Starting phenix.real_space_refine on Mon Aug 25 23:12:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ic5_35355/08_2025/8ic5_35355_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ic5_35355/08_2025/8ic5_35355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ic5_35355/08_2025/8ic5_35355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ic5_35355/08_2025/8ic5_35355.map" model { file = "/net/cci-nas-00/data/ceres_data/8ic5_35355/08_2025/8ic5_35355_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ic5_35355/08_2025/8ic5_35355_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.042 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 9 5.49 5 S 151 5.16 5 C 20201 2.51 5 N 5337 2.21 5 O 5741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31445 Number of models: 1 Model: "" Number of chains: 27 Chain: "AA" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3157 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 15, 'TRANS': 387} Chain breaks: 2 Chain: "AB" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3097 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 10, 'TRANS': 402} Chain breaks: 1 Chain: "AC" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2988 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 350} Chain: "AD" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1896 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "AE" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1397 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain breaks: 2 Chain: "AF" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 855 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "AG" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 634 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "AH" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "AI" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 328 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 5, 'TRANS': 42} Chain breaks: 3 Chain: "AJ" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 332 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "AK" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 355 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "Aa" Number of atoms: 3131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3131 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 15, 'TRANS': 384} Chain breaks: 2 Chain: "Ab" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3128 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 10, 'TRANS': 406} Chain: "Ac" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2956 Classifications: {'peptide': 369} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 347} Chain breaks: 1 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: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1436 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 2 Chain: "Af" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 864 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "Ag" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 643 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "Ah" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "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: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "AC" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'HEM': 2, 'UQ6': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 15 Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "Ac" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'3PE': 2, 'HEM': 2, 'U10': 1, 'UQ6': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 92 Planarities with less than four sites: {'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1, 'UQ6:plan-4': 1, 'UQ6:plan-5': 1, 'UQ6:plan-6': 1, 'UQ6:plan-7': 1} Unresolved non-hydrogen planarities: 52 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 Time building chain proxies: 8.34, per 1000 atoms: 0.27 Number of scatterers: 31445 At special positions: 0 Unit cell: (156.87, 143.59, 172.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 151 16.00 P 9 15.00 O 5741 8.00 N 5337 7.00 C 20201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYSAA 338 " - pdb=" SG CYSAA 360 " distance=2.01 Simple disulfide: pdb=" SG CYSAE 222 " - pdb=" SG CYSAE 238 " distance=2.05 Simple disulfide: pdb=" SG CYSAH 51 " - pdb=" SG CYSAH 65 " distance=2.05 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 35 " - pdb=" SG CYSAh 79 " distance=2.12 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: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7302 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 18 sheets defined 59.9% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 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: 3.556A pdb=" N ILEAA 116 " --> pdb=" O GLUAA 112 " (cutoff:3.500A) Processing helix chain 'AA' and resid 139 through 152 Processing helix chain 'AA' and resid 157 through 176 Processing helix chain 'AA' and resid 178 through 192 Processing helix chain 'AA' and resid 204 through 210 Processing helix chain 'AA' and resid 212 through 224 Processing helix chain 'AA' and resid 225 through 227 No H-bonds generated for 'chain 'AA' and resid 225 through 227' Processing helix chain 'AA' and resid 238 through 249 Processing helix chain 'AA' and resid 299 through 312 removed outlier: 4.195A pdb=" N THRAA 303 " --> pdb=" O PROAA 299 " (cutoff:3.500A) Processing helix chain 'AA' and resid 363 through 382 removed outlier: 4.250A pdb=" N ASPAA 367 " --> pdb=" O METAA 363 " (cutoff:3.500A) Processing helix chain 'AA' and resid 384 through 397 Processing helix chain 'AA' and resid 398 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 85 Processing helix chain 'AB' and resid 86 through 89 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: 4.715A pdb=" N SERAB 156 " --> pdb=" O ALAAB 152 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLNAB 157 " --> pdb=" O ALAAB 153 " (cutoff:3.500A) Processing helix chain 'AB' and resid 168 through 182 removed outlier: 3.869A pdb=" N ARGAB 172 " --> pdb=" O ASNAB 168 " (cutoff:3.500A) Processing helix chain 'AB' and resid 201 through 213 Processing helix chain 'AB' and resid 214 through 216 No H-bonds generated for 'chain 'AB' and resid 214 through 216' Processing helix chain 'AB' and resid 226 through 237 removed outlier: 3.596A pdb=" N LEUAB 230 " --> pdb=" O SERAB 226 " (cutoff:3.500A) Processing helix chain 'AB' and resid 280 through 294 removed outlier: 3.828A pdb=" N ASNAB 284 " --> pdb=" O ASNAB 280 " (cutoff:3.500A) Processing helix chain 'AB' and resid 307 through 315 Processing helix chain 'AB' and resid 346 through 363 Processing helix chain 'AB' and resid 367 through 387 Processing helix chain 'AB' and resid 388 through 404 Processing helix chain 'AB' and resid 408 through 419 Processing helix chain 'AB' and resid 420 through 434 Processing helix chain 'AC' and resid 10 through 19 removed outlier: 3.609A pdb=" N ILEAC 14 " --> pdb=" O LEUAC 10 " (cutoff:3.500A) Processing helix chain 'AC' and resid 28 through 31 Processing helix chain 'AC' and resid 32 through 53 Processing helix chain 'AC' and resid 61 through 72 Processing helix chain 'AC' and resid 75 through 104 Processing helix chain 'AC' and resid 105 through 108 removed outlier: 3.579A 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: 3.563A pdb=" N TRPAC 141 " --> pdb=" O GLNAC 137 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SERAC 151 " --> pdb=" O THRAC 147 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALAAC 152 " --> pdb=" O ASNAC 148 " (cutoff:3.500A) Processing helix chain 'AC' and resid 156 through 166 Processing helix chain 'AC' and resid 171 through 202 removed outlier: 3.552A pdb=" N ARGAC 177 " --> pdb=" O ALAAC 173 " (cutoff:3.500A) Proline residue: AC 186 - end of helix Processing helix chain 'AC' and resid 212 through 215 removed outlier: 4.576A pdb=" N ALAAC 215 " --> pdb=" O ASNAC 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 212 through 215' Processing helix chain 'AC' and resid 224 through 244 Processing helix chain 'AC' and resid 252 through 257 Processing helix chain 'AC' and resid 271 through 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: 3.507A pdb=" N ILEAC 298 " --> pdb=" O LEUAC 294 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEUAC 301 " --> pdb=" O SERAC 297 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALAAC 302 " --> pdb=" O ILEAC 298 " (cutoff:3.500A) Processing helix chain 'AC' and resid 305 through 308 removed outlier: 3.962A pdb=" N HISAC 308 " --> pdb=" O PROAC 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 305 through 308' Processing helix chain 'AC' and resid 318 through 341 removed outlier: 3.758A pdb=" N GLYAC 340 " --> pdb=" O THRAC 336 " (cutoff:3.500A) Processing helix chain 'AC' and resid 346 through 364 Processing helix chain 'AC' and resid 364 through 377 Processing helix chain 'AD' and resid 106 through 120 Processing helix chain 'AD' and resid 121 through 124 removed outlier: 3.512A pdb=" N CYSAD 124 " --> pdb=" O CYSAD 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 121 through 124' Processing helix chain 'AD' and resid 131 through 136 removed outlier: 3.868A pdb=" N LEUAD 135 " --> pdb=" O ALAAD 131 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VALAD 136 " --> pdb=" O TYRAD 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 131 through 136' Processing helix chain 'AD' and resid 141 through 152 removed outlier: 4.173A pdb=" N VALAD 152 " --> pdb=" O LEUAD 148 " (cutoff:3.500A) Processing helix chain 'AD' and resid 181 through 189 Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 206 through 216 Processing helix chain 'AD' and resid 237 through 241 removed outlier: 4.098A pdb=" N ALAAD 241 " --> pdb=" O PROAD 238 " (cutoff:3.500A) Processing helix chain 'AD' and resid 262 through 279 Processing helix chain 'AD' and resid 281 through 317 Proline residue: AD 301 - end of helix removed outlier: 3.864A 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 79 through 83 Processing helix chain 'AE' and resid 107 through 140 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 155 through 159 Processing helix chain 'AE' and resid 168 through 172 Processing helix chain 'AE' and resid 180 through 190 Processing helix chain 'AE' and resid 200 through 205 Processing helix chain 'AF' and resid 15 through 26 removed outlier: 3.720A pdb=" N GLYAF 26 " --> pdb=" O TYRAF 22 " (cutoff:3.500A) Processing helix chain 'AF' and resid 33 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 91 through 110 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: 5.322A 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 38 Processing