0.8554 (t80) REVERT: Aa 463 GLU cc_start: 0.8483 (tt0) cc_final: 0.8131 (tt0) REVERT: Ab 40 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8360 (t80) REVERT: Ab 157 GLN cc_start: 0.8684 (tp40) cc_final: 0.8319 (tp40) REVERT: Ab 218 MET cc_start: 0.8915 (mtm) cc_final: 0.8517 (mtt) REVERT: Ab 390 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8880 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8680 (tm-30) REVERT: Ab 453 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8439 (tt) REVERT: Ac 42 MET cc_start: 0.8259 (mtt) cc_final: 0.8011 (tpp) REVERT: Ac 51 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8959 (mm) REVERT: Ac 85 ASN cc_start: 0.9123 (m-40) cc_final: 0.8893 (m-40) REVERT: Ac 119 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8534 (mp) REVERT: Ac 171 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: Ac 198 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8466 (tt) REVERT: Ac 275 LEU cc_start: 0.8605 (mt) cc_final: 0.8226 (mt) REVERT: Ac 352 GLN cc_start: 0.8876 (mt0) cc_final: 0.8400 (mt0) REVERT: Ad 181 ASN cc_start: 0.8952 (p0) cc_final: 0.8614 (p0) REVERT: Ad 196 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (t70) REVERT: Ae 90 ASP cc_start: 0.9012 (m-30) cc_final: 0.8758 (t0) REVERT: Ae 135 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: Ae 140 MET cc_start: 0.8209 (mtp) cc_final: 0.7973 (mtp) REVERT: Ae 170 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7788 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6590 (tm-30) cc_final: 0.6356 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7830 (pm20) cc_final: 0.7316 (pt0) REVERT: Ae 231 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6608 (t80) REVERT: Ae 234 TYR cc_start: 0.8412 (m-80) cc_final: 0.8168 (m-10) REVERT: Ag 37 ASN cc_start: 0.8563 (t0) cc_final: 0.8314 (t0) REVERT: Ah 35 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7453 (t) REVERT: Ah 45 ARG cc_start: 0.8562 (ptp-110) cc_final: 0.8074 (ptp-110) REVERT: Aj 13 LEU cc_start: 0.8877 (tp) cc_final: 0.8655 (mt) REVERT: Aj 14 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8056 (pt) REVERT: Aj 16 ARG cc_start: 0.7993 (ttt180) cc_final: 0.7222 (ptm-80) REVERT: Aj 30 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8480 (tt) REVERT: Ak 47 TYR cc_start: 0.7960 (t80) cc_final: 0.7270 (t80) outliers start: 107 outliers final: 77 residues processed: 636 average time/residue: 0.4329 time to fit residues: 448.8063 Evaluate side-chains 638 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 543 time to evaluate : 3.862 ------------------------------------------------------------------------------- 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 268 CYS Chi-restraints excluded: chain AA residue 275 ILE 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 384 THR 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 309 LEU Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AC residue 43 VAL 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 129 MET Chi-restraints excluded: chain AC residue 192 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 262 LEU Chi-restraints excluded: chain AD residue 130 VAL 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 161 GLU Chi-restraints excluded: chain AE residue 270 VAL 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 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain Aa residue 87 ASN 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 216 LEU 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 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 Ab residue 453 LEU 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 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 331 ASN Chi-restraints excluded: chain Ac residue 334 ILE Chi-restraints excluded: chain Ad residue 146 LYS 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 151 LYS Chi-restraints excluded: chain Ae residue 185 ASP Chi-restraints excluded: chain Ae residue 231 PHE 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 35 CYS 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 Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 30 LEU Chi-restraints excluded: chain Ak residue 16 ASN Chi-restraints excluded: chain Ak residue 18 ILE Chi-restraints excluded: chain Ak residue 32 LEU Chi-restraints excluded: chain Ak residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 358 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 294 optimal weight: 0.7980 chunk 271 optimal weight: 0.4980 chunk 333 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 210 GLN AB 236 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 399 GLN Aa 87 ASN Ac 331 ASN Ae 186 GLN Ah 82 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.108886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.085693 restraints weight = 71951.198| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.79 