Starting phenix.real_space_refine on Fri Jun 27 06:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ic5_35355/06_2025/8ic5_35355_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ic5_35355/06_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_35355/06_2025/8ic5_35355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ic5_35355/06_2025/8ic5_35355.map" model { file = "/net/cci-nas-00/data/ceres_data/8ic5_35355/06_2025/8ic5_35355_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ic5_35355/06_2025/8ic5_35355_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-5': 1} Unresolved non-hydrogen planarities: 15 Chain: "AD" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 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: {'UQ6:plan-6': 1, 'UQ6:plan-7': 1, 'UQ6:plan-4': 1, 'UQ6:plan-5': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 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: 21.27, per 1000 atoms: 0.68 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: 9.03 Conformation dependent library (CDL) restraints added in 4.1 seconds 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: 3.62 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: 11.81 Time building geometry restraints manager: 10.51 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 325 or resid 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 74.500 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.510 ------------------------------------------------------------------------------- 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 : 28.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (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 TRP 0.019 0.002 TRPAc 141 HIS 0.008 0.001 HISAc 196 PHE 0.049 0.002 PHEAc 183 TYR 0.049 0.002 TYRAE 235 ARG 0.007 0.001 ARGAE 250 Details of bonding type rmsd hydrogen bonds : bond 0.18817 ( 1849) hydrogen bonds : angle 7.37074 ( 5301) SS BOND : bond 0.03600 ( 7) SS BOND : angle 16.54457 ( 14) covalent geometry : bond 0.00784 (32216) covalent geometry : angle 1.12782 (43727) 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 : 3.559 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: symmetry clash revert: symmetry clash REVERT: AA 187 LEU cc_start: 0.8036 (tp) cc_final: 0.7708 (tt) REVERT: AA 219 TYR cc_start: 0.7074 (t80) cc_final: 0.6806 (t80) REVERT: AA 441 LEU cc_start: 0.8419 (tt) cc_final: 0.8200 (tp) REVERT: AA 462 ILE cc_start: 0.8085 (pt) cc_final: 0.7855 (tt) REVERT: AB 89 LEU cc_start: 0.8311 (mt) cc_final: 0.8104 (mt) REVERT: AC 113 TRP cc_start: 0.7572 (t-100) cc_final: 0.7334 (t-100) REVERT: AC 327 ILE cc_start: 0.8832 (mt) cc_final: 0.8552 (tp) REVERT: AD 213 SER cc_start: 0.7857 (m) cc_final: 0.7572 (p) REVERT: AD 306 MET cc_start: 0.8262 (mtp) cc_final: 0.8025 (ttm) REVERT: AE 158 ASP cc_start: 0.5959 (m-30) cc_final: 0.5686 (t0) 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: 0.8035 (t) REVERT: AI 14 VAL cc_start: 0.7341 (t) cc_final: 0.7036 (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: 0.8088 (tp) REVERT: Aa 202 GLU cc_start: 0.8730 (mp0) cc_final: 0.8436 (mp0) REVERT: Ac 174 THR cc_start: 0.5986 (m) cc_final: 0.5274 (p) REVERT: Ac 233 LEU cc_start: 0.8019 (tp) cc_final: 0.7663 (tt) REVERT: Ac 240 MET cc_start: 0.7931 (mmm) cc_final: 0.7563 (mmt) REVERT: Ac 242 LEU cc_start: 0.8315 (tp) cc_final: 0.8108 (tp) REVERT: Ac 268 ILE cc_start: 0.7351 (mp) cc_final: 0.6899 (tp) REVERT: Ad 94 TYR cc_start: 0.6663 (m-80) cc_final: 0.6014 (m-10) REVERT: Ad 288 MET cc_start: 0.7191 (mmp) cc_final: 0.6943 (mmp) REVERT: Ad 291 LYS cc_start: 0.8671 (mttt) cc_final: 0.8462 (ttpt) REVERT: Af 58 ASP cc_start: 0.7591 (m-30) cc_final: 0.7348 (t0) REVERT: Ag 64 ASN cc_start: 0.7696 (m-40) cc_final: 0.7427 (m110) outliers start: 8 outliers final: 3 residues processed: 1193 average time/residue: 0.4863 time to fit residues: 895.0847 Evaluate side-chains 629 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 626 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 2.9990 chunk 289 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 154 optimal weight: 0.9990 chunk 299 optimal weight: 0.0030 chunk 115 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 346 optimal weight: 7.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- 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** AA 469 ASN AB 170 GLN AC 44 GLN AC 68 HIS ** AC 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 352 GLN AG 69 GLN AH 34 HIS AJ 48 ASN Aa 128 HIS Aa 173 GLN Aa 181 ASN Aa 402 HIS Ab 284 ASN ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 137 GLN ** Ac 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 115 GLN Ad 155 GLN ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.072878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.057581 restraints weight = 177635.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.059237 restraints weight = 109891.