helix chain 'AH' and resid 38 through 58 Processing helix chain 'AH' and resid 65 through 83 Processing helix chain 'AI' and resid 5 through 9 Processing helix chain 'AI' and resid 10 through 16 Proline residue: AI 13 - end of helix 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 removed outlier: 3.527A pdb=" N GLUAK 12 " --> pdb=" O PROAK 8 " (cutoff:3.500A) Proline residue: AK 19 - end of helix Processing helix chain 'AK' and resid 38 through 43 Processing helix chain 'Aa' and resid 78 through 82 Processing helix chain 'Aa' and resid 88 through 97 Processing helix chain 'Aa' and resid 106 through 116 removed outlier: 4.177A pdb=" N GLUAa 110 " --> pdb=" O GLYAa 106 " (cutoff:3.500A) removed outlier: 3.555A 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 311 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 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: 3.665A 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: 3.868A 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: 3.597A pdb=" N LEUAb 230 " --> pdb=" O SERAb 226 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 280 through 294 removed outlier: 3.621A pdb=" N ASNAb 284 " --> pdb=" O ASNAb 280 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 307 through 315 Processing helix chain 'Ab' and resid 346 through 363 Processing helix chain 'Ab' and resid 367 through 387 Processing helix chain 'Ab' and resid 388 through 404 Processing helix chain 'Ab' and resid 408 through 419 Processing helix chain 'Ab' and resid 420 through 434 Processing helix chain 'Ac' and resid 9 through 18 Processing helix chain 'Ac' and resid 28 through 31 Processing helix chain 'Ac' and resid 32 through 53 Processing helix chain 'Ac' and resid 61 through 72 Processing helix chain 'Ac' and resid 75 through 104 Processing helix chain 'Ac' and resid 105 through 108 removed outlier: 3.578A pdb=" N THRAc 108 " --> pdb=" O GLYAc 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 105 through 108' Processing helix chain 'Ac' and resid 109 through 133 Processing helix chain 'Ac' and resid 136 through 151 removed outlier: 3.702A pdb=" N SERAc 151 " --> pdb=" O THRAc 147 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 157 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: 4.576A pdb=" N ALAAc 215 " --> pdb=" O ASNAc 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ac' and resid 212 through 215' Processing helix chain 'Ac' and resid 224 through 244 Processing helix chain 'Ac' and resid 252 through 257 Processing helix chain 'Ac' and resid 271 through 273 No H-bonds generated for 'chain 'Ac' and resid 271 through 273' Processing helix chain 'Ac' and resid 274 through 284 Processing helix chain 'Ac' and resid 286 through 304 removed outlier: 3.506A pdb=" N ILEAc 298 " --> pdb=" O LEUAc 294 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEUAc 301 " --> pdb=" O SERAc 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALAAc 302 " --> pdb=" O ILEAc 298 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 305 through 307 No H-bonds generated for 'chain 'Ac' and resid 305 through 307' Processing helix chain 'Ac' and resid 318 through 341 removed outlier: 3.760A pdb=" N GLYAc 340 " --> pdb=" O THRAc 336 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 346 through 364 Processing helix chain 'Ac' and resid 364 through 377 Processing helix chain 'Ad' and resid 106 through 120 Processing helix chain 'Ad' and resid 121 through 124 removed outlier: 3.510A pdb=" N CYSAd 124 " --> pdb=" O CYSAd 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 121 through 124' Processing helix chain 'Ad' and resid 131 through 136 removed outlier: 3.954A pdb=" N LEUAd 135 " --> pdb=" O ALAAd 131 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VALAd 136 " --> pdb=" O TYRAd 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ad' and resid 131 through 136' Processing helix chain 'Ad' and resid 141 through 151 Processing helix chain 'Ad' and resid 181 through 189 Processing helix chain 'Ad' and resid 199 through 204 Processing helix chain 'Ad' and resid 206 through 216 Processing helix chain 'Ad' and resid 237 through 241 removed outlier: 4.098A pdb=" N ALAAd 241 " --> pdb=" O PROAd 238 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 262 through 279 Processing helix chain 'Ad' and resid 281 through 317 Proline residue: Ad 301 - end of helix removed outlier: 3.864A pdb=" N VALAd 313 " --> pdb=" O HISAd 309 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEUAd 314 " --> pdb=" O LYSAd 310 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 79 through 83 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 149 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 Processing helix chain 'Af' and resid 33 through 38 Processing helix chain 'Af' and resid 41 through 51 Processing helix chain 'Af' and resid 52 through 72 Processing helix chain 'Af' and resid 91 through 111 Processing helix chain 'Ag' and resid 20 through 24 Processing helix chain 'Ag' and resid 29 through 72 removed outlier: 3.850A pdb=" N ILEAg 35 " --> pdb=" O PHEAg 31 " (cutoff:3.500A) Proline residue: Ag 36 - end of helix removed outlier: 5.323A pdb=" N LEUAg 47 " --> pdb=" O ARGAg 43 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARGAg 48 " --> pdb=" O GLUAg 44 " (cutoff:3.500A) Proline residue: Ag 51 - end of helix Processing helix chain 'Ah' and resid 26 through 38 Processing helix chain 'Ah' and resid 38 through 58 Processing helix chain 'Ah' and resid 65 through 83 Processing helix chain 'Aj' and resid 9 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 37 Proline residue: Ak 19 - end of helix Processing helix chain 'Ak' and resid 38 through 45 Processing helix chain 'Ak' and resid 45 through 50 Processing sheet with id=AA1, first strand: chain 'AA' and resid 49 through 50 removed outlier: 6.611A pdb=" N ARGAA 58 " --> pdb=" O LEUAA 231 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALAAA 233 " --> pdb=" O ARGAA 58 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALAAA 60 " --> pdb=" O ALAAA 233 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLYAA 235 " --> pdb=" O ALAAA 60 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLUAA 62 " --> pdb=" O GLYAA 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 344 through 348 removed outlier: 3.540A pdb=" N ARGAA 278 " --> pdb=" O VALAG 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 39 through 42 removed outlier: 6.151A pdb=" N VALAB 48 " --> pdb=" O LEUAB 220 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N GLYAB 222 " --> pdb=" O VALAB 48 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALAAB 50 " --> pdb=" O GLYAB 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 256 through 261 removed outlier: 6.890A pdb=" N GLYAB 256 " --> pdb=" O METAB 438 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ALAAB 440 " --> pdb=" O GLYAB 256 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILEAB 258 " --> pdb=" O ALAAB 440 " (cutoff:3.500A) removed outlier: 8.548A 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: 3.639A pdb=" N GLYAB 334 " --> pdb=" O SERAB 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AC' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'AD' and resid 155 through 158 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: 6.660A pdb=" N HISAE 242 " --> pdb=" O ARGAE 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AE' and resid 263 through 267 removed outlier: 6.043A pdb=" N VALAE 270 " --> pdb=" O THRAE 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AI' and resid 75 through 76 removed outlier: 6.228A pdb=" N VALAb 48 " --> pdb=" O LEUAb 220 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLYAb 222 " --> pdb=" O VALAb 48 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALAAb 50 " --> pdb=" O GLYAb 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Aa' and resid 49 through 52 Processing sheet with id=AB3, first strand: chain 'Aa' and resid 340 through 348 removed outlier: 3.855A pdb=" N SERAa 340 " --> pdb=" O VALAa 359 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLYAa 458 " --> pdb=" O ILEAa 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Ab' and resid 256 through 261 removed outlier: 6.894A pdb=" N GLYAb 256 " --> pdb=" O METAb 438 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ALAAb 440 " --> pdb=" O GLYAb 256 " (cutoff:3.500A) removed outlier: 6.488A 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: 6.010A pdb=" N GLUAb 260 " --> pdb=" O GLYAb 442 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLYAb 334 " --> pdb=" O SERAb 275 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Ac' and resid 23 through 24 Processing sheet with id=AB6, first strand: chain 'Ad' and resid 153 through 155 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) Processing sheet with id=AB9, first strand: chain 'Ae' and resid 263 through 264 1849 hydrogen bonds defined for protein. 5301 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: 7.03 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 11045 1.38 - 1.56: 20869 1.56 - 1.74: 26 1.74 - 1.92: 253 1.92 - 2.11: 23 Bond restraints: 32216 Sorted by residual: bond pdb=" C GLUAC 271 " pdb=" N TRPAC 272 " ideal model delta sigma weight residual 1.335 1.516 -0.181 1.32e-02 5.74e+03 1.87e+02 bond pdb=" C GLUAc 271 " pdb=" N TRPAc 272 " ideal model delta sigma weight residual 1.335 1.515 -0.179 1.32e-02 5.74e+03 1.84e+02 bond pdb=" C3 U10Ac 405 " pdb=" O3 U10Ac 405 " ideal model delta sigma weight residual 1.230 1.407 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" C8 U10Ac 405 " pdb=" C9 U10Ac 405 " ideal model delta sigma weight residual 1.470 1.324 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" C13 U10Ac 405 " pdb=" C14 U10Ac 405 " ideal model delta sigma weight residual 1.470 1.329 0.141 2.00e-02 2.50e+03 5.00e+01 ... (remaining 32211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 42885 3.45 - 6.89: 739 6.89 - 10.34: 91 10.34 - 13.79: 10 13.79 - 17.23: 2 Bond angle restraints: 43727 Sorted by residual: angle pdb=" N THRAh 66 " pdb=" CA THRAh 66 " pdb=" C THRAh 66 " ideal model delta sigma weight residual 111.36 97.16 14.20 1.09e+00 8.42e-01 1.70e+02 angle pdb=" N GLUAD 144 " pdb=" CA GLUAD 144 " pdb=" C GLUAD 144 " ideal model delta sigma weight residual 111.07 99.01 12.06 1.07e+00 8.73e-01 1.27e+02 angle pdb=" N CYSAA 360 " pdb=" CA CYSAA 360 " pdb=" C CYSAA 360 " ideal model delta sigma weight residual 108.24 121.97 -13.73 1.32e+00 5.74e-01 1.08e+02 angle pdb=" N ASPAH 52 " pdb=" CA ASPAH 52 " pdb=" C ASPAH 52 " ideal model delta sigma weight residual 111.36 102.66 8.70 1.09e+00 8.42e-01 6.37e+01 angle pdb=" N CYSAa 360 " pdb=" CA