r_work: 0.3148 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.505 33045 Z= 0.135 Angle : 0.653 14.701 44806 Z= 0.317 Chirality : 0.042 0.226 4839 Planarity : 0.004 0.062 5666 Dihedral : 11.443 130.950 4868 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.86 % Allowed : 20.02 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3916 helix: 1.54 (0.11), residues: 2093 sheet: -0.22 (0.25), residues: 407 loop : 0.06 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPAK 34 HIS 0.011 0.001 HISAE 178 PHE 0.020 0.001 PHEAJ 32 TYR 0.020 0.001 TYRAa 468 ARG 0.004 0.000 ARGAf 34 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 1856) hydrogen bonds : angle 4.46618 ( 5328) SS BOND : bond 0.00603 ( 6) SS BOND : angle 0.90758 ( 12) covalent geometry : bond 0.00320 (33031) covalent geometry : angle 0.65299 (44794) Misc. bond : bond 0.27864 ( 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 673 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 577 time to evaluate : 3.837 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: 0.8282 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: AA 174 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8382 (tm-30) REVERT: AA 179 MET cc_start: 0.7603 (mtm) cc_final: 0.7380 (mtm) REVERT: AA 368 MET cc_start: 0.8451 (mmm) cc_final: 0.8177 (tpt) REVERT: AB 173 ILE cc_start: 0.8434 (tp) cc_final: 0.8137 (tt) REVERT: AB 322 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: AC 100 ARG cc_start: 0.8333 (tmm-80) cc_final: 0.8076 (tmm-80) REVERT: AC 271 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7897 (mt-10) REVERT: AC 311 LYS cc_start: 0.8854 (mptt) cc_final: 0.8512 (mmtp) REVERT: AC 341 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7722 (mm-40) REVERT: AD 127 MET cc_start: 0.8750 (mmm) cc_final: 0.8542 (mmm) REVERT: AD 142 GLU cc_start: 0.8222 (tm-30) cc_final: 0.8019 (tm-30) REVERT: AD 227 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7815 (pp) REVERT: AD 234 ASN cc_start: 0.8853 (t0) cc_final: 0.8053 (m110) REVERT: AD 255 TYR cc_start: 0.7460 (m-80) cc_final: 0.7030 (m-80) REVERT: AD 263 MET cc_start: 0.8303 (tpp) cc_final: 0.7991 (tpt) REVERT: AD 284 HIS cc_start: 0.7904 (t70) cc_final: 0.7559 (t70) REVERT: AE 110 ARG cc_start: 0.7341 (mtm180) cc_final: 0.6919 (ptt180) REVERT: AE 169 TRP cc_start: 0.8627 (t60) cc_final: 0.8299 (t60) REVERT: AE 170 ARG cc_start: 0.8791 (mtm180) cc_final: 0.8520 (mtt-85) REVERT: AE 175 PHE cc_start: 0.8111 (m-80) cc_final: 0.7789 (m-80) REVERT: AE 200 HIS cc_start: 0.6803 (t-90) cc_final: 0.6176 (t70) REVERT: AF 64 LYS cc_start: 0.9052 (tptm) cc_final: 0.8721 (tptt) REVERT: AF 110 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8037 (mmtt) REVERT: AG 72 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7773 (tpt170) REVERT: AH 23 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7221 (pm20) REVERT: AH 73 LEU cc_start: 0.9043 (mp) cc_final: 0.8719 (mt) REVERT: AH 77 ASP cc_start: 0.8731 (m-30) cc_final: 0.8517 (m-30) REVERT: AI 78 PHE cc_start: 0.6890 (m-80) cc_final: 0.6473 (m-10) REVERT: AJ 32 PHE cc_start: 0.8601 (t80) cc_final: 0.8246 (t80) REVERT: AJ 33 GLU cc_start: 0.8010 (tt0) cc_final: 0.7351 (tt0) REVERT: AK 16 ASN cc_start: 0.7339 (t0) cc_final: 0.6917 (t0) REVERT: Aa 87 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8486 (t0) REVERT: Aa 129 THR cc_start: 0.9376 (m) cc_final: 0.9060 (p) REVERT: Aa 450 TYR cc_start: 0.8795 (t80) cc_final: 0.8479 (t80) REVERT: Aa 463 GLU cc_start: 0.8481 (tt0) cc_final: 0.8187 (tt0) REVERT: Ab 40 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8371 (t80) REVERT: Ab 157 GLN cc_start: 0.8599 (tp40) cc_final: 0.7753 (tm-30) REVERT: Ab 218 MET cc_start: 0.8857 (mtm) cc_final: 0.8576 (mtt) REVERT: Ab 390 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8888 (tm-30) REVERT: Ab 414 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: Ab 453 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8375 (tt) REVERT: Ac 42 MET cc_start: 0.8252 (mtt) cc_final: 0.8002 (tpp) REVERT: Ac 51 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8920 (mm) REVERT: Ac 85 ASN cc_start: 0.9102 (m-40) cc_final: 0.8874 (m-40) REVERT: Ac 118 LEU cc_start: 0.9081 (tp) cc_final: 0.8860 (tt) REVERT: Ac 119 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8543 (mp) REVERT: Ac 171 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: Ac 198 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (tt) REVERT: Ac 244 LEU cc_start: 0.9238 (tp) cc_final: 0.8726 (tp) REVERT: Ac 275 LEU cc_start: 0.8458 (mt) cc_final: 0.8061 (mt) REVERT: Ac 352 GLN cc_start: 0.8866 (mt0) cc_final: 0.8379 (mt0) REVERT: Ad 181 ASN cc_start: 0.8908 (p0) cc_final: 0.8669 (p0) REVERT: Ad 196 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8477 (t70) REVERT: Ad 273 PHE cc_start: 0.9355 (t80) cc_final: 0.8850 (t80) REVERT: Ae 90 ASP cc_start: 