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.060459 restraints weight = 78232.551| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.632 32231 Z= 0.199 Angle : 0.754 16.771 43741 Z= 0.379 Chirality : 0.045 0.270 4751 Planarity : 0.005 0.074 5547 Dihedral : 10.946 141.119 4562 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.39 % Allowed : 4.09 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 3844 helix: 0.86 (0.11), residues: 2110 sheet: -0.09 (0.27), residues: 377 loop : -0.43 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPAA 376 HIS 0.014 0.002 HISAH 82 PHE 0.037 0.002 PHEAd 233 TYR 0.034 0.002 TYRAD 236 ARG 0.011 0.001 ARGAE 110 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 1849) hydrogen bonds : angle 5.39926 ( 5301) SS BOND : bond 0.02393 ( 7) SS BOND : angle 1.70533 ( 14) covalent geometry : bond 0.00438 (32216) covalent geometry : angle 0.75385 (43727) Misc. bond : bond 0.36319 ( 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 826 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 813 time to evaluate : 4.034 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: AA 187 LEU cc_start: 0.9181 (tp) cc_final: 0.8965 (tt) REVERT: AA 219 TYR cc_start: 0.8781 (t80) cc_final: 0.8240 (t80) REVERT: AA 373 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7996 (mm-40) REVERT: AA 376 TRP cc_start: 0.8666 (m-10) cc_final: 0.8059 (m-90) REVERT: AA 377 MET cc_start: 0.9024 (tpp) cc_final: 0.8824 (tpp) REVERT: AA 448 TYR cc_start: 0.8685 (m-80) cc_final: 0.8440 (m-80) REVERT: AA 469 ASN cc_start: 0.8886 (m-40) cc_final: 0.8625 (m110) REVERT: AB 89 LEU cc_start: 0.9170 (mt) cc_final: 0.8894 (mp) REVERT: AB 119 MET cc_start: 0.8490 (ttm) cc_final: 0.8026 (ttm) REVERT: AB 121 TYR cc_start: 0.8192 (m-10) cc_final: 0.7925 (m-80) REVERT: AB 133 LEU cc_start: 0.9568 (mt) cc_final: 0.9350 (mt) REVERT: AB 134 MET cc_start: 0.9241 (ptp) cc_final: 0.9038 (ptp) REVERT: AB 213 PHE cc_start: 0.8620 (m-80) cc_final: 0.8258 (m-80) REVERT: AB 237 PHE cc_start: 0.8912 (m-80) cc_final: 0.8631 (m-80) REVERT: AB 384 MET cc_start: 0.9182 (mtm) cc_final: 0.8903 (mtm) REVERT: AC 113 TRP cc_start: 0.9116 (t-100) cc_final: 0.8598 (t-100) REVERT: AC 178 PHE cc_start: 0.8768 (m-10) cc_final: 0.8529 (m-80) REVERT: AC 280 ILE cc_start: 0.9284 (mm) cc_final: 0.9066 (mm) REVERT: AD 174 TYR cc_start: 0.8582 (m-80) cc_final: 0.8373 (m-80) REVERT: AD 213 SER cc_start: 0.8057 (m) cc_final: 0.7736 (p) REVERT: AD 214 LEU cc_start: 0.9643 (tp) cc_final: 0.9275 (tp) REVERT: AD 303 THR cc_start: 0.9575 (m) cc_final: 0.9367 (p) REVERT: AE 220 LEU cc_start: 0.8385 (mt) cc_final: 0.7887 (mt) REVERT: AF 108 TRP cc_start: 0.9220 (t-100) cc_final: 0.8388 (t-100) REVERT: AG 19 LEU cc_start: 0.9185 (tp) cc_final: 0.8641 (tp) REVERT: AH 47 ARG cc_start: 0.8907 (tmt-80) cc_final: 0.8685 (tpt90) REVERT: AI 4 VAL cc_start: 0.7896 (m) cc_final: 0.7685 (p) REVERT: AJ 23 LEU cc_start: 0.7123 (mt) cc_final: 0.6764 (mt) REVERT: AJ 32 PHE cc_start: 0.8661 (t80) cc_final: 0.8431 (m-80) REVERT: AK 27 VAL cc_start: 0.3991 (t) cc_final: 0.3779 (t) REVERT: AK 39 ARG cc_start: 0.7418 (mtt90) cc_final: 0.7130 (pmt170) REVERT: Aa 74 TRP cc_start: 0.7600 (m-90) cc_final: 0.5687 (m-90) REVERT: Aa 134 LYS cc_start: 0.8382 (tptp) cc_final: 0.7866 (tptt) REVERT: Aa 220 LEU cc_start: 0.9307 (tp) cc_final: 0.8633 (tp) REVERT: Aa 224 TYR cc_start: 0.7908 (m-80) cc_final: 0.7697 (m-80) REVERT: Aa 275 ILE cc_start: 0.8970 (tt) cc_final: 0.8673 (tt) REVERT: Aa 276 ARG cc_start: 0.8504 (mtt-85) cc_final: 0.8125 (mmt90) REVERT: Aa 377 MET cc_start: 0.8984 (mmm) cc_final: 0.8757 (mmm) REVERT: Aa 400 VAL cc_start: 0.8693 (t) cc_final: 0.8401 (t) REVERT: Aa 406 THR cc_start: 0.9046 (p) cc_final: 0.8499 (p) REVERT: Ab 319 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7997 (pt0) REVERT: Ab 407 MET cc_start: 0.8763 (tmm) cc_final: 0.8219 (tmm) REVERT: Ac 53 MET cc_start: 0.8157 (ptm) cc_final: 0.7914 (ptp) REVERT: Ac 111 GLU cc_start: 0.8303 (mp0) cc_final: 0.8019 (mm-30) REVERT: Ac 165 TRP cc_start: 0.7504 (m-10) cc_final: 0.7125 (m-10) REVERT: Ac 170 VAL cc_start: 0.8920 (p) cc_final: 0.8540 (p) REVERT: Ac 174 THR cc_start: 0.9067 (m) cc_final: 0.8513 (p) REVERT: Ac 178 PHE cc_start: 0.9167 (m-80) cc_final: 0.8481 (m-80) REVERT: Ac 316 MET cc_start: 0.8989 (tpp) cc_final: 0.8765 (mmm) REVERT: Ad 306 MET cc_start: 0.8534 (mmp) cc_final: 0.8286 (mmm) REVERT: Af 54 ASP cc_start: 0.8997 (p0) cc_final: 0.8779 (p0) REVERT: Af 58 ASP cc_start: 0.8522 (m-30) cc_final: 0.8280 (m-30) REVERT: Af 60 MET cc_start: 0.8833 (mmm) cc_final: 0.8569 (mmm) REVERT: Af 83 LYS cc_start: 0.7053 (mptt) cc_final: 0.6779 (mmtt) REVERT: Ag 19 LEU cc_start: 0.9282 (tp) cc_final: 0.8906 (tt) REVERT: Ag 47 LEU cc_start: 0.9287 (tp) cc_final: 0.9063 (tp) REVERT: Ah 77 ASP cc_start: 0.8758 (t0) cc_final: 0.8455 (t0) REVERT: Aj 23 LEU cc_start: 0.9567 (tp) cc_final: 0.9222 (mt) REVERT: Ak 23 MET cc_start: 0.8548 (mmm) cc_final: 0.8142 (mtt) REVERT: Ak 49 ASN cc_start: 0.6194 (t0) cc_final: 0.5990 (t0) outliers start: 13 outliers final: 5 residues processed: 820 average time/residue: 0.5851 time to fit residues: 765.8733 Evaluate side-chains 574 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 569 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 9.9990 chunk 64 optimal weight: 0.0770 chunk 264 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN ** 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** AD 155 GLN AD 189 ASN 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 415 GLN ** Ac 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 148 ASN ** Ac 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3628 r_free = 0.3628 target = 0.068746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053986 restraints weight = 186644.