CYSAa 360 " pdb=" C CYSAa 360 " ideal model delta sigma weight residual 109.14 120.99 -11.85 1.49e+00 4.50e-01 6.33e+01 ... (remaining 43722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 18698 31.28 - 62.57: 351 62.57 - 93.85: 61 93.85 - 125.14: 3 125.14 - 156.42: 3 Dihedral angle restraints: 19116 sinusoidal: 7777 harmonic: 11339 Sorted by residual: 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 -80.93 80.93 2 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" C11 U10Ac 405 " pdb=" C12 U10Ac 405 " pdb=" C13 U10Ac 405 " pdb=" C14 U10Ac 405 " ideal model delta sinusoidal sigma weight residual 126.68 -76.90 -156.42 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C2B HEMAC 402 " pdb=" C3B HEMAC 402 " pdb=" CAB HEMAC 402 " pdb=" CBB HEMAC 402 " ideal model delta sinusoidal sigma weight residual -0.00 -76.12 76.12 2 1.00e+01 1.00e-02 4.52e+01 ... (remaining 19113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 4150 0.084 - 0.168: 536 0.168 - 0.252: 50 0.252 - 0.337: 10 0.337 - 0.421: 5 Chirality restraints: 4751 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 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA LYSAH 83 " pdb=" N LYSAH 83 " pdb=" C LYSAH 83 " pdb=" CB LYSAH 83 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA VALAa 50 " pdb=" N VALAa 50 " pdb=" C VALAa 50 " pdb=" CB VALAa 50 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 4748 not shown) Planarity restraints: 5547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10Ac 405 " -0.096 2.00e-02 2.50e+03 8.38e-02 1.23e+02 pdb=" C1M U10Ac 405 " 0.100 2.00e-02 2.50e+03 pdb=" C2 U10Ac 405 " -0.103 2.00e-02 2.50e+03 pdb=" C3 U10Ac 405 " 0.049 2.00e-02 2.50e+03 pdb=" C4 U10Ac 405 " 0.093 2.00e-02 2.50e+03 pdb=" C5 U10Ac 405 " -0.082 2.00e-02 2.50e+03 pdb=" C6 U10Ac 405 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HECAD 401 " 0.020 2.00e-02 2.50e+03 5.91e-02 7.85e+01 pdb=" C2C HECAD 401 " -0.162 2.00e-02 2.50e+03 pdb=" C3C HECAD 401 " 0.023 2.00e-02 2.50e+03 pdb=" C4C HECAD 401 " 0.003 2.00e-02 2.50e+03 pdb=" CAC HECAD 401 " 0.033 2.00e-02 2.50e+03 pdb=" CHC HECAD 401 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HECAD 401 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HECAD 401 " 0.048 2.00e-02 2.50e+03 pdb=" NC HECAD 401 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HECAd 401 " -0.021 2.00e-02 2.50e+03 5.86e-02 7.73e+01 pdb=" C2C HECAd 401 " 0.160 2.00e-02 2.50e+03 pdb=" C3C HECAd 401 " -0.022 2.00e-02 2.50e+03 pdb=" C4C HECAd 401 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HECAd 401 " -0.032 2.00e-02 2.50e+03 pdb=" CHC HECAd 401 " -0.029 2.00e-02 2.50e+03 pdb=" CHD HECAd 401 " 0.003 2.00e-02 2.50e+03 pdb=" CMC HECAd 401 " -0.048 2.00e-02 2.50e+03 pdb=" NC HECAd 401 " -0.009 2.00e-02 2.50e+03 ... (remaining 5544 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 712 2.65 - 3.21: 32528 3.21 - 3.77: 54089 3.77 - 4.34: 75517 4.34 - 4.90: 116577 Nonbonded interactions: 279423 Sorted by model distance: nonbonded pdb=" NE2 HISAc 182 " pdb="FE HEMAc 402 " model vdw 2.084 3.080 nonbonded pdb=" NE2 HISAC 182 " pdb="FE HEMAC 401 " model vdw 2.085 3.080 nonbonded pdb=" SG CYSAA 360 " pdb=" N ASPAA 361 " model vdw 2.125 3.480 nonbonded pdb=" NE2 HISAd 125 " pdb="FE HECAd 401 " model vdw 2.211 3.080 nonbonded pdb=" NE2 HISAD 125 " pdb="FE HECAD 401 " model vdw 2.211 3.080 ... (remaining 279418 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 254 or resid 267 through 311 or resid 337 thro \ ugh 479)) selection = (chain 'Aa' and resid 44 through 479) } ncs_group { reference = chain 'AB' selection = (chain 'Ab' and (resid 38 through 300 or resid 304 through 453)) } ncs_group { reference = (chain 'AC' and (resid 8 through 151 or resid 156 through 380 or resid 402)) selection = (chain 'Ac' and (resid 8 through 380 or resid 402)) } ncs_group { reference = chain 'AD' selection = (chain 'Ad' and resid 88 through 401) } ncs_group { reference = (chain 'AE' and (resid 79 through 148 or resid 152 through 274)) selection = (chain 'Ae' and (resid 79 through 92 or resid 106 through 148 or resid 152 throu \ gh 274)) } ncs_group { reference = chain 'AF' selection = (chain 'Af' and resid 14 through 110) } ncs_group { reference = chain 'AG' selection = (chain 'Ag' and resid 5 through 79) } ncs_group { reference = chain 'AH' selection = chain 'Ah' } ncs_group { reference = chain 'AJ' selection = chain 'Aj' } ncs_group { reference = (chain 'AK' and resid 6 through 44) selection = (chain 'Ak' and resid 6 through 44) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.900 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 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 : 0.008 0.262 32231 Z= 0.506 Angle : 1.166 58.633 43741 Z= 0.746 Chirality : 0.057 0.421 4751 Planarity : 0.007 0.084 5547 Dihedral : 13.400 156.421 11793 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.24 % Allowed : 2.03 % Favored : 97.73 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.12), residues: 3844 helix: -0.53 (0.10), residues: 2055 sheet: -0.02 (0.27), residues: 361 loop : -1.11 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAE 250 TYR 0.049 0.002 TYRAE 235 PHE 0.049 0.002 PHEAc 183 TRP 0.019 0.002 TRPAc 141 HIS 0.008 0.001 HISAc 196 Details of bonding type rmsd covalent geometry : bond 0.00784 (32216) covalent geometry : angle 1.12782 (43727) SS BOND : bond 0.03600 ( 7) SS BOND : angle 16.54457 ( 14) hydrogen bonds : bond 0.18817 ( 1849) hydrogen bonds : angle 7.37074 ( 5301) Misc. bond : bond 0.15478 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1187 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 187 LEU cc_start: 0.8036 (tp) cc_final: 0.7706 (tt) REVERT: AA 219 TYR cc_start: 0.7074 (t80) cc_final: 0.6801 (t80) REVERT: AA 441 LEU cc_start: 0.8419 (tt) cc_final: 0.8193 (tp) REVERT: AA 462 ILE cc_start: 0.8085 (pt) cc_final: 0.7845 (tt) REVERT: AB 89 LEU cc_start: 0.8311 (mt) cc_final: 0.8103 (mt) REVERT: AC 41 LEU cc_start: 0.9009 (tp) cc_final: 0.8790 (tp) REVERT: AC 113 TRP cc_start: 0.7572 (t-100) cc_final: 0.7341 (t-100) REVERT: AC 327 ILE cc_start: 0.8832 (mt) cc_final: 0.8550 (tp) REVERT: AD 110 ILE cc_start: 0.8854 (mt) cc_final: 0.8650 (mt) REVERT: AD 213 SER cc_start: 0.7857 (m) cc_final: 0.7593 (p) REVERT: AD 306 MET cc_start: 0.8262 (mtp) cc_final: 0.8022 (ttm) REVERT: AH 66 THR cc_start: 0.7246 (m) cc_final: 0.6952 (m) REVERT: AH 80 VAL cc_start: 0.8630 (t) cc_final: 0.8021 (t) REVERT: AI 14 VAL cc_start: 0.7341 (t) cc_final: 0.7041 (t) REVERT: Aa 74 TRP cc_start: 0.7250 (m-90) cc_final: 0.6718 (m-90) REVERT: Aa 187 LEU cc_start: 0.8411 (tp) cc_final: 0.8085 (tp) REVERT: Aa 202 GLU cc_start: 0.8730 (mp0) cc_final: 0.8379 (mp0) REVERT: Ac 174 THR cc_start: 0.5986 (m) cc_final: 0.5290 (p) REVERT: Ac 233 LEU cc_start: 0.8019 (tp) cc_final: 0.7674 (tt) REVERT: Ac 240 MET cc_start: 0.7931 (mmm) cc_final: 0.7553 (mmt) REVERT: Ac 242 LEU cc_start: 0.8315 (tp) cc_final: 0.8059 (tp) REVERT: Ac 268 ILE cc_start: 0.7351 (mp) cc_final: 0.6892 (tp) REVERT: Ad 94 TYR cc_start: 0.6663 (m-80) cc_final: 0.6015 (m-10) REVERT: Ad 288 MET cc_start: 0.7191 (mmp) cc_final: 0.6948 (mmp) REVERT: Af 58 ASP cc_start: 0.7591 (m-30) cc_final: 0.7346 (t0) REVERT: Ag 64 ASN cc_start: 0.7696 (m-40) cc_final: 0.7424 (m110) outliers start: 8 outliers final: 3 residues processed: 1193 average time/residue: 0.2366 time to fit residues: 437.3767 Evaluate side-chains 630 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 627 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 55 ASN ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 160 GLN AA 286 HIS ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 170 GLN AC 68 HIS ** AD 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 69 GLN AJ 48 ASN Aa 128 HIS Aa 173 GLN Aa 181 ASN Aa 402 HIS ** Ab 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 137 GLN Ac 148 ASN Ad 115 GLN Ad 155 GLN ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 242 HIS Af 80 GLN ** Ag 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 87 ASN Aj 48 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.057543 restraints weight = 179908.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.059267 restraints weight = 110477.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.060455 restraints weight = 77906.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.061258 restraints weight = 60473.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.061852 restraints weight = 50482.963| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.633 32231 Z= 0.208 Angle : 0.766 17.810 43741 Z= 0.385 Chirality : 0.045 0.253 4751 Planarity : 0.005 0.051 5547 Dihedral : 10.985 141.628 4562 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.27 % Allowed : 4.18 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.13), residues: 3844 helix: 0.81 (0.11), residues: 2113 sheet: -0.12 (0.26), residues: 379 loop : -0.47 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGAA 278 TYR 0.034 0.002 TYRAK 10 PHE 0.037 0.002 PHEAd 233 TRP 0.031 0.002 TRPAD 96 HIS 0.012 0.002 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00458 (32216) covalent geometry : angle 0.76572 (43727) SS BOND : bond 0.00921 ( 7) SS BOND : angle 1.77487 ( 14) hydrogen bonds : bond 0.05554 ( 1849) hydrogen bonds : angle 5.46038 ( 5301) Misc. bond : bond 0.37168 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 805 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 373 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7908 (mm-40) REVERT: AA 376 TRP cc_start: 0.8818 (m-10) cc_final: 0.8255 (m-90) REVERT: AA 410 CYS cc_start: 0.9077 (t) cc_final: 0.8875 (t) REVERT: AA 448 TYR cc_start: 0.8679 (m-80) cc_final: 0.8430 (m-80) REVERT: AB 89 LEU cc_start: 0.9150 (mt) cc_final: 0.8853 (mp) REVERT: AB 119 MET cc_start: 0.8506 (ttm) cc_final: 0.8003 (ttm) REVERT: AB 121 TYR cc_start: 0.8195 (m-10) cc_final: 0.7933 (m-80) REVERT: AB 133 LEU cc_start: 0.9570 (mt) cc_final: 0.9348 (mt) REVERT: AB 161 ASP cc_start: 0.9272 (t0) cc_final: 0.9071 (t0) REVERT: AB 213 PHE cc_start: 0.8563 (m-80) cc_final: 0.8237 (m-80) REVERT: AB 237 PHE cc_start: 0.8875 (m-80) cc_final: 0.8602 (m-80) REVERT: AB 384 MET cc_start: 0.9199 (mtm) cc_final: 0.8907 (mtm) REVERT: AC 174 THR cc_start: 0.8164 (m) cc_final: 0.7931 (m) REVERT: AC 280 ILE cc_start: 0.9269 (mm) cc_final: 0.9051 (mm) REVERT: AD 174 TYR cc_start: 0.8579 (m-80) cc_final: 0.8332 (m-80) REVERT: AD 213 SER cc_start: 0.8109 (m) cc_final: 0.7813 (p) REVERT: AD 214 LEU cc_start: 0.9639 (tp) cc_final: 0.9305 (tp) REVERT: AD 255 TYR cc_start: 0.6921 (m-10) cc_final: 0.6602 (m-80) REVERT: AD 259 THR cc_start: 0.7516 (t) cc_final: 0.7294 (p) REVERT: AD 303 THR cc_start: 0.9570 (m) cc_final: 0.9327 (p) REVERT: AE 211 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8662 (p) REVERT: AE 220 LEU cc_start: 0.8333 (mt) cc_final: 0.7543 (mt) REVERT: AF 62 ARG cc_start: 0.9163 (mtm110) cc_final: 0.8506 (mtm180) REVERT: AF 108 TRP cc_start: 0.9204 (t-100) cc_final: 0.8501 (t-100) REVERT: AG 19 LEU cc_start: 0.9078 (tp) cc_final: 0.8570 (tp) REVERT: AG 45 ARG cc_start: 0.2555 (mtt180) cc_final: 0.2263 (mtt180) REVERT: AH 47 ARG cc_start: 0.8926 (tmt-80) cc_final: 0.8696 (tpt90) REVERT: AJ 23 LEU cc_start: 0.7116 (mt) cc_final: 0.6751 (mt) REVERT: AJ 32 PHE cc_start: 0.8682 (t80) cc_final: 0.8380 (m-80) REVERT: AK 39 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7104 (pmt170) REVERT: Aa 68 THR cc_start: 0.8999 (p) cc_final: 0.8522 (p) REVERT: Aa 74 TRP cc_start: 0.7607 (m-90) cc_final: 0.5672 (m-90) REVERT: Aa 220 LEU cc_start: 0.9316 (tp) cc_final: 0.8674 (tp) REVERT: Aa 224 TYR cc_start: 0.7889 (m-80) cc_final: 0.7683 (m-80) REVERT: Aa 275 ILE cc_start: 0.9010 (tt) cc_final: 0.8744 (tt) REVERT: Aa 276 ARG cc_start: 0.8521 (mtt-85) cc_final: 0.8033 (mmt90) REVERT: Aa 354 LEU cc_start: 0.8927 (tp) cc_final: 0.8719 (tp) REVERT: Aa 377 MET cc_start: 0.9087 (mmm) cc_final: 0.8338 (mmm) REVERT: Aa 400 VAL cc_start: 0.8663 (t) cc_final: 0.8401 (t) REVERT: Aa 406 THR cc_start: 0.8883 (p) cc_final: 0.8544 (p) REVERT: Aa 477 TRP cc_start: 0.8164 (m-10) cc_final: 0.7659 (m-10) REVERT: Ab 260 GLU cc_start: 0.7395 (mp0) cc_final: 0.7152 (mp0) REVERT: Ac 53 MET cc_start: 0.8264 (ptm) cc_final: 0.7995 (ptp) REVERT: Ac 111 GLU cc_start: 0.8323 (mp0) cc_final: 0.8019 (mm-30) REVERT: Ac 165 TRP cc_start: 0.7382 (m-10) cc_final: 0.7010 (m-10) REVERT: Ac 170 VAL cc_start: 0.9113 (p) cc_final: 0.8841 (p) REVERT: Ac 174 THR cc_start: 0.9093 (m) cc_final: 0.8431 (p) REVERT: Ac 178 PHE cc_start: 0.9202 (m-80) cc_final: 0.8458 (m-80) REVERT: Ad 288 MET cc_start: 0.7419 (mmp) cc_final: 0.7132 (mmp) REVERT: Ad 306 MET cc_start: 0.8606 (mmp) cc_final: 0.8327 (mmm) REVERT: Ae 130 LYS cc_start: 0.9074 (pptt) cc_final: 0.8707 (pttp) REVERT: Af 54 ASP cc_start: 0.8965 (p0) cc_final: 0.8745 (p0) REVERT: Af 58 ASP cc_start: 0.8493 (m-30) cc_final: 0.8181 (m-30) REVERT: Af 60 MET cc_start: 0.8799 (mmm) cc_final: 0.8529 (mmm) REVERT: Af 83 LYS cc_start: 0.7017 (mptt) cc_final: 0.6752 (mmtt) REVERT: Ag 19 LEU cc_start: 0.9302 (tp) cc_final: 0.8921 (tt) REVERT: Ag 47 LEU cc_start: 0.9305 (tp) cc_final: 0.9079 (tp) REVERT: Ah 77 ASP cc_start: 0.8763 (t0) cc_final: 0.8479 (t0) REVERT: Aj 23 LEU cc_start: 0.9575 (tp) cc_final: 0.9234 (mt) REVERT: Ak 23 MET cc_start: 0.8570 (mmm) cc_final: 0.8146 (mtt) REVERT: Ak 49 ASN cc_start: 0.6180 (t0) cc_final: 0.5968 (t0) outliers start: 9 outliers final: 2 residues processed: 811 average time/residue: 0.2178 time to fit residues: 281.8786 Evaluate side-chains 572 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 569 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 6 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 352 GLN ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 284 HIS ** AE 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 128 HIS Aa 240 GLN Aa 402 HIS Aa 469 ASN ** Ab 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 263 ASN ** Ac 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 115 GLN Ad 189 ASN ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Ah 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.067824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.053255 restraints weight = 191006.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054748 restraints weight = 119956.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055768 restraints weight = 86151.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.056495 restraints weight = 68174.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.056941 restraints weight = 57486.789| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.919 32231 Z= 0.309 Angle : 0.844 21.709 43741 Z= 0.416 Chirality : 0.046 0.198 4751 Planarity : 0.005 0.061 5547 Dihedral : 10.555 145.236 4562 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.13), residues: 3844 helix: 0.76 (0.11), residues: 2120 sheet: -0.41 (0.25), residues: 398 loop : -0.39 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARGAA 415 TYR 0.047 0.003 TYRAD 117 PHE 0.034 0.003 PHEAC 183 TRP 0.032 0.002 TRPAD 96 HIS 0.013 0.002 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00674 (32216) covalent geometry : angle 0.84361 (43727) SS BOND : bond 0.00707 ( 7) SS BOND : angle 1.30266 ( 14) hydrogen bonds : bond 0.05201 ( 1849) hydrogen bonds : angle 5.41573 ( 5301) Misc. bond : bond 0.47898 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 672 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 126 ARG cc_start: 0.8578 (mpt-90) cc_final: 0.8222 (mpt-90) REVERT: AA 131 TYR cc_start: 0.7584 (m-80) cc_final: 0.7380 (m-80) REVERT: AA 224 TYR cc_start: 0.9152 (m-10) cc_final: 0.8777 (m-80) REVERT: AA 244 ASP cc_start: 0.8720 (m-30) cc_final: 0.8367 (m-30) REVERT: AA 376 TRP cc_start: 0.8968 (m-10) cc_final: 0.8057 (m-90) REVERT: AA 462 ILE cc_start: 0.9241 (pt) cc_final: 0.9004 (tt) REVERT: AB 89 LEU cc_start: 0.9424 (mt) cc_final: 0.9188 (mp) REVERT: AB 119 MET cc_start: 0.8610 (ttm) cc_final: 0.8209 (ttm) REVERT: AC 53 MET cc_start: 0.8940 (mtp) cc_final: 0.8320 (mtp) REVERT: AC 82 MET cc_start: 0.8858 (mtt) cc_final: 0.8618 (mtt) REVERT: AC 113 TRP cc_start: 0.9235 (t-100) cc_final: 0.8934 (t-100) REVERT: AD 175 PHE cc_start: 0.8229 (m-80) cc_final: 0.7553 (m-80) REVERT: AD 213 SER cc_start: 0.8133 (m) cc_final: 0.7781 (p) REVERT: AD 214 LEU cc_start: 0.9587 (tp) cc_final: 0.9354 (tp) REVERT: AD 237 PHE cc_start: 0.9106 (t80) cc_final: 0.8863 (t80) REVERT: AD 255 TYR cc_start: 0.6652 (m-10) cc_final: 0.6448 (m-80) REVERT: AD 296 MET cc_start: 0.9491 (mmm) cc_final: 0.8985 (mmm) REVERT: AF 62 ARG cc_start: 0.8934 (mtm110) cc_final: 0.8443 (mtm180) REVERT: AF 108 TRP cc_start: 0.9214 (t-100) cc_final: 0.8548 (t-100) REVERT: AG 19 LEU cc_start: 0.8948 (tp) cc_final: 0.8647 (tp) REVERT: AG 33 LYS cc_start: 0.9292 (mttp) cc_final: 0.8958 (mmmm) REVERT: AH 36 GLU cc_start: 0.8559 (tp30) cc_final: 0.8248 (tp30) REVERT: AH 47 ARG cc_start: 0.9055 (tmt-80) cc_final: 0.8820 (tpt90) REVERT: AK 39 ARG cc_start: 0.7270 (mtt90) cc_final: 0.7006 (pmt170) REVERT: Aa 211 LEU cc_start: 0.8558 (mt) cc_final: 0.8293 (mt) REVERT: Aa 224 TYR cc_start: 0.8233 (m-80) cc_final: 0.8022 (m-80) REVERT: Aa 377 MET cc_start: 0.9152 (mmm) cc_final: 0.8876 (mmm) REVERT: Aa 440 MET cc_start: 0.9566 (mtm) cc_final: 0.9175 (mtt) REVERT: Aa 477 TRP cc_start: 0.8497 (m-10) cc_final: 0.7767 (m-10) REVERT: Ab 157 GLN cc_start: 0.9512 (tp40) cc_final: 0.9259 (tp40) REVERT: Ab 218 MET cc_start: 0.8704 (mtt) cc_final: 0.7826 (mtt) REVERT: Ab 292 LEU cc_start: 0.9186 (mt) cc_final: 0.8984 (tt) REVERT: Ac 82 MET cc_start: 0.9503 (mtp) cc_final: 0.9261 (mmm) REVERT: Ac 174 THR cc_start: 0.9095 (m) cc_final: 0.8617 (p) REVERT: Ac 178 PHE cc_start: 0.9284 (m-80) cc_final: 0.8802 (m-80) REVERT: Ac 312 GLN cc_start: 0.7533 (mm110) cc_final: 0.7274 (mm110) REVERT: Ac 316 MET cc_start: 0.9207 (tpp) cc_final: 0.8746 (mmm) REVERT: Ac 376 MET cc_start: 0.9311 (mmp) cc_final: 0.8943 (mmm) REVERT: Ae 130 LYS cc_start: 0.9267 (pptt) cc_final: 0.8975 (pttp) REVERT: Af 33 MET cc_start: 0.8662 (mmm) cc_final: 0.8434 (mmm) REVERT: Af 54 ASP cc_start: 0.9052 (p0) cc_final: 0.8793 (p0) REVERT: Af 69 LEU cc_start: 0.9613 (mm) cc_final: 0.9404 (mm) REVERT: Af 71 MET cc_start: 0.9075 (tmm) cc_final: 0.8697 (tmm) REVERT: Af 83 LYS cc_start: 0.7510 (mptt) cc_final: 0.7085 (mmtt) REVERT: Ag 47 LEU cc_start: 0.9370 (tp) cc_final: 0.9160 (tp) REVERT: Ah 77 ASP cc_start: 0.8962 (t0) cc_final: 0.8718 (t0) REVERT: Ak 41 ILE cc_start: 0.9399 (mm) cc_final: 0.9188 (mm) outliers start: 4 outliers final: 3 residues processed: 676 average time/residue: 0.2162 time to fit residues: 234.8022 Evaluate side-chains 509 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 506 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 270 optimal weight: 0.0060 chunk 25 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 273 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 overall best weight: 1.9800 ------------------------------------------------------------------------------- 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 44 GLN AC 68 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 155 GLN ** AD 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 242 HIS AH 34 HIS ** AH 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 16 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 128 HIS Aa 181 ASN Aa 373 GLN ** Ab 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 298 HIS ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 23 ASN Ag 24 GLN ** Ag 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.069603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054926 restraints weight = 184290.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056523 restraints weight = 113395.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.057622 restraints weight = 80158.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058411 restraints weight = 62535.