0.8983 (m-30) cc_final: 0.8745 (t0) REVERT: Ae 135 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8420 (mp10) REVERT: Ae 140 MET cc_start: 0.8114 (mtp) cc_final: 0.7864 (mtp) REVERT: Ae 170 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7742 (mpt-90) REVERT: Ae 194 GLN cc_start: 0.6654 (tm-30) cc_final: 0.6415 (tm-30) REVERT: Ae 209 GLU cc_start: 0.7828 (pm20) cc_final: 0.7311 (pt0) REVERT: Ae 231 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6731 (t80) REVERT: Ae 234 TYR cc_start: 0.8510 (m-80) cc_final: 0.8267 (m-10) REVERT: Af 88 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8662 (pttp) REVERT: Ah 35 CYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7403 (t) REVERT: Ah 45 ARG cc_start: 0.8567 (ptp-110) cc_final: 0.8093 (ptp-110) REVERT: Aj 13 LEU cc_start: 0.8872 (tp) cc_final: 0.8642 (mt) REVERT: Aj 14 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8053 (pt) REVERT: Aj 16 ARG cc_start: 0.7923 (ttt180) cc_final: 0.7193 (ptm-80) REVERT: Aj 30 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (tt) REVERT: Ak 47 TYR cc_start: 0.7980 (t80) cc_final: 0.7219 (t80) outliers start: 96 outliers final: 71 residues processed: 636 average time/residue: 0.4326 time to fit residues: 448.7767 Evaluate side-chains 636 residues out of total 3361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 547 time to evaluate : 3.729 ------------------------------------------------------------------------------- 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 216 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 384 THR Chi-restraints excluded: chain AA residue 401 SER Chi-restraints excluded: chain AA residue 407 THR Chi-restraints excluded: chain AB residue 36 GLN 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 278 ILE Chi-restraints excluded: chain AB residue 322 ASP Chi-restraints excluded: chain AC residue 43 VAL 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 192 LEU Chi-restraints excluded: chain AC residue 197 LEU Chi-restraints excluded: chain AC residue 233 LEU Chi-restraints excluded: chain AC residue 262 LEU Chi-restraints excluded: chain AD residue 130 VAL 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 174 LEU Chi-restraints excluded: chain AE residue 182 LYS Chi-restraints excluded: chain AE residue 270 VAL 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 70 LEU Chi-restraints excluded: chain AI residue 72 VAL Chi-restraints excluded: chain AJ residue 8 SER Chi-restraints excluded: chain Aa residue 87 ASN 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 Ab residue 40 PHE Chi-restraints excluded: chain Ab residue 133 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 Ab residue 453 LEU 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 292 LEU Chi-restraints excluded: chain Ac residue 300 ILE Chi-restraints excluded: chain Ac residue 331 ASN 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 Ae residue 123 VAL Chi-restraints excluded: chain Ae residue 135 GLN Chi-restraints excluded: chain Ae residue 151 LYS 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 35 CYS 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 Aj residue 14 LEU Chi-restraints excluded: chain Aj residue 20 THR Chi-restraints excluded: chain Aj residue 30 LEU 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 45 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 265 optimal weight: 0.7980 chunk 320 optimal weight: 0.9980 chunk 290 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 376 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 36 GLN AB 210 GLN AB 236 GLN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 87 ASN Aa 434 GLN ** Ac 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 80 GLN Ah 82 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085542 restraints weight = 71995.644| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.78 r_work: 0.3146 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.518 33045 Z= 0.144 Angle : 0.659 14.766 44806 Z= 0.319 Chirality : 0.042 0.206 4839 Planarity : 0.004 0.064 5666 Dihedral : 11.344 130.004 4868 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.77 % Allowed : 20.44 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3916 helix: 1.53 (0.11), residues: 2092 sheet: -0.19 (0.25), residues: 406 loop : 0.07 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRPAK 34 HIS 0.011 0.001 HISAE 178 PHE 0.025 0.001 PHEAK 5 TYR 0.033 0.001 TYRAF 21 ARG 0.005 0.000 ARGAf 34 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 1856) hydrogen bonds : angle 4.45776 ( 5328) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.95143 ( 12) covalent geometry : bond 0.00344 (33031) covalent geometry : angle 0.65900 (44794) Misc. bond : bond 0.27646 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16174.07 seconds wall clock time: 281 minutes 46.13 seconds (16906.13 seconds total)