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.055549 restraints weight = 116357.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.056597 restraints weight = 82825.402| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.843 32231 Z= 0.252 Angle : 0.781 18.681 43741 Z= 0.388 Chirality : 0.045 0.173 4751 Planarity : 0.005 0.043 5547 Dihedral : 10.442 139.580 4562 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.18 % Allowed : 4.48 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 3844 helix: 0.86 (0.11), residues: 2123 sheet: -0.28 (0.26), residues: 394 loop : -0.35 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRPAk 34 HIS 0.013 0.002 HISAH 82 PHE 0.039 0.003 PHEAC 183 TYR 0.039 0.002 TYRAD 117 ARG 0.010 0.001 ARGAA 415 Details of bonding type rmsd hydrogen bonds : bond 0.05001 ( 1849) hydrogen bonds : angle 5.27211 ( 5301) SS BOND : bond 0.01018 ( 7) SS BOND : angle 1.35415 ( 14) covalent geometry : bond 0.00547 (32216) covalent geometry : angle 0.78031 (43727) Misc. bond : bond 0.43459 ( 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 705 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 699 time to evaluate : 3.575 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: AA 126 ARG cc_start: 0.8559 (mpt-90) cc_final: 0.8241 (mpt-90) REVERT: AA 131 TYR cc_start: 0.7510 (m-80) cc_final: 0.7305 (m-80) REVERT: AA 187 LEU cc_start: 0.9392 (tp) cc_final: 0.9147 (tt) REVERT: AA 219 TYR cc_start: 0.8892 (t80) cc_final: 0.8466 (t80) REVERT: AA 224 TYR cc_start: 0.9204 (m-10) cc_final: 0.8769 (m-10) REVERT: AA 238 GLU cc_start: 0.8193 (pp20) cc_final: 0.7983 (pp20) REVERT: AA 241 GLN cc_start: 0.9001 (pt0) cc_final: 0.8681 (pt0) REVERT: AA 244 ASP cc_start: 0.8676 (m-30) cc_final: 0.8298 (m-30) REVERT: AA 373 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8195 (mm-40) REVERT: AA 376 TRP cc_start: 0.8991 (m-10) cc_final: 0.8066 (m-90) REVERT: AA 410 CYS cc_start: 0.8991 (t) cc_final: 0.8754 (t) REVERT: AA 462 ILE cc_start: 0.9329 (pt) cc_final: 0.9083 (tt) REVERT: AA 469 ASN cc_start: 0.9087 (m-40) cc_final: 0.8629 (m110) REVERT: AB 89 LEU cc_start: 0.9457 (mt) cc_final: 0.9154 (mp) REVERT: AB 119 MET cc_start: 0.8578 (ttm) cc_final: 0.8144 (ttm) REVERT: AC 49 LEU cc_start: 0.9537 (tt) cc_final: 0.9211 (tt) REVERT: AC 113 TRP cc_start: 0.9205 (t-100) cc_final: 0.8857 (t-100) REVERT: AC 115 ILE cc_start: 0.9447 (mm) cc_final: 0.9099 (mm) REVERT: AC 178 PHE cc_start: 0.8857 (m-10) cc_final: 0.8632 (m-80) REVERT: AC 187 PHE cc_start: 0.9391 (m-80) cc_final: 0.8911 (m-80) REVERT: AC 199 PHE cc_start: 0.9010 (m-80) cc_final: 0.8079 (m-80) REVERT: AC 269 LYS cc_start: 0.7809 (mmmm) cc_final: 0.7546 (tppt) REVERT: AC 271 GLU cc_start: 0.8886 (tp30) cc_final: 0.7579 (tp30) REVERT: AD 175 PHE cc_start: 0.8241 (m-80) cc_final: 0.7831 (m-80) REVERT: AD 213 SER cc_start: 0.8267 (m) cc_final: 0.7892 (p) REVERT: AD 214 LEU cc_start: 0.9638 (tp) cc_final: 0.9351 (tp) REVERT: AD 255 TYR cc_start: 0.6986 (m-10) cc_final: 0.6725 (m-80) REVERT: AF 62 ARG cc_start: 0.9019 (mtm110) cc_final: 0.8752 (mtm180) REVERT: AF 108 TRP cc_start: 0.9227 (t-100) cc_final: 0.8398 (t-100) REVERT: AG 19 LEU cc_start: 0.8931 (tp) cc_final: 0.8628 (tp) REVERT: AG 33 LYS cc_start: 0.9286 (mttp) cc_final: 0.8965 (mmmm) REVERT: AH 36 GLU cc_start: 0.8624 (tp30) cc_final: 0.7899 (tp30) REVERT: AH 47 ARG cc_start: 0.9072 (tmt-80) cc_final: 0.8710 (tpt90) REVERT: AI 20 ARG cc_start: 0.7274 (ttt-90) cc_final: 0.6331 (mtm-85) REVERT: AI 67 THR cc_start: 0.8388 (m) cc_final: 0.7923 (p) REVERT: AJ 36 PHE cc_start: 0.8142 (t80) cc_final: 0.7931 (t80) REVERT: AK 39 ARG cc_start: 0.7266 (mtt90) cc_final: 0.7001 (pmt170) REVERT: Aa 68 THR cc_start: 0.9396 (p) cc_final: 0.9160 (t) REVERT: Aa 185 ASP cc_start: 0.8910 (m-30) cc_final: 0.8707 (m-30) REVERT: Aa 211 LEU cc_start: 0.8522 (mt) cc_final: 0.8284 (mt) REVERT: Aa 224 TYR cc_start: 0.8199 (m-80) cc_final: 0.7883 (m-80) REVERT: Aa 354 LEU cc_start: 0.9028 (tp) cc_final: 0.8678 (tp) REVERT: Aa 377 MET cc_start: 0.9099 (mmm) cc_final: 0.8304 (mmm) REVERT: Aa 406 THR cc_start: 0.9146 (p) cc_final: 0.8935 (t) REVERT: Aa 477 TRP cc_start: 0.8516 (m-10) cc_final: 0.7620 (m-10) REVERT: Ab 218 MET cc_start: 0.8792 (mtt) cc_final: 0.7917 (mtt) REVERT: Ab 292 LEU cc_start: 0.9320 (mt) cc_final: 0.9055 (tt) REVERT: Ab 407 MET cc_start: 0.9055 (tmm) cc_final: 0.8647 (tmm) REVERT: Ac 82 MET cc_start: 0.9483 (mtp) cc_final: 0.9205 (mmm) REVERT: Ac 174 THR cc_start: 0.9080 (m) cc_final: 0.8609 (p) REVERT: Ac 178 PHE cc_start: 0.9292 (m-80) cc_final: 0.8829 (m-80) REVERT: Af 54 ASP cc_start: 0.9082 (p0) cc_final: 0.8771 (p0) REVERT: Af 58 ASP cc_start: 0.8640 (m-30) cc_final: 0.8392 (m-30) REVERT: Af 69 LEU cc_start: 0.9606 (mm) cc_final: 0.9383 (mm) REVERT: Af 71 MET cc_start: 0.9037 (tmm) cc_final: 0.8659 (tmm) REVERT: Af 83 LYS cc_start: 0.7448 (mptt) cc_final: 0.7023 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7925 (mt) cc_final: 0.7705 (mt) REVERT: Ag 47 LEU cc_start: 0.9411 (tp) cc_final: 0.9194 (tp) REVERT: Ah 77 ASP cc_start: 0.9039 (t0) cc_final: 0.8795 (t0) REVERT: Ah 85 PHE cc_start: 0.6313 (m-80) cc_final: 0.5710 (m-80) REVERT: Ak 41 ILE cc_start: 0.9369 (mm) cc_final: 0.9131 (mm) outliers start: 6 outliers final: 3 residues processed: 704 average time/residue: 0.4477 