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058865 restraints weight = 52278.652| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.721 32231 Z= 0.166 Angle : 0.679 15.949 43741 Z= 0.335 Chirality : 0.043 0.262 4751 Planarity : 0.004 0.087 5547 Dihedral : 10.154 138.062 4562 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.13), residues: 3844 helix: 1.04 (0.11), residues: 2124 sheet: -0.08 (0.26), residues: 389 loop : -0.31 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAC 282 TYR 0.041 0.002 TYRAD 236 PHE 0.031 0.002 PHEAh 70 TRP 0.023 0.002 TRPAD 96 HIS 0.016 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00371 (32216) covalent geometry : angle 0.67891 (43727) SS BOND : bond 0.01698 ( 7) SS BOND : angle 1.42704 ( 14) hydrogen bonds : bond 0.04475 ( 1849) hydrogen bonds : angle 5.06393 ( 5301) Misc. bond : bond 0.37737 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 673 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 74 TRP cc_start: 0.7159 (m-90) cc_final: 0.6790 (m-90) REVERT: AA 126 ARG cc_start: 0.8335 (mpt-90) cc_final: 0.8060 (mpt-90) REVERT: AA 224 TYR cc_start: 0.9143 (m-10) cc_final: 0.8709 (m-10) REVERT: AA 244 ASP cc_start: 0.8615 (m-30) cc_final: 0.8018 (m-30) REVERT: AA 376 TRP cc_start: 0.8926 (m-10) cc_final: 0.8313 (m-90) REVERT: AA 410 CYS cc_start: 0.8763 (t) cc_final: 0.8476 (t) REVERT: AA 440 MET cc_start: 0.9174 (tmm) cc_final: 0.8905 (tmm) REVERT: AB 89 LEU cc_start: 0.9383 (mt) cc_final: 0.9071 (mp) REVERT: AB 119 MET cc_start: 0.8506 (ttm) cc_final: 0.8036 (ttm) REVERT: AC 49 LEU cc_start: 0.9520 (tt) cc_final: 0.9300 (tt) REVERT: AC 53 MET cc_start: 0.8903 (mtp) cc_final: 0.8504 (mtp) REVERT: AC 82 MET cc_start: 0.8826 (mtt) cc_final: 0.8593 (mtt) REVERT: AC 268 ILE cc_start: 0.7970 (mt) cc_final: 0.7717 (mt) REVERT: AC 269 LYS cc_start: 0.7731 (mmmm) cc_final: 0.7459 (tppt) REVERT: AC 271 GLU cc_start: 0.8434 (tp30) cc_final: 0.7854 (tp30) REVERT: AD 213 SER cc_start: 0.8248 (m) cc_final: 0.7905 (p) REVERT: AD 214 LEU cc_start: 0.9598 (tp) cc_final: 0.9338 (tp) REVERT: AF 62 ARG cc_start: 0.8988 (mtm110) cc_final: 0.8594 (ptp90) REVERT: AF 101 GLU cc_start: 0.8692 (pt0) cc_final: 0.8491 (pt0) REVERT: AF 108 TRP cc_start: 0.9171 (t-100) cc_final: 0.8450 (t-100) REVERT: AG 19 LEU cc_start: 0.8892 (tp) cc_final: 0.8459 (tp) REVERT: AG 33 LYS cc_start: 0.9260 (mttp) cc_final: 0.8943 (mmmm) REVERT: AH 68 GLU cc_start: 0.8776 (mp0) cc_final: 0.8494 (mp0) REVERT: AI 20 ARG cc_start: 0.7189 (ttt-90) cc_final: 0.6267 (mtm-85) REVERT: AI 67 THR cc_start: 0.8373 (m) cc_final: 0.7856 (p) REVERT: AK 39 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6921 (pmt170) REVERT: Aa 185 ASP cc_start: 0.8883 (m-30) cc_final: 0.8676 (m-30) REVERT: Aa 211 LEU cc_start: 0.8441 (mt) cc_final: 0.8176 (mt) REVERT: Aa 220 LEU cc_start: 0.9423 (tp) cc_final: 0.9030 (tp) REVERT: Aa 224 TYR cc_start: 0.8085 (m-80) cc_final: 0.7735 (m-80) REVERT: Aa 440 MET cc_start: 0.9575 (mtm) cc_final: 0.9237 (mtt) REVERT: Aa 477 TRP cc_start: 0.8485 (m-10) cc_final: 0.8182 (m-10) REVERT: Ab 157 GLN cc_start: 0.9441 (tp40) cc_final: 0.9219 (tp40) REVERT: Ac 53 MET cc_start: 0.8716 (ptp) cc_final: 0.8338 (ptp) REVERT: Ac 113 TRP cc_start: 0.8972 (t-100) cc_final: 0.8660 (t-100) REVERT: Ac 121 PHE cc_start: 0.8173 (m-80) cc_final: 0.7955 (m-80) REVERT: Ac 174 THR cc_start: 0.8943 (m) cc_final: 0.8402 (p) REVERT: Ac 178 PHE cc_start: 0.9248 (m-80) cc_final: 0.8775 (m-80) REVERT: Ac 275 LEU cc_start: 0.8940 (mt) cc_final: 0.8694 (mt) REVERT: Ac 316 MET cc_start: 0.9229 (tpp) cc_final: 0.8842 (mmm) REVERT: Ac 366 MET cc_start: 0.9156 (mmp) cc_final: 0.8952 (mmm) REVERT: Ac 376 MET cc_start: 0.9021 (mmp) cc_final: 0.8754 (mmm) REVERT: Ad 276 TRP cc_start: 0.8692 (t60) cc_final: 0.8328 (t60) REVERT: Ad 292 MET cc_start: 0.8869 (ttp) cc_final: 0.8127 (tmm) REVERT: Ae 168 LYS cc_start: 0.8687 (pttp) cc_final: 0.8138 (mmmt) REVERT: Af 33 MET cc_start: 0.8535 (mmm) cc_final: 0.8200 (mmm) REVERT: Af 54 ASP cc_start: 0.9005 (p0) cc_final: 0.8740 (p0) REVERT: Af 56 TYR cc_start: 0.8610 (t80) cc_final: 0.8338 (t80) REVERT: Af 83 LYS cc_start: 0.7447 (mptt) cc_final: 0.7063 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7982 (mt) cc_final: 0.7756 (mt) REVERT: Ah 77 ASP cc_start: 0.8919 (t0) cc_final: 0.8667 (t0) REVERT: Ak 49 ASN cc_start: 0.7150 (t0) cc_final: 0.6759 (m-40) outliers start: 1 outliers final: 0 residues processed: 673 average time/residue: 0.2065 time to fit residues: 226.7409 Evaluate side-chains 512 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 175 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 82 optimal weight: 0.0060 chunk 105 optimal weight: 0.0980 chunk 330 optimal weight: 7.9990 chunk 275 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 128 HIS ** AA 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN AA 342 GLN ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 68 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 227 ASN AE 242 HIS ** AH 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 55 ASN ** Aa 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 128 HIS ** Aa 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 452 GLN ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.070153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055293 restraints weight = 182877.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.056902 restraints weight = 112696.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.058006 restraints weight = 80072.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058710 restraints weight = 62607.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059311 restraints weight = 52921.087| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.653 32231 Z= 0.147 Angle : 0.668 14.262 43741 Z= 0.331 Chirality : 0.043 0.283 4751 Planarity : 0.004 0.102 5547 Dihedral : 9.923 136.612 4562 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.15 % Allowed : 2.18 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 3844 helix: 1.07 (0.11), residues: 2119 sheet: -0.06 (0.27), residues: 371 loop : -0.22 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGAH 45 TYR 0.041 0.002 TYRAD 236 PHE 0.045 0.002 PHEAC 183 TRP 0.026 0.001 TRPAC 165 HIS 0.012 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00336 (32216) covalent geometry : angle 0.66786 (43727) SS BOND : bond 0.00480 ( 7) SS BOND : angle 1.17694 ( 14) hydrogen bonds : bond 0.04293 ( 1849) hydrogen bonds : angle 4.95609 ( 5301) Misc. bond : bond 0.33955 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 678 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 74 TRP cc_start: 0.7415 (m-90) cc_final: 0.7043 (m-90) REVERT: AA 244 ASP cc_start: 0.8469 (m-30) cc_final: 0.8171 (m-30) REVERT: AA 376 TRP cc_start: 0.8791 (m-10) cc_final: 0.7823 (m-90) REVERT: AA 410 CYS cc_start: 0.8695 (t) cc_final: 0.8457 (t) REVERT: AA 440 MET cc_start: 0.9148 (tmm) cc_final: 0.8900 (tmm) REVERT: AB 65 VAL cc_start: 0.9455 (m) cc_final: 0.8578 (m) REVERT: AB 89 LEU cc_start: 0.9361 (mt) cc_final: 0.9031 (mp) REVERT: AB 119 MET cc_start: 0.8495 (ttm) cc_final: 0.8005 (ttm) REVERT: AB 177 LEU cc_start: 0.9389 (tp) cc_final: 0.9175 (tp) REVERT: AC 53 MET cc_start: 0.8911 (mtp) cc_final: 0.8699 (mtp) REVERT: AC 82 MET cc_start: 0.8762 (mtt) cc_final: 0.8483 (mtt) REVERT: AC 113 TRP cc_start: 0.9212 (t-100) cc_final: 0.8847 (t-100) REVERT: AC 165 TRP cc_start: 0.6848 (m-10) cc_final: 0.6358 (m-10) REVERT: AC 187 PHE cc_start: 0.9387 (m-80) cc_final: 0.9015 (m-80) REVERT: AC 268 ILE cc_start: 0.7884 (mt) cc_final: 0.7600 (mt) REVERT: AC 269 LYS cc_start: 0.7745 (mmmm) cc_final: 0.7330 (tppt) REVERT: AC 271 GLU cc_start: 0.8431 (tp30) cc_final: 0.7839 (tp30) REVERT: AC 344 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8219 (pm20) REVERT: AD 174 TYR cc_start: 0.8626 (m-80) cc_final: 0.8412 (m-80) REVERT: AD 213 SER cc_start: 0.8718 (m) cc_final: 0.7989 (p) REVERT: AD 214 LEU cc_start: 0.9538 (tp) cc_final: 0.9311 (tp) REVERT: AE 80 HIS cc_start: 0.5583 (p-80) cc_final: 0.5374 (p-80) REVERT: AF 62 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8601 (ptp90) REVERT: AF 76 LEU cc_start: 0.9344 (mt) cc_final: 0.9137 (mt) REVERT: AF 108 TRP cc_start: 0.9148 (t-100) cc_final: 0.8432 (t-100) REVERT: AG 19 LEU cc_start: 0.8870 (tp) cc_final: 0.8646 (tp) REVERT: AG 33 LYS cc_start: 0.9234 (mttp) cc_final: 0.8924 (mmmm) REVERT: AH 32 ARG cc_start: 0.9195 (tmt-80) cc_final: 0.8925 (ttm-80) REVERT: AI 20 ARG cc_start: 0.7101 (ttt-90) cc_final: 0.6297 (mtm-85) REVERT: AI 67 THR cc_start: 0.8442 (m) cc_final: 0.7927 (p) REVERT: AK 39 ARG cc_start: 0.7224 (mtt90) cc_final: 0.6934 (pmt170) REVERT: Aa 99 LYS cc_start: 0.7879 (mmtp) cc_final: 0.7495 (mmtm) REVERT: Aa 185 ASP cc_start: 0.8865 (m-30) cc_final: 0.8653 (m-30) REVERT: Aa 211 LEU cc_start: 0.8415 (mt) cc_final: 0.8170 (mt) REVERT: Aa 243 LEU cc_start: 0.9271 (mm) cc_final: 0.9037 (mm) REVERT: Aa 440 MET cc_start: 0.9555 (mtm) cc_final: 0.9226 (mtt) REVERT: Ab 157 GLN cc_start: 0.9408 (tp40) cc_final: 0.9160 (tp40) REVERT: Ab 218 MET cc_start: 0.8657 (mtt) cc_final: 0.7901 (mtt) REVERT: Ac 82 MET cc_start: 0.9310 (mtp) cc_final: 0.8955 (mmm) REVERT: Ac 88 SER cc_start: 0.8599 (m) cc_final: 0.8200 (p) REVERT: Ac 121 PHE cc_start: 0.8099 (m-80) cc_final: 0.7849 (m-80) REVERT: Ac 174 THR cc_start: 0.8845 (m) cc_final: 0.8180 (p) REVERT: Ac 178 PHE cc_start: 0.9257 (m-80) cc_final: 0.8846 (m-80) REVERT: Ac 183 PHE cc_start: 0.8884 (m-10) cc_final: 0.8673 (m-80) REVERT: Ac 232 ILE cc_start: 0.9515 (tp) cc_final: 0.9294 (tp) REVERT: Ac 275 LEU cc_start: 0.8880 (mt) cc_final: 0.8501 (mt) REVERT: Ac 316 MET cc_start: 0.9108 (tpp) cc_final: 0.8738 (mmm) REVERT: Ad 276 TRP cc_start: 0.8692 (t60) cc_final: 0.8307 (t60) REVERT: Ad 288 MET cc_start: 0.7736 (mmt) cc_final: 0.7247 (mmt) REVERT: Ae 121 THR cc_start: 0.9292 (m) cc_final: 0.9041 (m) REVERT: Ae 168 LYS cc_start: 0.8639 (pttp) cc_final: 0.7946 (mmmt) REVERT: Af 33 MET cc_start: 0.8426 (mmm) cc_final: 0.7861 (mmm) REVERT: Af 54 ASP cc_start: 0.8933 (p0) cc_final: 0.8707 (p0) REVERT: Af 56 TYR cc_start: 0.8676 (t80) cc_final: 0.8359 (t80) REVERT: Af 69 LEU cc_start: 0.9584 (mm) cc_final: 0.9313 (mm) REVERT: Af 71 MET cc_start: 0.9092 (tmm) cc_final: 0.8745 (tmm) REVERT: Af 83 LYS cc_start: 0.7478 (mptt) cc_final: 0.7085 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7887 (mt) cc_final: 0.7621 (mt) REVERT: Aj 23 LEU cc_start: 0.9621 (tp) cc_final: 0.9361 (mt) REVERT: Ak 34 TRP cc_start: 0.8328 (t60) cc_final: 0.8069 (t60) REVERT: Ak 49 ASN cc_start: 0.7177 (t0) cc_final: 0.6852 (t0) outliers start: 5 outliers final: 1 residues processed: 681 average time/residue: 0.2087 time to fit residues: 231.2334 Evaluate side-chains 512 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 362 optimal weight: 6.9990 chunk 281 optimal weight: 0.2980 chunk 94 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 44 GLN AC 68 HIS AC 221 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 242 HIS AH 34 HIS Aa 128 HIS Aa 373 GLN Ab 227 HIS Ac 341 GLN ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.070338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.055480 restraints weight = 181158.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057055 restraints weight = 111501.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058221 restraints weight = 79511.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.059001 restraints weight = 62049.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.059474 restraints weight = 51678.959| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.615 32231 Z= 0.141 Angle : 0.664 13.795 43741 Z= 0.326 Chirality : 0.043 0.336 4751 Planarity : 0.004 0.071 5547 Dihedral : 9.751 135.974 4562 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.09 % Allowed : 1.55 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.14), residues: 3844 helix: 1.11 (0.11), residues: 2119 sheet: -0.07 (0.26), residues: 378 loop : -0.18 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARGAb 196 TYR 0.037 0.002 TYRAB 71 PHE 0.024 0.002 PHEAJ 36 TRP 0.021 0.001 TRPAD 96 HIS 0.019 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00323 (32216) covalent geometry : angle 0.66333 (43727) SS BOND : bond 0.00447 ( 7) SS BOND : angle 1.08858 ( 14) hydrogen bonds : bond 0.04149 ( 1849) hydrogen bonds : angle 4.90175 ( 5301) Misc. bond : bond 0.32404 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 667 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 224 TYR cc_start: 0.9184 (m-10) cc_final: 0.8769 (m-10) REVERT: AA 244 ASP cc_start: 0.8506 (m-30) cc_final: 0.7967 (m-30) REVERT: AA 376 TRP cc_start: 0.8834 (m-10) cc_final: 0.7912 (m-90) REVERT: AA 440 MET cc_start: 0.9162 (tmm) cc_final: 0.8914 (tmm) REVERT: AB 39 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7894 (mp0) REVERT: AB 89 LEU cc_start: 0.9351 (mt) cc_final: 0.9079 (mp) REVERT: AB 119 MET cc_start: 0.8536 (ttm) cc_final: 0.8154 (ttm) REVERT: AB 407 MET cc_start: 0.9266 (tpt) cc_final: 0.8986 (tpt) REVERT: AB 438 MET cc_start: 0.6486 (ptt) cc_final: 0.6283 (ptt) REVERT: AC 82 MET cc_start: 0.8791 (mtt) cc_final: 0.8519 (mtt) REVERT: AC 165 TRP cc_start: 0.7308 (m-10) cc_final: 0.6604 (m-10) REVERT: AC 187 PHE cc_start: 0.9239 (m-80) cc_final: 0.9005 (m-80) REVERT: AC 271 GLU cc_start: 0.8477 (tp30) cc_final: 0.7960 (tp30) REVERT: AD 214 LEU cc_start: 0.9497 (tp) cc_final: 0.9205 (tp) REVERT: AE 90 ASP cc_start: 0.8584 (p0) cc_final: 0.8372 (p0) REVERT: AF 101 GLU cc_start: 0.8949 (pt0) cc_final: 0.8738 (pt0) REVERT: AF 108 TRP cc_start: 0.9107 (t-100) cc_final: 0.8361 (t-100) REVERT: AG 19 LEU cc_start: 0.8809 (tp) cc_final: 0.8577 (tp) REVERT: AH 73 LEU cc_start: 0.9569 (mt) cc_final: 0.9358 (mt) REVERT: AI 20 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6410 (mtm-85) REVERT: AK 39 ARG cc_start: 0.7181 (mtt90) cc_final: 0.6853 (pmt170) REVERT: Aa 179 MET cc_start: 0.7582 (mtm) cc_final: 0.7344 (mtm) REVERT: Aa 211 LEU cc_start: 0.8373 (mt) cc_final: 0.8102 (mt) REVERT: Aa 220 LEU cc_start: 0.9358 (tp) cc_final: 0.8486 (tp) REVERT: Aa 243 LEU cc_start: 0.9266 (mm) cc_final: 0.9029 (mm) REVERT: Aa 440 MET cc_start: 0.9551 (mtm) cc_final: 0.9228 (mtt) REVERT: Aa 445 CYS cc_start: 0.7753 (t) cc_final: 0.7433 (t) REVERT: Ab 134 MET cc_start: 0.8938 (ptt) cc_final: 0.8720 (ptt) REVERT: Ab 157 GLN cc_start: 0.9403 (tp40) cc_final: 0.9182 (tp40) REVERT: Ab 218 MET cc_start: 0.8741 (mtt) cc_final: 0.7948 (mtt) REVERT: Ac 88 SER cc_start: 0.8615 (m) cc_final: 0.8201 (p) REVERT: Ac 121 PHE cc_start: 0.8070 (m-80) cc_final: 0.7805 (m-80) REVERT: Ac 174 THR cc_start: 0.8839 (m) cc_final: 0.8525 (p) REVERT: Ac 178 PHE cc_start: 0.9273 (m-80) cc_final: 0.8962 (m-80) REVERT: Ac 183 PHE cc_start: 0.8861 (m-10) cc_final: 0.8659 (m-80) REVERT: Ac 275 LEU cc_start: 0.8772 (mt) cc_final: 0.8482 (mt) REVERT: Ac 312 GLN cc_start: 0.7390 (mm110) cc_final: 0.6626 (tp-100) REVERT: Ac 316 MET cc_start: 0.9080 (tpp) cc_final: 0.8869 (mmm) REVERT: Ac 328 LEU cc_start: 0.9031 (tp) cc_final: 0.8816 (tp) REVERT: Ad 276 TRP cc_start: 0.8680 (t60) cc_final: 0.8321 (t60) REVERT: Ad 288 MET cc_start: 0.7744 (mmt) cc_final: 0.7249 (mmt) REVERT: Ad 292 MET cc_start: 0.8753 (ttp) cc_final: 0.8179 (tmm) REVERT: Ae 168 LYS cc_start: 0.8620 (pttp) cc_final: 0.7917 (mmmt) REVERT: Af 33 MET cc_start: 0.8407 (mmm) cc_final: 0.8000 (mmm) REVERT: Af 54 ASP cc_start: 0.8915 (p0) cc_final: 0.8683 (p0) REVERT: Af 56 TYR cc_start: 0.8659 (t80) cc_final: 0.8131 (t80) REVERT: Af 60 MET cc_start: 0.9232 (mmm) cc_final: 0.8892 (mtp) REVERT: Af 69 LEU cc_start: 0.9582 (mm) cc_final: 0.9296 (mm) REVERT: Af 83 LYS cc_start: 0.7558 (mptt) cc_final: 0.7210 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7832 (mt) cc_final: 0.7585 (mt) REVERT: Ah 45 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8825 (ttp80) REVERT: Ah 84 LEU cc_start: 0.8443 (tp) cc_final: 0.8237 (tp) REVERT: Aj 23 LEU cc_start: 0.9615 (tp) cc_final: 0.9370 (mt) REVERT: Ak 23 MET cc_start: 0.8159 (mtt) cc_final: 0.7949 (mtt) REVERT: Ak 49 ASN cc_start: 0.7249 (t0) cc_final: 0.6930 (t0) outliers start: 3 outliers final: 0 residues processed: 669 average time/residue: 0.1873 time to fit residues: 203.9311 Evaluate side-chains 507 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 123 optimal weight: 20.0000 chunk 365 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 327 optimal weight: 6.9990 chunk 283 optimal weight: 0.6980 chunk 306 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 258 optimal weight: 0.6980 chunk 354 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 160 GLN AB 188 ASN ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 68 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS AE 242 HIS AH 34 HIS Aa 95 HIS Aa 128 HIS Ac 345 HIS ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.070779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.056070 restraints weight = 181490.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057646 restraints weight = 112184.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.058759 restraints weight = 80048.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059503 restraints weight = 62753.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.059968 restraints weight = 52705.673| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.586 32231 Z= 0.135 Angle : 0.655 12.934 43741 Z= 0.321 Chirality : 0.042 0.337 4751 Planarity : 0.004 0.067 5547 Dihedral : 9.598 137.848 4562 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.03 % Allowed : 1.24 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.14), residues: 3844 helix: 1.14 (0.11), residues: 2125 sheet: -0.12 (0.26), residues: 377 loop : -0.17 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAB 217 TYR 0.026 0.001 TYRAB 71 PHE 0.048 0.002 PHEAC 183 TRP 0.033 0.001 TRPAK 34 HIS 0.013 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00306 (32216) covalent geometry : angle 0.65475 (43727) SS BOND : bond 0.00152 ( 7) SS BOND : angle 0.81776 ( 14) hydrogen bonds : bond 0.03975 ( 1849) hydrogen bonds : angle 4.78301 ( 5301) Misc. bond : bond 0.30615 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 657 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 107 ASN cc_start: 0.9171 (p0) cc_final: 0.8835 (p0) REVERT: AA 185 ASP cc_start: 0.8962 (m-30) cc_final: 0.8757 (m-30) REVERT: AA 224 TYR cc_start: 0.9194 (m-10) cc_final: 0.8736 (m-10) REVERT: AA 244 ASP cc_start: 0.8357 (m-30) cc_final: 0.8048 (m-30) REVERT: AA 376 TRP cc_start: 0.8847 (m-10) cc_final: 0.7859 (m-90) REVERT: AA 441 LEU cc_start: 0.9658 (tt) cc_final: 0.9383 (mt) REVERT: AB 39 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7934 (mp0) REVERT: AB 89 LEU cc_start: 0.9367 (mt) cc_final: 0.9120 (mp) REVERT: AB 119 MET cc_start: 0.8559 (ttm) cc_final: 0.8251 (ttm) REVERT: AB 438 MET cc_start: 0.6521 (ptt) cc_final: 0.6254 (ptt) REVERT: AC 111 GLU cc_start: 0.8977 (pp20) cc_final: 0.8461 (pp20) REVERT: AC 271 GLU cc_start: 0.8494 (tp30) cc_final: 0.7982 (tp30) REVERT: AD 214 LEU cc_start: 0.9431 (tp) cc_final: 0.9152 (tp) REVERT: AD 215 LEU cc_start: 0.8830 (mm) cc_final: 0.8558 (mm) REVERT: AE 90 ASP cc_start: 0.8647 (p0) cc_final: 0.8425 (p0) REVERT: AF 62 ARG cc_start: 0.8981 (mtm110) cc_final: 0.8556 (mtm180) REVERT: AF 108 TRP cc_start: 0.9104 (t-100) cc_final: 0.8419 (t-100) REVERT: AF 110 LYS cc_start: 0.8188 (pttp) cc_final: 0.7979 (pptt) REVERT: AG 15 ILE cc_start: 0.8885 (mp) cc_final: 0.8595 (tp) REVERT: AG 19 LEU cc_start: 0.8745 (tp) cc_final: 0.8293 (tp) REVERT: AG 33 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8856 (mmmm) REVERT: AH 47 ARG cc_start: 0.9072 (tmt-80) cc_final: 0.8846 (tpt90) REVERT: AH 73 LEU cc_start: 0.9586 (mt) cc_final: 0.9345 (mt) REVERT: AI 20 ARG cc_start: 0.7008 (ttt-90) cc_final: 0.6422 (mtm-85) REVERT: AI 67 THR cc_start: 0.8338 (m) cc_final: 0.7841 (p) REVERT: AK 39 ARG cc_start: 0.7130 (mtt90) cc_final: 0.6762 (pmt170) REVERT: Aa 211 LEU cc_start: 0.8360 (mt) cc_final: 0.8077 (mt) REVERT: Aa 220 LEU cc_start: 0.9447 (tp) cc_final: 0.9018 (tp) REVERT: Aa 243 LEU cc_start: 0.9301 (mm) cc_final: 0.9074 (mm) REVERT: Aa 440 MET cc_start: 0.9574 (mtm) cc_final: 0.9242 (mtt) REVERT: Aa 445 CYS cc_start: 0.7823 (t) cc_final: 0.7507 (t) REVERT: Aa 477 TRP cc_start: 0.8690 (m-10) cc_final: 0.8438 (m-10) REVERT: Ab 134 MET cc_start: 0.8966 (ptt) cc_final: 0.8731 (ptt) REVERT: Ab 157 GLN cc_start: 0.9408 (tp40) cc_final: 0.9072 (tp40) REVERT: Ab 218 MET cc_start: 0.8804 (mtt) cc_final: 0.7999 (mtt) REVERT: Ab 240 MET cc_start: 0.7844 (pmm) cc_final: 0.7642 (pmm) REVERT: Ac 64 SER cc_start: 0.9678 (m) cc_final: 0.9393 (p) REVERT: Ac 88 SER cc_start: 0.8598 (m) cc_final: 0.8281 (p) REVERT: Ac 121 PHE cc_start: 0.8053 (m-80) cc_final: 0.7791 (m-80) REVERT: Ac 174 THR cc_start: 0.8726 (m) cc_final: 0.8384 (p) REVERT: Ac 178 PHE cc_start: 0.9274 (m-80) cc_final: 0.8974 (m-80) REVERT: Ac 240 MET cc_start: 0.8932 (mmm) cc_final: 0.8634 (mmt) REVERT: Ac 254 ASP cc_start: 0.7869 (t0) cc_final: 0.7600 (t0) REVERT: Ac 304 MET cc_start: 0.8644 (tpp) cc_final: 0.8388 (tpt) REVERT: Ac 312 GLN cc_start: 0.7299 (mm110) cc_final: 0.6888 (tp-100) REVERT: Ac 328 LEU cc_start: 0.9072 (tp) cc_final: 0.8856 (tp) REVERT: Ad 127 MET cc_start: 0.8737 (mmm) cc_final: 0.8341 (mmm) REVERT: Ad 276 TRP cc_start: 0.8712 (t60) cc_final: 0.8376 (t60) REVERT: Ad 292 MET cc_start: 0.8874 (ttp) cc_final: 0.8208 (tmm) REVERT: Ae 168 LYS cc_start: 0.8601 (pttp) cc_final: 0.7905 (mmmt) REVERT: Af 32 LEU cc_start: 0.8318 (tp) cc_final: 0.8071 (tp) REVERT: Af 33 MET cc_start: 0.8471 (mmm) cc_final: 0.7874 (mmm) REVERT: Af 54 ASP cc_start: 0.8970 (p0) cc_final: 0.8617 (p0) REVERT: Af 56 TYR cc_start: 0.8725 (t80) cc_final: 0.8464 (t80) REVERT: Af 58 ASP cc_start: 0.8288 (m-30) cc_final: 0.8074 (m-30) REVERT: Af 69 LEU cc_start: 0.9585 (mm) cc_final: 0.9278 (mm) REVERT: Af 71 MET cc_start: 0.9084 (tmm) cc_final: 0.8721 (tmm) REVERT: Af 83 LYS cc_start: 0.7616 (mptt) cc_final: 0.7259 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7770 (mt) cc_final: 0.7450 (mt) REVERT: Ag 17 TYR cc_start: 0.8753 (m-80) cc_final: 0.8529 (m-80) REVERT: Ah 45 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8708 (ttp80) REVERT: Aj 23 LEU cc_start: 0.9608 (tp) cc_final: 0.9361 (mt) REVERT: Ak 23 MET cc_start: 0.8101 (mtt) cc_final: 0.7855 (mtt) REVERT: Ak 49 ASN cc_start: 0.7367 (t0) cc_final: 0.7068 (t0) outliers start: 1 outliers final: 0 residues processed: 658 average time/residue: 0.1852 time to fit residues: 200.1516 Evaluate side-chains 514 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 171 optimal weight: 0.5980 chunk 316 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 191 optimal weight: 30.0000 chunk 254 optimal weight: 6.