time to fit residues: 501.0862 Evaluate side-chains 539 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 536 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 255 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 128 HIS ** AA 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 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** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 68 HIS AD 115 GLN ** AD 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 219 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 452 GLN ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 415 GLN Ac 263 ASN ** Ac 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 115 GLN Ad 119 GLN ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 23 ASN Ag 24 GLN Ah 87 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.067466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.052881 restraints weight = 189134.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054385 restraints weight = 117216.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055440 restraints weight = 83571.337| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.889 32231 Z= 0.251 Angle : 0.751 17.115 43741 Z= 0.371 Chirality : 0.045 0.256 4751 Planarity : 0.005 0.088 5547 Dihedral : 10.199 139.227 4562 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.03 % Allowed : 4.03 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 3844 helix: 0.86 (0.11), residues: 2130 sheet: -0.12 (0.26), residues: 389 loop : -0.42 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPAk 34 HIS 0.017 0.002 HISAH 82 PHE 0.025 0.002 PHEAC 121 TYR 0.037 0.002 TYRAD 236 ARG 0.007 0.001 ARGAA 278 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 1849) hydrogen bonds : angle 5.17545 ( 5301) SS BOND : bond 0.00791 ( 7) SS BOND : angle 1.21882 ( 14) covalent geometry : bond 0.00557 (32216) covalent geometry : angle 0.75073 (43727) Misc. bond : bond 0.45986 ( 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 639 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 3.677 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: AA 98 PHE cc_start: 0.7265 (m-10) cc_final: 0.6996 (m-80) REVERT: AA 126 ARG cc_start: 0.8458 (mpt-90) cc_final: 0.8184 (mpt-90) REVERT: AA 185 ASP cc_start: 0.8912 (m-30) cc_final: 0.8709 (m-30) REVERT: AA 187 LEU cc_start: 0.9409 (tp) cc_final: 0.9122 (tt) REVERT: AA 224 TYR cc_start: 0.9218 (m-10) cc_final: 0.8777 (m-10) REVERT: AA 376 TRP cc_start: 0.9017 (m-10) cc_final: 0.8335 (m-90) REVERT: AA 469 ASN cc_start: 0.9036 (m-40) cc_final: 0.8526 (m-40) REVERT: AB 89 LEU cc_start: 0.9500 (mt) cc_final: 0.9224 (mp) REVERT: AB 119 MET cc_start: 0.8507 (ttm) cc_final: 0.8135 (ttm) REVERT: AB 133 LEU cc_start: 0.9537 (mt) cc_final: 0.9327 (mt) REVERT: AB 177 LEU cc_start: 0.9470 (tp) cc_final: 0.9254 (tp) REVERT: AC 111 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8469 (tm-30) REVERT: AC 113 TRP cc_start: 0.9212 (t-100) cc_final: 0.8805 (t-100) REVERT: AC 115 ILE cc_start: 0.9548 (mm) cc_final: 0.9310 (mm) REVERT: AC 178 PHE cc_start: 0.8955 (m-10) cc_final: 0.8701 (m-80) REVERT: AC 198 LEU cc_start: 0.9156 (tp) cc_final: 0.8906 (mt) REVERT: AC 271 GLU cc_start: 0.8874 (tp30) cc_final: 0.7587 (tp30) REVERT: AD 174 TYR cc_start: 0.8365 (m-80) cc_final: 0.8149 (m-80) REVERT: AD 175 PHE cc_start: 0.8151 (m-80) cc_final: 0.7770 (m-80) REVERT: AD 213 SER cc_start: 0.8249 (m) cc_final: 0.7981 (p) REVERT: AD 214 LEU cc_start: 0.9569 (tp) cc_final: 0.9341 (tp) REVERT: AF 101 GLU cc_start: 0.9065 (pt0) cc_final: 0.8842 (pt0) REVERT: AF 108 TRP cc_start: 0.9192 (t-100) cc_final: 0.8430 (t-100) REVERT: AG 19 LEU cc_start: 0.8943 (tp) cc_final: 0.8592 (tp) REVERT: AG 33 LYS cc_start: 0.9278 (mttp) cc_final: 0.8983 (mmmm) REVERT: AI 20 ARG cc_start: 0.7245 (ttt-90) cc_final: 0.6357 (mtm-85) REVERT: AK 39 ARG cc_start: 0.7235 (mtt90) cc_final: 0.6952 (pmt170) REVERT: Aa 99 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7876 (mmtm) REVERT: Aa 211 LEU cc_start: 0.8415 (mt) cc_final: 0.8206 (mt) REVERT: Aa 224 TYR cc_start: 0.8238 (m-80) cc_final: 0.7975 (m-80) REVERT: Aa 354 LEU cc_start: 0.9080 (tp) cc_final: 0.8755 (tp) REVERT: Aa 445 CYS cc_start: 0.7737 (t) cc_final: 0.7491 (t) REVERT: Ab 218 MET cc_start: 0.8915 (mtt) cc_final: 0.7981 (mtt) REVERT: Ab 240 MET cc_start: 0.8267 (mpp) cc_final: 0.7456 (ppp) REVERT: Ab 407 MET cc_start: 0.9145 (tmm) cc_final: 0.8893 (tmm) REVERT: Ac 53 MET cc_start: 0.8851 (ptp) cc_final: 0.8501 (ptp) REVERT: Ac 82 MET cc_start: 0.9149 (mtp) cc_final: 0.8937 (mmm) REVERT: Ac 88 SER cc_start: 0.8509 (m) cc_final: 0.8135 (p) REVERT: Ac 121 PHE cc_start: 0.8357 (m-80) cc_final: 0.8041 (m-80) REVERT: Ac 149 LEU cc_start: 0.8619 (mt) cc_final: 0.8300 (mt) REVERT: Ac 174 THR cc_start: 0.8804 (m) cc_final: 0.8421 (p) REVERT: Ac 178 PHE cc_start: 0.9237 (m-80) cc_final: 0.8771 (m-80) REVERT: Ac 183 PHE cc_start: 0.8896 (m-10) cc_final: 0.8686 (m-80) REVERT: Ac 237 LEU cc_start: 0.9544 (tt) cc_final: 0.9250 (tp) REVERT: Ac 316 MET cc_start: 0.9070 (tpp) cc_final: 0.8675 (mmm) REVERT: Ad 276 TRP cc_start: 0.8800 (t60) cc_final: 0.8497 (t60) REVERT: Af 83 LYS cc_start: 0.7650 (mptt) cc_final: 0.7222 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7989 (mt) cc_final: 0.7788 (mt) REVERT: Ag 47 LEU cc_start: 0.9434 (tp) cc_final: 0.9225 (tp) REVERT: Ah 77 ASP cc_start: 0.9046 (t0) cc_final: 0.8800 (t0) REVERT: Ah 84 LEU cc_start: 0.8902 (tp) cc_final: 0.8657 (tp) REVERT: Aj 18 THR cc_start: 0.8523 (m) cc_final: 0.8124 (t) REVERT: Ak 34 TRP cc_start: 0.8563 (t-100) cc_final: 0.8312 (t-100) outliers start: 1 outliers final: 1 residues processed: 639 average time/residue: 0.4119 time to fit residues: 425.7372 Evaluate side-chains 503 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 502 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 321 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 258 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 339 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 188 ASN ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS ** AE 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 34 HIS Aa 55 ASN Aa 95 HIS Aa 128 HIS ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ab 446 HIS ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.067761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053066 restraints weight = 185916.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054602 restraints weight = 115353.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055673 restraints weight = 82241.123| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.6062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.814 32231 Z= 0.192 Angle : 0.697 15.525 43741 Z= 0.342 Chirality : 0.043 0.258 4751 Planarity : 0.005 0.080 5547 Dihedral : 9.987 138.121 4562 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3844 helix: 0.95 (0.11), residues: 2137 sheet: -0.04 (0.26), residues: 379 loop : -0.39 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPAA 74 HIS 0.014 0.001 HISAH 82 PHE 0.036 0.002 PHEAC 183 TYR 0.039 0.002 TYRAD 236 ARG 0.006 0.001 ARGAA 278 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 1849) hydrogen bonds : angle 5.02510 ( 5301) SS BOND : bond 0.00502 ( 7) SS BOND : angle 0.90963 ( 14) covalent geometry : bond 0.00436 (32216) covalent geometry : angle 0.69689 (43727) Misc. bond : bond 0.41767 ( 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 643 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 641 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 126 ARG cc_start: 0.8390 (mpt-90) cc_final: 0.8145 (mpt-90) REVERT: AA 185 ASP cc_start: 0.8857 (m-30) cc_final: 0.8650 (m-30) REVERT: AA 187 LEU cc_start: 0.9397 (tp) cc_final: 0.9133 (tt) REVERT: AA 224 TYR cc_start: 0.9250 (m-10) cc_final: 0.8815 (m-10) REVERT: AA 244 ASP cc_start: 0.8615 (m-30) cc_final: 0.8249 (m-30) REVERT: AA 376 TRP cc_start: 0.8998 (m-10) cc_final: 0.8061 (m-90) REVERT: AA 469 ASN cc_start: 0.9049 (m-40) cc_final: 0.8510 (m-40) REVERT: AB 39 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7914 (mp0) REVERT: AB 89 LEU cc_start: 0.9505 (mt) cc_final: 0.9207 (mp) REVERT: AB 119 MET cc_start: 0.8512 (ttm) cc_final: 0.8144 (ttm) REVERT: AB 177 LEU cc_start: 0.9421 (tp) cc_final: 0.9196 (tp) REVERT: AB 407 MET cc_start: 0.9438 (tpp) cc_final: 0.9201 (tpt) REVERT: AC 111 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8503 (tm-30) REVERT: AC 113 TRP cc_start: 0.9209 (t-100) cc_final: 0.8768 (t-100) REVERT: AC 115 ILE cc_start: 0.9552 (mm) cc_final: 0.9220 (mm) REVERT: AC 181 PHE cc_start: 0.8767 (m-80) cc_final: 0.8400 (m-80) REVERT: AC 271 GLU cc_start: 0.8855 (tp30) cc_final: 0.7560 (tp30) REVERT: AD 213 SER cc_start: 0.8808 (m) cc_final: 0.8043 (p) REVERT: AF 62 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8579 (mtm180) REVERT: AF 101 GLU cc_start: 0.9046 (pt0) cc_final: 0.8830 (pt0) REVERT: AF 108 TRP cc_start: 0.9196 (t-100) cc_final: 0.8460 (t-100) REVERT: AG 19 LEU cc_start: 0.8925 (tp) cc_final: 0.8643 (tp) REVERT: AG 33 LYS cc_start: 0.9246 (mttp) cc_final: 0.8901 (mmmm) REVERT: AI 20 ARG cc_start: 0.7259 (ttt-90) cc_final: 0.6345 (mtm-85) REVERT: AK 39 ARG cc_start: 0.7168 (mtt90) cc_final: 0.6923 (pmt170) REVERT: Aa 128 HIS cc_start: 0.7946 (m-70) cc_final: 0.7682 (m170) REVERT: Aa 185 ASP cc_start: 0.8981 (m-30) cc_final: 0.8758 (m-30) REVERT: Aa 220 LEU cc_start: 0.9402 (tp) cc_final: 0.8621 (tp) REVERT: Aa 243 LEU cc_start: 0.9300 (mm) cc_final: 0.9067 (mm) REVERT: Aa 354 LEU cc_start: 0.8969 (tp) cc_final: 0.8700 (tp) REVERT: Aa 445 CYS cc_start: 0.7773 (t) cc_final: 0.7528 (t) REVERT: Aa 477 TRP cc_start: 0.8873 (m-10) cc_final: 0.8459 (m-10) REVERT: Ab 218 MET cc_start: 0.8975 (mtt) cc_final: 0.7986 (mtt) REVERT: Ab 407 MET cc_start: 0.9065 (tmm) cc_final: 0.8486 (tmm) REVERT: Ac 53 MET cc_start: 0.8806 (ptp) cc_final: 0.8515 (ptp) REVERT: Ac 88 SER cc_start: 0.8526 (m) cc_final: 0.8171 (p) REVERT: Ac 121 PHE cc_start: 0.8360 (m-80) cc_final: 0.8074 (m-80) REVERT: Ac 174 THR cc_start: 0.8784 (m) cc_final: 0.8422 (p) REVERT: Ac 178 PHE cc_start: 0.9259 (m-80) cc_final: 0.8819 (m-80) REVERT: Ac 237 LEU cc_start: 0.9522 (tt) cc_final: 0.9271 (tp) REVERT: Ac 316 MET cc_start: 0.9179 (tpp) cc_final: 0.8960 (mmm) REVERT: Ac 328 LEU cc_start: 0.9060 (tp) cc_final: 0.8830 (tp) REVERT: Ad 166 MET cc_start: 0.8848 (mmt) cc_final: 0.8634 (mmp) REVERT: Ad 276 TRP cc_start: 0.8833 (t60) cc_final: 0.8551 (t60) REVERT: Af 69 LEU cc_start: 0.9597 (mm) cc_final: 0.9343 (mm) REVERT: Af 83 LYS cc_start: 0.7735 (mptt) cc_final: 0.7326 (mmtt) REVERT: Ag 8 LEU cc_start: 0.7889 (mt) cc_final: 0.7673 (mt) outliers start: 2 outliers final: 0 residues processed: 642 average time/residue: 0.4429 time to fit residues: 466.5914 Evaluate side-chains 506 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 233 optimal weight: 0.9990 chunk 306 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 283 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 44 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 ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.068608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053881 restraints weight = 182466.