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 95 HIS AA 181 ASN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 267 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN AE 200 HIS AE 242 HIS Aa 128 HIS ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 446 HIS ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 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 = 0.3593 r_free = 0.3593 target = 0.067119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052480 restraints weight = 187571.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053996 restraints weight = 117126.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055026 restraints weight = 83808.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055754 restraints weight = 66080.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.056177 restraints weight = 55718.826| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.823 32231 Z= 0.238 Angle : 0.749 18.219 43741 Z= 0.369 Chirality : 0.044 0.349 4751 Planarity : 0.005 0.071 5547 Dihedral : 9.688 140.844 4562 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 1.36 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.14), residues: 3844 helix: 0.94 (0.11), residues: 2126 sheet: -0.18 (0.26), residues: 377 loop : -0.32 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGAJ 34 TYR 0.025 0.002 TYRAd 236 PHE 0.026 0.002 PHEAC 121 TRP 0.043 0.002 TRPAK 34 HIS 0.015 0.002 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00533 (32216) covalent geometry : angle 0.74827 (43727) SS BOND : bond 0.00631 ( 7) SS BOND : angle 1.46980 ( 14) hydrogen bonds : bond 0.04382 ( 1849) hydrogen bonds : angle 5.01748 ( 5301) Misc. bond : bond 0.40604 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 597 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 131 TYR cc_start: 0.7775 (m-80) cc_final: 0.7492 (m-80) REVERT: AA 185 ASP cc_start: 0.8998 (m-30) cc_final: 0.8777 (m-30) REVERT: AA 224 TYR cc_start: 0.9297 (m-10) cc_final: 0.8886 (m-10) REVERT: AA 244 ASP cc_start: 0.8567 (m-30) cc_final: 0.8204 (m-30) REVERT: AA 354 LEU cc_start: 0.8957 (tp) cc_final: 0.8726 (tp) REVERT: AA 368 MET cc_start: 0.7676 (mmm) cc_final: 0.7399 (mtp) REVERT: AA 376 TRP cc_start: 0.9013 (m-10) cc_final: 0.8006 (m-90) REVERT: AA 377 MET cc_start: 0.8721 (tpp) cc_final: 0.8333 (tpp) REVERT: AB 39 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7901 (mp0) REVERT: AB 89 LEU cc_start: 0.9522 (mt) cc_final: 0.9214 (mp) REVERT: AB 119 MET cc_start: 0.8645 (ttm) cc_final: 0.8183 (ttm) REVERT: AB 121 TYR cc_start: 0.8438 (m-10) cc_final: 0.7808 (m-10) REVERT: AB 177 LEU cc_start: 0.9512 (tp) cc_final: 0.9291 (tp) REVERT: AB 407 MET cc_start: 0.9559 (tpp) cc_final: 0.9110 (tpt) REVERT: AB 438 MET cc_start: 0.6690 (ptt) cc_final: 0.6486 (ptt) REVERT: AC 82 MET cc_start: 0.8665 (mtp) cc_final: 0.8418 (mtp) REVERT: AC 111 GLU cc_start: 0.8971 (pp20) cc_final: 0.8392 (pp20) REVERT: AC 181 PHE cc_start: 0.8862 (m-80) cc_final: 0.8659 (m-80) REVERT: AC 312 GLN cc_start: 0.7445 (tp-100) cc_final: 0.6989 (tp-100) REVERT: AD 127 MET cc_start: 0.7893 (mtm) cc_final: 0.7200 (mtp) REVERT: AD 214 LEU cc_start: 0.9443 (tp) cc_final: 0.9235 (tp) REVERT: AD 259 THR cc_start: 0.8064 (t) cc_final: 0.7819 (p) REVERT: AE 90 ASP cc_start: 0.8776 (p0) cc_final: 0.8519 (p0) REVERT: AE 140 MET cc_start: 0.6598 (tmm) cc_final: 0.6201 (tmm) REVERT: AF 62 ARG cc_start: 0.8930 (mtm110) cc_final: 0.8606 (mtm180) REVERT: AF 108 TRP cc_start: 0.9104 (t-100) cc_final: 0.8549 (t-100) REVERT: AG 11 ILE cc_start: 0.8706 (mp) cc_final: 0.8495 (mp) REVERT: AG 19 LEU cc_start: 0.8864 (tp) cc_final: 0.8321 (tp) REVERT: AH 47 ARG cc_start: 0.9102 (tmt-80) cc_final: 0.8837 (tpt90) REVERT: AI 20 ARG cc_start: 0.7158 (ttt-90) cc_final: 0.6483 (mtm-85) REVERT: AK 27 VAL cc_start: 0.4200 (t) cc_final: 0.3956 (t) REVERT: AK 39 ARG cc_start: 0.7128 (mtt90) cc_final: 0.6784 (pmt170) REVERT: Aa 76 ASP cc_start: 0.8723 (p0) cc_final: 0.8348 (p0) REVERT: Aa 128 HIS cc_start: 0.8027 (m-70) cc_final: 0.7805 (m170) REVERT: Aa 172 MET cc_start: 0.8504 (ppp) cc_final: 0.8254 (ppp) REVERT: Aa 185 ASP cc_start: 0.8971 (m-30) cc_final: 0.8755 (m-30) REVERT: Aa 211 LEU cc_start: 0.8582 (mt) cc_final: 0.8245 (mt) REVERT: Aa 243 LEU cc_start: 0.9363 (mm) cc_final: 0.9097 (mm) REVERT: Aa 440 MET cc_start: 0.9598 (mtm) cc_final: 0.9101 (mpp) REVERT: Aa 445 CYS cc_start: 0.7737 (t) cc_final: 0.7405 (t) REVERT: Ab 134 MET cc_start: 0.9046 (ptt) cc_final: 0.8814 (ptt) REVERT: Ab 218 MET cc_start: 0.8998 (mtt) cc_final: 0.8174 (mtt) REVERT: Ab 240 MET cc_start: 0.7915 (pmm) cc_final: 0.7661 (pmm) REVERT: Ac 88 SER cc_start: 0.8647 (m) cc_final: 0.8348 (p) REVERT: Ac 113 TRP cc_start: 0.8977 (t-100) cc_final: 0.8628 (t-100) REVERT: Ac 121 PHE cc_start: 0.8452 (m-80) cc_final: 0.8143 (m-80) REVERT: Ac 178 PHE cc_start: 0.9276 (m-80) cc_final: 0.8857 (m-80) REVERT: Ac 183 PHE cc_start: 0.8857 (m-10) cc_final: 0.8582 (t80) REVERT: Ac 254 ASP cc_start: 0.8180 (t0) cc_final: 0.7806 (t0) REVERT: Ac 304 MET cc_start: 0.8784 (tpp) cc_final: 0.8456 (tpt) REVERT: Ac 312 GLN cc_start: 0.7353 (mm110) cc_final: 0.6991 (tp-100) REVERT: Ad 276 TRP cc_start: 0.8889 (t60) cc_final: 0.8577 (t60) REVERT: Ad 288 MET cc_start: 0.7771 (mmt) cc_final: 0.7260 (mmt) REVERT: Ae 149 MET cc_start: 0.8767 (mmp) cc_final: 0.8503 (mmp) REVERT: Ae 161 GLU cc_start: 0.6071 (mm-30) cc_final: 0.5531 (tp30) REVERT: Ae 175 PHE cc_start: 0.8227 (m-10) cc_final: 0.7970 (m-10) REVERT: Af 32 LEU cc_start: 0.8236 (tp) cc_final: 0.7916 (tp) REVERT: Af 33 MET cc_start: 0.8629 (mmm) cc_final: 0.8294 (mmm) REVERT: Af 54 ASP cc_start: 0.9035 (p0) cc_final: 0.8731 (p0) REVERT: Af 56 TYR cc_start: 0.8839 (t80) cc_final: 0.8347 (t80) REVERT: Af 58 ASP cc_start: 0.8477 (m-30) cc_final: 0.8276 (m-30) REVERT: Af 60 MET cc_start: 0.9322 (mmm) cc_final: 0.9000 (mtp) REVERT: Af 71 MET cc_start: 0.9113 (tmm) cc_final: 0.8683 (tmm) REVERT: Ag 17 TYR cc_start: 0.8893 (m-80) cc_final: 0.8688 (m-80) REVERT: Ah 45 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8770 (ttp80) REVERT: Aj 23 LEU cc_start: 0.9633 (tp) cc_final: 0.9408 (mt) REVERT: Ak 23 MET cc_start: 0.8177 (mtt) cc_final: 0.7905 (mtt) REVERT: Ak 34 TRP cc_start: 0.8232 (t60) cc_final: 0.7948 (t60) REVERT: Ak 49 ASN cc_start: 0.7421 (t0) cc_final: 0.7120 (t0) outliers start: 1 outliers final: 0 residues processed: 598 average time/residue: 0.1715 time to fit residues: 167.6654 Evaluate side-chains 483 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 296 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 290 optimal weight: 0.9990 chunk 171 optimal weight: 0.3980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 227 HIS ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 68 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS AE 242 HIS Aa 207 ASN ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.069383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054547 restraints weight = 181558.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.056121 restraints weight = 112565.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.057177 restraints weight = 80382.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057841 restraints weight = 63327.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058409 restraints weight = 53821.910| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.628 32231 Z= 0.138 Angle : 0.676 13.519 43741 Z= 0.330 Chirality : 0.043 0.351 4751 Planarity : 0.004 0.061 5547 Dihedral : 9.467 137.730 4562 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.14), residues: 3844 helix: 1.10 (0.11), residues: 2128 sheet: -0.05 (0.26), residues: 363 loop : -0.24 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGAb 172 TYR 0.021 0.001 TYRAf 21 PHE 0.040 0.002 PHEAC 183 TRP 0.021 0.001 TRPAa 376 HIS 0.014 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00319 (32216) covalent geometry : angle 0.67573 (43727) SS BOND : bond 0.00745 ( 7) SS BOND : angle 1.31050 ( 14) hydrogen bonds : bond 0.04001 ( 1849) hydrogen bonds : angle 4.82076 ( 5301) Misc. bond : bond 0.30497 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 630 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 185 ASP cc_start: 0.8959 (m-30) cc_final: 0.8722 (m-30) REVERT: AA 224 TYR cc_start: 0.9250 (m-10) cc_final: 0.8851 (m-10) REVERT: AA 244 ASP cc_start: 0.8533 (m-30) cc_final: 0.8052 (m-30) REVERT: AA 368 MET cc_start: 0.7642 (mmm) cc_final: 0.7250 (mtp) REVERT: AA 410 CYS cc_start: 0.8973 (t) cc_final: 0.8771 (t) REVERT: AB 89 LEU cc_start: 0.9466 (mt) cc_final: 0.9201 (mp) REVERT: AB 119 MET cc_start: 0.8605 (ttm) cc_final: 0.7834 (ttm) REVERT: AB 121 TYR cc_start: 0.8422 (m-80) cc_final: 0.7799 (m-10) REVERT: AB 133 LEU cc_start: 0.9523 (mt) cc_final: 0.9316 (mt) REVERT: AB 197 MET cc_start: 0.9360 (mpp) cc_final: 0.8849 (mpp) REVERT: AB 384 MET cc_start: 0.9113 (mtm) cc_final: 0.8738 (ptm) REVERT: AB 407 MET cc_start: 0.9530 (tpp) cc_final: 0.9076 (tpt) REVERT: AB 438 MET cc_start: 0.6580 (ptt) cc_final: 0.6178 (ptt) REVERT: AC 111 GLU cc_start: 0.8980 (pp20) cc_final: 0.8704 (tm-30) REVERT: AC 271 GLU cc_start: 0.8708 (tp30) cc_final: 0.7930 (tp30) REVERT: AD 127 MET cc_start: 0.7789 (mtm) cc_final: 0.7084 (mtp) REVERT: AD 214 LEU cc_start: 0.9423 (tp) cc_final: 0.9193 (tp) REVERT: AD 259 THR cc_start: 0.8006 (t) cc_final: 0.7662 (p) REVERT: AE 90 ASP cc_start: 0.8782 (p0) cc_final: 0.8495 (p0) REVERT: AF 62 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8615 (mtm180) REVERT: AF 101 GLU cc_start: 0.8981 (pt0) cc_final: 0.8731 (pt0) REVERT: AF 108 TRP cc_start: 0.9069 (t-100) cc_final: 0.8280 (t-100) REVERT: AG 19 LEU cc_start: 0.8827 (tp) cc_final: 0.8230 (tt) REVERT: AG 33 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8807 (mmmm) REVERT: AH 47 ARG cc_start: 0.9126 (tmt-80) cc_final: 0.8839 (tpt90) REVERT: AI 20 ARG cc_start: 0.7025 (ttt-90) cc_final: 0.6456 (mtm-85) REVERT: AI 67 THR cc_start: 0.8450 (m) cc_final: 0.7928 (p) REVERT: AK 27 VAL cc_start: 0.4327 (t) cc_final: 0.4016 (t) REVERT: AK 39 ARG cc_start: 0.7179 (mtt90) cc_final: 0.6790 (pmt170) REVERT: Aa 76 ASP cc_start: 0.8685 (p0) cc_final: 0.8463 (p0) REVERT: Aa 128 HIS cc_start: 0.8191 (m-70) cc_final: 0.7927 (m170) REVERT: Aa 179 MET cc_start: 0.7853 (mtm) cc_final: 0.7621 (mtm) REVERT: Aa 211 LEU cc_start: 0.8448 (mt) cc_final: 0.8092 (mt) REVERT: Aa 220 LEU cc_start: 0.9326 (tp) cc_final: 0.9113 (tp) REVERT: Aa 224 TYR cc_start: 0.7865 (m-80) cc_final: 0.7444 (m-80) REVERT: Aa 243 LEU cc_start: 0.9345 (mm) cc_final: 0.9098 (mm) REVERT: Aa 368 MET cc_start: 0.6328 (mtm) cc_final: 0.5407 (ttm) REVERT: Aa 440 MET cc_start: 0.9592 (mtm) cc_final: 0.9285 (mtt) REVERT: Aa 445 CYS cc_start: 0.7705 (t) cc_final: 0.7355 (t) REVERT: Aa 477 TRP cc_start: 0.8690 (m-10) cc_final: 0.8140 (m-10) REVERT: Ab 134 MET cc_start: 0.9006 (ptt) cc_final: 0.8776 (ptt) REVERT: Ab 218 MET cc_start: 0.8939 (mtt) cc_final: 0.8158 (mtt) REVERT: Ab 387 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6354 (tp30) REVERT: Ac 53 MET cc_start: 0.8573 (ptm) cc_final: 0.8359 (ptm) REVERT: Ac 64 SER cc_start: 0.9700 (m) cc_final: 0.9318 (p) REVERT: Ac 88 SER cc_start: 0.8693 (m) cc_final: 0.8281 (t) REVERT: Ac 121 PHE cc_start: 0.8180 (m-80) cc_final: 0.7920 (m-80) REVERT: Ac 178 PHE cc_start: 0.9283 (m-80) cc_final: 0.8853 (m-80) REVERT: Ac 183 PHE cc_start: 0.8870 (m-10) cc_final: 0.8607 (t80) REVERT: Ac 197 LEU cc_start: 0.9495 (mm) cc_final: 0.9279 (tt) REVERT: Ac 254 ASP cc_start: 0.8212 (t0) cc_final: 0.7735 (t0) REVERT: Ac 312 GLN cc_start: 0.7417 (mm110) cc_final: 0.7190 (tp-100) REVERT: Ac 315 LEU cc_start: 0.8814 (mt) cc_final: 0.8566 (tp) REVERT: Ac 358 TYR cc_start: 0.8456 (t80) cc_final: 0.8216 (t80) REVERT: Ad 127 MET cc_start: 0.8707 (mmm) cc_final: 0.8257 (mmm) REVERT: Ad 276 TRP cc_start: 0.8820 (t60) cc_final: 0.8517 (t60) REVERT: Ad 288 MET cc_start: 0.7697 (mmt) cc_final: 0.7237 (mmt) REVERT: Af 32 LEU cc_start: 0.8237 (tp) cc_final: 0.7914 (tp) REVERT: Af 33 MET cc_start: 0.8476 (mmm) cc_final: 0.8245 (mmm) REVERT: Af 54 ASP cc_start: 0.9058 (p0) cc_final: 0.8809 (p0) REVERT: Af 56 TYR cc_start: 0.8778 (t80) cc_final: 0.8225 (t80) REVERT: Af 60 MET cc_start: 0.9295 (mmm) cc_final: 0.8972 (mtp) REVERT: Af 71 MET cc_start: 0.9131 (tmm) cc_final: 0.8722 (tmm) REVERT: Ag 8 LEU cc_start: 0.7846 (mt) cc_final: 0.7631 (mt) REVERT: Ah 45 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8731 (ttp80) REVERT: Aj 23 LEU cc_start: 0.9619 (tp) cc_final: 0.9376 (mt) REVERT: Ak 23 MET cc_start: 0.8002 (mtt) cc_final: 0.7727 (mtt) REVERT: Ak 34 TRP cc_start: 0.8176 (t60) cc_final: 0.7850 (t60) REVERT: Ak 49 ASN cc_start: 0.7450 (t0) cc_final: 0.7155 (t0) outliers start: 1 outliers final: 0 residues processed: 631 average time/residue: 0.1750 time to fit residues: 182.2269 Evaluate side-chains 501 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 132 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 294 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 overall best weight: 2.4162 ------------------------------------------------------------------------------- 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 68 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 189 ASN AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS AE 242 HIS ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.068444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053713 restraints weight = 183891.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055254 restraints weight = 114833.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.056286 restraints weight = 82131.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.057000 restraints weight = 65031.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057444 restraints weight = 54926.497| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.707 32231 Z= 0.171 Angle : 0.707 14.660 43741 Z= 0.351 Chirality : 0.044 0.322 4751 Planarity : 0.004 0.076 5547 Dihedral : 9.422 139.226 4562 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.14), residues: 3844 helix: 1.02 (0.11), residues: 2131 sheet: -0.19 (0.26), residues: 373 loop : -0.23 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAD 285 TYR 0.022 0.002 TYRAf 21 PHE 0.031 0.002 PHEAJ 36 TRP 0.023 0.002 TRPAC 77 HIS 0.014 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00398 (32216) covalent geometry : angle 0.70649 (43727) SS BOND : bond 0.00554 ( 7) SS BOND : angle 1.83878 ( 14) hydrogen bonds : bond 0.04145 ( 1849) hydrogen bonds : angle 4.93667 ( 5301) Misc. bond : bond 0.34751 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7688 Ramachandran restraints generated. 3844 Oldfield, 0 Emsley, 3844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 599 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 107 ASN cc_start: 0.9277 (p0) cc_final: 0.9004 (p0) REVERT: AA 131 TYR cc_start: 0.7630 (m-80) cc_final: 0.7403 (m-80) REVERT: AA 185 ASP cc_start: 0.8921 (m-30) cc_final: 0.8690 (m-30) REVERT: AA 224 TYR cc_start: 0.9182 (m-10) cc_final: 0.8980 (m-10) REVERT: AA 244 ASP cc_start: 0.8386 (m-30) cc_final: 0.8144 (m-30) REVERT: AA 354 LEU cc_start: 0.8921 (tp) cc_final: 0.8658 (tp) REVERT: AA 368 MET cc_start: 0.7580 (mmm) cc_final: 0.7302 (mtp) REVERT: AB 39 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7635 (mp0) REVERT: AB 89 LEU cc_start: 0.9483 (mt) cc_final: 0.9212 (mp) REVERT: AB 119 MET cc_start: 0.8518 (ttm) cc_final: 0.7784 (ttm) REVERT: AB 121 TYR cc_start: 0.8378 (m-80) cc_final: 0.7720 (m-10) REVERT: AB 197 MET cc_start: 0.9356 (mpp) cc_final: 0.8799 (mpp) REVERT: AB 407 MET cc_start: 0.9522 (tpp) cc_final: 0.9101 (tpt) REVERT: AC 82 MET cc_start: 0.8613 (mtp) cc_final: 0.8368 (mtp) REVERT: AC 111 GLU cc_start: 0.8983 (pp20) cc_final: 0.8658 (tm-30) REVERT: AC 235 MET cc_start: 0.9417 (tmm) cc_final: 0.9093 (tmm) REVERT: AC 271 GLU cc_start: 0.8770 (tp30) cc_final: 0.7999 (tp30) REVERT: AC 379 LEU cc_start: 0.8967 (mt) cc_final: 0.8551 (mt) REVERT: AD 127 MET cc_start: 0.7884 (mtm) cc_final: 0.7162 (mtp) REVERT: AE 90 ASP cc_start: 0.8833 (p0) cc_final: 0.8515 (p0) REVERT: AF 62 ARG cc_start: 0.8893 (mtm110) cc_final: 0.8592 (mtm180) REVERT: AF 101 GLU cc_start: 0.9012 (pt0) cc_final: 0.8797 (pt0) REVERT: AF 108 TRP cc_start: 0.9079 (t-100) cc_final: 0.8393 (t-100) REVERT: AG 19 LEU cc_start: 0.8861 (tp) cc_final: 0.8333 (tp) REVERT: AH 47 ARG cc_start: 0.9119 (tmt-80) cc_final: 0.8887 (tpt90) REVERT: AI 20 ARG cc_start: 0.7047 (ttt-90) cc_final: 0.6501 (mtm-85) REVERT: AI 67 THR cc_start: 0.8471 (m) cc_final: 0.7910 (p) REVERT: AJ 9 ARG cc_start: 0.8406 (mpp-170) cc_final: 0.8117 (mpt180) REVERT: AK 23 MET cc_start: 0.8424 (tpt) cc_final: 0.8220 (tpt) REVERT: AK 27 VAL cc_start: 0.4150 (t) cc_final: 0.3859 (t) REVERT: AK 39 ARG cc_start: 0.7062 (mtt90) cc_final: 0.6699 (pmt170) REVERT: Aa 76 ASP cc_start: 0.8507 (p0) cc_final: 0.8219 (p0) REVERT: Aa 128 HIS cc_start: 0.8137 (m-70) cc_final: 0.7886 (m170) REVERT: Aa 179 MET cc_start: 0.7824 (mtm) cc_final: 0.7573 (mtm) REVERT: Aa 211 LEU cc_start: 0.8536 (mt) cc_final: 0.8192 (mt) REVERT: Aa 220 LEU cc_start: 0.9231 (tp) cc_final: 0.8953 (tp) REVERT: Aa 224 TYR cc_start: 0.7884 (m-80) cc_final: 0.7562 (m-80) REVERT: Aa 243 LEU cc_start: 0.9302 (mm) cc_final: 0.9082 (mm) REVERT: Aa 363 MET cc_start: 0.8923 (mmp) cc_final: 0.8690 (mmp) REVERT: Aa 368 MET cc_start: 0.6036 (mtm) cc_final: 0.4937 (ttm) REVERT: Aa 440 MET cc_start: 0.9563 (mtm) cc_final: 0.9231 (mtt) REVERT: Aa 445 CYS cc_start: 0.7755 (t) cc_final: 0.7412 (t) REVERT: Aa 477 TRP cc_start: 0.8760 (m-10) cc_final: 0.8297 (m-10) REVERT: Ab 218 MET cc_start: 0.8997 (mtt) cc_final: 0.8213 (mtt) REVERT: Ab 240 MET cc_start: 0.7794 (pmm) cc_final: 0.7533 (pmm) REVERT: Ab 387 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6430 (tp30) REVERT: Ac 53 MET cc_start: 0.8614 (ptm) cc_final: 0.8410 (ptm) REVERT: Ac 64 SER cc_start: 0.9655 (m) cc_final: 0.9329 (p) REVERT: Ac 121 PHE cc_start: 0.8202 (m-80) cc_final: 0.7970 (m-80) REVERT: Ac 178 PHE cc_start: 0.9236 (m-80) cc_final: 0.8810 (m-80) REVERT: Ac 197 LEU cc_start: 0.9472 (mm) cc_final: 0.9255 (tt) REVERT: Ac 254 ASP cc_start: 0.8175 (t0) cc_final: 0.7679 (t0) REVERT: Ac 312 GLN cc_start: 0.7390 (mm110) cc_final: 0.7132 (tp-100) REVERT: Ac 328 LEU cc_start: 0.9032 (tp) cc_final: 0.8796 (tp) REVERT: Ad 276 TRP cc_start: 0.8828 (t60) cc_final: 0.8564 (t60) REVERT: Ad 292 MET cc_start: 0.8921 (ttp) cc_final: 0.8187 (tmm) REVERT: Ae 149 MET cc_start: 0.8646 (mmp) cc_final: 0.8437 (mmp) REVERT: Ae 175 PHE cc_start: 0.8144 (m-10) cc_final: 0.7886 (m-10) REVERT: Af 32 LEU cc_start: 0.8301 (tp) cc_final: 0.7955 (tp) REVERT: Af 33 MET cc_start: 0.8489 (mmm) cc_final: 0.8209 (mmm) REVERT: Af 54 ASP cc_start: 0.8972 (p0) cc_final: 0.8645 (p0) REVERT: Af 56 TYR cc_start: 0.8739 (t80) cc_final: 0.8194 (t80) REVERT: Af 60 MET cc_start: 0.9240 (mmm) cc_final: 0.8917 (mtp) REVERT: Af 71 MET cc_start: 0.9085 (tmm) cc_final: 0.8700 (tmm) REVERT: Ak 23 MET cc_start: 0.7997 (mtt) cc_final: 0.7702 (mtt) REVERT: Ak 49 ASN cc_start: 0.7443 (t0) cc_final: 0.7151 (t0) outliers start: 1 outliers final: 0 residues processed: 600 average time/residue: 0.1744 time to fit residues: 173.3713 Evaluate side-chains 482 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 176 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 319 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 346 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 366 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 347 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 63 GLN ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 313 HIS ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 68 HIS ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS AE 242 HIS ** Ab 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.068885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054225 restraints weight = 183128.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.055736 restraints weight = 113547.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.056741 restraints weight = 81290.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057504 restraints weight = 64373.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.057946 restraints weight = 54048.466| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.625 32231 Z= 0.147 Angle : 0.690 13.919 43741 Z= 0.343 Chirality : 0.043 0.296 4751 Planarity : 0.004 0.055 5547 Dihedral : 9.348 138.150 4562 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.06 % Allowed : 0.18 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.14), residues: 3844 helix: 1.06 (0.11), residues: 2125 sheet: -0.10 (0.26), residues: 365 loop : -0.20 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARGAb 60 TYR 0.022 0.002 TYRAf 21 PHE 0.035 0.002 PHEAc 183 TRP 0.021 0.002 TRPAk 34 HIS 0.014 0.001 HISAH 82 Details of bonding type rmsd covalent geometry : bond 0.00342 (32216) covalent geometry : angle 0.68950 (43727) SS BOND : bond 0.00514 ( 7) SS BOND : angle 1.68286 ( 14) hydrogen bonds : bond 0.04037 ( 1849) hydrogen bonds : angle 4.87394 ( 5301) Misc. bond : bond 0.30838 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7747.06 seconds wall clock time: 134 minutes 18.48 seconds (8058.48 seconds total)