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055434 restraints weight = 112721.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.056522 restraints weight = 80202.169| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.725 32231 Z= 0.152 Angle : 0.678 14.304 43741 Z= 0.332 Chirality : 0.043 0.286 4751 Planarity : 0.004 0.063 5547 Dihedral : 9.810 136.182 4562 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3844 helix: 1.07 (0.11), residues: 2125 sheet: 0.08 (0.27), residues: 356 loop : -0.29 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPAk 34 HIS 0.018 0.001 HISAH 82 PHE 0.034 0.002 PHEAJ 21 TYR 0.042 0.002 TYRAD 236 ARG 0.014 0.001 ARGAb 196 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 1849) hydrogen bonds : angle 4.89025 ( 5301) SS BOND : bond 0.00485 ( 7) SS BOND : angle 0.89488 ( 14) covalent geometry : bond 0.00352 (32216) covalent geometry : angle 0.67750 (43727) Misc. bond : bond 0.37743 ( 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 646 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 644 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 126 ARG cc_start: 0.8381 (mpt-90) cc_final: 0.8164 (mpt-90) REVERT: AA 185 ASP cc_start: 0.8895 (m-30) cc_final: 0.8676 (m-30) REVERT: AA 224 TYR cc_start: 0.9278 (m-10) cc_final: 0.8790 (m-10) REVERT: AA 244 ASP cc_start: 0.8633 (m-30) cc_final: 0.8247 (m-30) REVERT: AA 376 TRP cc_start: 0.8907 (m-10) cc_final: 0.7964 (m-90) REVERT: AA 469 ASN cc_start: 0.9144 (m-40) cc_final: 0.8507 (m-40) REVERT: AB 71 TYR cc_start: 0.8513 (m-10) cc_final: 0.8226 (m-10) REVERT: AB 89 LEU cc_start: 0.9552 (mt) cc_final: 0.9267 (mp) REVERT: AB 119 MET cc_start: 0.8550 (ttm) cc_final: 0.8191 (ttm) REVERT: AB 407 MET cc_start: 0.9442 (tpp) cc_final: 0.9148 (tpt) REVERT: AB 438 MET cc_start: 0.6797 (ptt) cc_final: 0.6472 (ptt) REVERT: AC 49 LEU cc_start: 0.9554 (tt) cc_final: 0.9259 (tt) REVERT: AC 53 MET cc_start: 0.8998 (ptp) cc_final: 0.8519 (ptp) REVERT: AC 113 TRP cc_start: 0.9242 (t-100) cc_final: 0.8812 (t-100) REVERT: AC 115 ILE cc_start: 0.9529 (mm) cc_final: 0.9206 (mm) REVERT: AC 181 PHE cc_start: 0.8813 (m-80) cc_final: 0.8442 (m-80) REVERT: AC 271 GLU cc_start: 0.8948 (tp30) cc_final: 0.7722 (tp30) REVERT: AC 272 TRP cc_start: 0.9183 (p-90) cc_final: 0.8913 (p-90) REVERT: AD 210 TYR cc_start: 0.8955 (t80) cc_final: 0.8641 (t80) REVERT: AD 213 SER cc_start: 0.8362 (m) cc_final: 0.8123 (p) REVERT: AD 214 LEU cc_start: 0.9526 (tp) cc_final: 0.8993 (mm) REVERT: AD 215 LEU cc_start: 0.8849 (mm) cc_final: 0.8635 (mm) REVERT: AF 62 ARG cc_start: 0.8908 (mtm110) cc_final: 0.8597 (mtm180) REVERT: AF 101 GLU cc_start: 0.9055 (pt0) cc_final: 0.8847 (pt0) REVERT: AF 108 TRP cc_start: 0.9206 (t-100) cc_final: 0.8458 (t-100) REVERT: AG 19 LEU cc_start: 0.8816 (tp) cc_final: 0.8400 (tp) REVERT: AG 33 LYS cc_start: 0.9239 (mttp) cc_final: 0.8888 (mmmm) REVERT: AH 68 GLU cc_start: 0.8828 (mp0) cc_final: 0.8293 (mp0) REVERT: AI 20 ARG cc_start: 0.7190 (ttt-90) cc_final: 0.6391 (mtm-85) REVERT: AI 67 THR cc_start: 0.8342 (m) cc_final: 0.7834 (p) REVERT: AK 23 MET cc_start: 0.7876 (ttt) cc_final: 0.7328 (tpp) REVERT: AK 39 ARG cc_start: 0.7130 (mtt90) cc_final: 0.6829 (pmt170) REVERT: Aa 128 HIS cc_start: 0.8108 (m-70) cc_final: 0.7803 (m170) REVERT: Aa 172 MET cc_start: 0.8729 (ppp) cc_final: 0.8458 (ppp) REVERT: Aa 211 LEU cc_start: 0.8350 (mt) cc_final: 0.8039 (mt) REVERT: Aa 220 LEU cc_start: 0.9544 (tp) cc_final: 0.9127 (tp) REVERT: Aa 243 LEU cc_start: 0.9350 (mm) cc_final: 0.9074 (mm) REVERT: Aa 445 CYS cc_start: 0.7831 (t) cc_final: 0.7547 (t) REVERT: Aa 477 TRP cc_start: 0.8803 (m-10) cc_final: 0.8274 (m-10) REVERT: Ab 72 GLU cc_start: 0.7612 (mp0) cc_final: 0.7346 (mp0) REVERT: Ab 218 MET cc_start: 0.9004 (mtt) cc_final: 0.8265 (mtt) REVERT: Ab 407 MET cc_start: 0.9096 (tmm) cc_final: 0.8617 (tmm) REVERT: Ac 88 SER cc_start: 0.8594 (m) cc_final: 0.8203 (p) REVERT: Ac 121 PHE cc_start: 0.8415 (m-80) cc_final: 0.8181 (m-80) REVERT: Ac 174 THR cc_start: 0.8811 (m) cc_final: 0.8483 (p) REVERT: Ac 178 PHE cc_start: 0.9258 (m-80) cc_final: 0.8837 (m-80) REVERT: Ac 183 PHE cc_start: 0.8937 (m-10) cc_final: 0.8723 (m-80) REVERT: Ac 232 ILE cc_start: 0.9716 (tt) cc_final: 0.9513 (tp) REVERT: Ac 316 MET cc_start: 0.9203 (tpp) cc_final: 0.8941 (mmm) REVERT: Ac 328 LEU cc_start: 0.9143 (tp) cc_final: 0.8925 (tp) REVERT: Ad 166 MET cc_start: 0.8831 (mmt) cc_final: 0.8620 (mmp) REVERT: Ad 276 TRP cc_start: 0.8883 (t60) cc_final: 0.8621 (t60) REVERT: Ae 121 THR cc_start: 0.9486 (m) cc_final: 0.9273 (p) REVERT: Ae 175 PHE cc_start: 0.8162 (m-10) cc_final: 0.7926 (m-10) REVERT: Af 33 MET cc_start: 0.8703 (mmp) cc_final: 0.8349 (mmm) REVERT: Af 69 LEU cc_start: 0.9648 (mm) cc_final: 0.9368 (mm) REVERT: Af 71 MET cc_start: 0.9076 (tmm) cc_final: 0.8682 (tmm) REVERT: Ag 8 LEU cc_start: 0.7919 (mt) cc_final: 0.7700 (mt) REVERT: Ah 77 ASP cc_start: 0.9080 (t0) cc_final: 0.8843 (t0) outliers start: 2 outliers final: 1 residues processed: 646 average time/residue: 0.4043 time to fit residues: 425.9046 Evaluate side-chains 497 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 496 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 282 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** AA 181 ASN ** AA 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 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** ** AB 327 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** AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS AE 242 HIS ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 199 GLN ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.067090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.052585 restraints weight = 188498.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054102 restraints weight = 117341.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.055146 restraints weight = 83424.702| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.843 32231 Z= 0.207 Angle : 0.717 15.688 43741 Z= 0.352 Chirality : 0.044 0.293 4751 Planarity : 0.005 0.095 5547 Dihedral : 9.815 137.702 4562 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.14), residues: 3844 helix: 0.97 (0.11), residues: 2129 sheet: 0.12 (0.27), residues: 358 loop : -0.34 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPAk 34 HIS 0.015 0.002 HISAA 286 PHE 0.032 0.002 PHEAC 183 TYR 0.027 0.002 TYRAd 236 ARG 0.009 0.001 ARGAH 32 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 1849) hydrogen bonds : angle 4.97998 ( 5301) SS BOND : bond 0.00545 ( 7) SS BOND : angle 1.39166 ( 14) covalent geometry : bond 0.00474 (32216) covalent geometry : angle 0.71646 (43727) Misc. bond : bond 0.43171 ( 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 593 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 592 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 131 TYR cc_start: 0.7616 (m-80) cc_final: 0.7404 (m-80) REVERT: AA 185 ASP cc_start: 0.8794 (m-30) cc_final: 0.8552 (m-30) REVERT: AA 224 TYR cc_start: 0.9270 (m-10) cc_final: 0.8814 (m-10) REVERT: AA 244 ASP cc_start: 0.8551 (m-30) cc_final: 0.7968 (m-30) REVERT: AA 354 LEU cc_start: 0.8968 (tp) cc_final: 0.8701 (tp) REVERT: AA 373 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8254 (mm-40) REVERT: AA 376 TRP cc_start: 0.8952 (m-10) cc_final: 0.7992 (m-90) REVERT: AA 440 MET cc_start: 0.9220 (tmm) cc_final: 0.8974 (tmm) REVERT: AB 71 TYR cc_start: 0.8487 (m-10) cc_final: 0.8261 (m-10) REVERT: AB 89 LEU cc_start: 0.9566 (mt) cc_final: 0.9280 (mp) REVERT: AB 119 MET cc_start: 0.8529 (ttm) cc_final: 0.8134 (ttm) REVERT: AB 177 LEU cc_start: 0.9435 (tp) cc_final: 0.9219 (tp) REVERT: AB 407 MET cc_start: 0.9371 (tpp) cc_final: 0.9124 (tpt) REVERT: AB 438 MET cc_start: 0.6892 (ptt) cc_final: 0.6605 (ptt) REVERT: AC 53 MET cc_start: 0.8996 (ptp) cc_final: 0.8794 (ptm) REVERT: AC 82 MET cc_start: 0.8887 (mtt) cc_final: 0.8639 (mtt) REVERT: AC 111 GLU cc_start: 0.8873 (pp20) cc_final: 0.8469 (tm-30) REVERT: AC 113 TRP cc_start: 0.9257 (t-100) cc_final: 0.8778 (t-100) REVERT: AC 181 PHE cc_start: 0.8815 (m-80) cc_final: 0.8475 (m-80) REVERT: AC 235 MET cc_start: 0.9435 (tmm) cc_final: 0.9122 (tmm) REVERT: AC 271 GLU cc_start: 0.8852 (tp30) cc_final: 0.7672 (tp30) REVERT: AC 272 TRP cc_start: 0.9262 (p-90) cc_final: 0.8961 (p-90) REVERT: AD 214 LEU cc_start: 0.9372 (tp) cc_final: 0.9116 (tp) REVERT: AF 62 ARG cc_start: 0.8914 (mtm110) cc_final: 0.8577 (mtm180) REVERT: AF 101 GLU cc_start: 0.9083 (pt0) cc_final: 0.8873 (pt0) REVERT: AF 108 TRP cc_start: 0.9163 (t-100) cc_final: 0.8506 (t-100) REVERT: AG 19 LEU cc_start: 0.8903 (tp) cc_final: 0.8472 (tp) REVERT: AG 23 GLU cc_start: 0.7668 (mp0) cc_final: 0.7382 (mp0) REVERT: AG 33 LYS cc_start: 0.9218 (mttp) cc_final: 0.8882 (mmmm) REVERT: AH 47 ARG cc_start: 0.9241 (tmt-80) cc_final: 0.8906 (tpt90) REVERT: AH 84 LEU cc_start: 0.9544 (mt) cc_final: 0.9262 (mt) REVERT: AI 20 ARG cc_start: 0.7268 (ttt-90) cc_final: 0.6434 (mtm-85) REVERT: AI 67 THR cc_start: 0.8338 (m) cc_final: 0.7819 (p) REVERT: AI 77 ARG cc_start: 0.7343 (tmt170) cc_final: 0.6805 (tmt170) REVERT: AK 39 ARG cc_start: 0.7027 (mtt90) cc_final: 0.6741 (pmt170) REVERT: Aa 74 TRP cc_start: 0.8337 (m-90) cc_final: 0.7488 (m-90) REVERT: Aa 172 MET cc_start: 0.8611 (ppp) cc_final: 0.8399 (ppp) REVERT: Aa 185 ASP cc_start: 0.8979 (m-30) cc_final: 0.8745 (m-30) REVERT: Aa 220 LEU cc_start: 0.9498 (tp) cc_final: 0.9106 (tp) REVERT: Aa 243 LEU cc_start: 0.9305 (mm) cc_final: 0.9047 (mm) REVERT: Aa 354 LEU cc_start: 0.8950 (tp) cc_final: 0.8640 (tp) REVERT: Aa 358 PHE cc_start: 0.8724 (p90) cc_final: 0.8524 (p90) REVERT: Aa 445 CYS cc_start: 0.7876 (t) cc_final: 0.7562 (t) REVERT: Aa 477 TRP cc_start: 0.8891 (m-10) cc_final: 0.8669 (m-10) REVERT: Ab 218 MET cc_start: 0.9114 (mtt) cc_final: 0.8109 (mtt) REVERT: Ab 240 MET cc_start: 0.8035 (pmm) cc_final: 0.7793 (pmm) REVERT: Ab 301 ARG cc_start: 0.6708 (ptt180) cc_final: 0.6225 (ptt180) REVERT: Ab 407 MET cc_start: 0.9160 (tmm) cc_final: 0.8649 (tmm) REVERT: Ac 88 SER cc_start: 0.8569 (m) cc_final: 0.8203 (p) REVERT: Ac 110 MET cc_start: 0.8608 (mmt) cc_final: 0.8254 (mmm) REVERT: Ac 121 PHE cc_start: 0.8497 (m-80) cc_final: 0.8184 (m-80) REVERT: Ac 174 THR cc_start: 0.8664 (m) cc_final: 0.8300 (p) REVERT: Ac 178 PHE cc_start: 0.9250 (m-80) cc_final: 0.8815 (m-80) REVERT: Ac 257 MET cc_start: 0.8682 (ttm) cc_final: 0.8458 (ttm) REVERT: Ac 328 LEU cc_start: 0.9071 (tp) cc_final: 0.8850 (tp) REVERT: Ad 166 MET cc_start: 0.8867 (mmt) cc_final: 0.8655 (mmp) REVERT: Ad 276 TRP cc_start: 0.8908 (t60) cc_final: 0.8685 (t60) REVERT: Ad 292 MET cc_start: 0.9194 (ttp) cc_final: 0.8963 (ttp) REVERT: Ae 175 PHE cc_start: 0.8233 (m-10) cc_final: 0.7938 (m-10) REVERT: Ae 213 LEU cc_start: 0.8081 (mm) cc_final: 0.7859 (pp) REVERT: Af 33 MET cc_start: 0.8710 (mmp) cc_final: 0.8380 (mmm) REVERT: Af 71 MET cc_start: 0.9027 (tmm) cc_final: 0.8653 (tmm) REVERT: Aj 18 THR cc_start: 0.8595 (m) cc_final: 0.8245 (t) outliers start: 1 outliers final: 0 residues processed: 593 average time/residue: 0.4130 time to fit residues: 399.4630 Evaluate side-chains 478 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 209 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 228 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AA 249 HIS ** AA 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 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** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 446 HIS ** AC 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 201 HIS AC 267 HIS ** AD 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN AE 200 HIS AE 242 HIS ** Aa 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.065598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051311 restraints weight = 192126.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.052715 restraints weight = 119332.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.053693 restraints weight = 85583.573| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.965 32231 Z= 0.266 Angle : 0.783 18.268 43741 Z= 0.382 Chirality : 0.045 0.300 4751 Planarity : 0.005 0.082 5547 Dihedral : 9.916 142.387 4562 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.03 % Allowed : 1.21 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 3844 helix: 0.67 (0.11), residues: 2143 sheet: -0.12 (0.27), residues: 343 loop : -0.46 (0.17), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRPAk 34 HIS 0.013 0.002 HISAH 82 PHE 0.040 0.003 PHEAB 40 TYR 0.024 0.002 TYRAd 236 ARG 0.007 0.001 ARGAA 278 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1849) hydrogen bonds : angle 5.12010 ( 5301) SS BOND : bond 0.00574 ( 7) SS BOND : angle 1.25593 ( 14) covalent geometry : bond 0.00593 (32216) covalent geometry : angle 0.78243 (43727) Misc. bond : bond 0.48371 ( 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 580 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 579 time to evaluate : 3.795 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: AA 185 ASP cc_start: 0.8768 (m-30) cc_final: 0.8525 (m-30) REVERT: AA 229 MET cc_start: 0.8555 (mtm) cc_final: 0.8193 (mtm) REVERT: AA 244 ASP cc_start: 0.8342 (m-30) cc_final: 0.8095 (m-30) REVERT: AA 354 LEU cc_start: 0.9049 (tp) cc_final: 0.8773 (tp) REVERT: AA 368 MET cc_start: 0.7942 (mmm) cc_final: 0.7543 (mtp) REVERT: AA 440 MET cc_start: 0.9257 (tmm) cc_final: 0.9045 (tmm) REVERT: AB 89 LEU cc_start: 0.9588 (mt) cc_final: 0.9311 (mp) REVERT: AB 119 MET cc_start: 0.8561 (ttm) cc_final: 0.8181 (ttm) REVERT: AB 177 LEU cc_start: 0.9482 (tp) cc_final: 0.9232 (tp) REVERT: AC 111 GLU cc_start: 0.8827 (pp20) cc_final: 0.8304 (tm-30) REVERT: AC 113 TRP cc_start: 0.9294 (t-100) cc_final: 0.8885 (t-100) REVERT: AC 115 ILE cc_start: 0.9508 (mm) cc_final: 0.9260 (mm) REVERT: AC 235 MET cc_start: 0.9495 (tmm) cc_final: 0.9172 (tmm) REVERT: AC 271 GLU cc_start: 0.8982 (tp30) cc_final: 0.7873 (tp30) REVERT: AC 272 TRP cc_start: 0.9370 (p-90) cc_final: 0.9045 (p-90) REVERT: AD 214 LEU cc_start: 0.9435 (tp) cc_final: 0.9235 (tp) REVERT: AF 62 ARG cc_start: 0.8881 (mtm110) cc_final: 0.8609 (mtm180) REVERT: AF 101 GLU cc_start: 0.9107 (pt0) cc_final: 0.8906 (pt0) REVERT: AF 108 TRP cc_start: 0.9176 (t-100) cc_final: 0.8541 (t-100) REVERT: AG 19 LEU cc_start: 0.8925 (tp) cc_final: 0.8426 (tp) REVERT: AG 33 LYS cc_start: 0.9214 (mttp) cc_final: 0.8897 (mmmm) REVERT: AG 77 MET cc_start: 0.7749 (tpt) cc_final: 0.7437 (tpt) REVERT: AH 32 ARG cc_start: 0.9354 (tmt-80) cc_final: 0.8962 (ttm-80) REVERT: AH 47 ARG cc_start: 0.9212 (tmt-80) cc_final: 0.8945 (tpt90) REVERT: AH 68 GLU cc_start: 0.8663 (mp0) cc_final: 0.8143 (mp0) REVERT: AH 84 LEU cc_start: 0.9525 (mt) cc_final: 0.9219 (mt) REVERT: AI 20 ARG cc_start: 0.7335 (ttt-90) cc_final: 0.6509 (mtm-85) REVERT: AK 39 ARG cc_start: 0.6971 (mtt90) cc_final: 0.6614 (pmt170) REVERT: Aa 172 MET cc_start: 0.8600 (ppp) cc_final: 0.8377 (ppp) REVERT: Aa 185 ASP cc_start: 0.9039 (m-30) cc_final: 0.8800 (m-30) REVERT: Aa 220 LEU cc_start: 0.9341 (tp) cc_final: 0.8953 (tt) REVERT: Aa 243 LEU cc_start: 0.9324 (mm) cc_final: 0.9030 (mm) REVERT: Aa 354 LEU cc_start: 0.9001 (tp) cc_final: 0.8713 (tp) REVERT: Aa 358 PHE cc_start: 0.8833 (p90) cc_final: 0.8627 (p90) REVERT: Aa 445 CYS cc_start: 0.7789 (t) cc_final: 0.7505 (t) REVERT: Aa 477 TRP cc_start: 0.8793 (m-10) cc_final: 0.8586 (m-10) REVERT: Ab 72 GLU cc_start: 0.7559 (mp0) cc_final: 0.7135 (mp0) REVERT: Ab 218 MET cc_start: 0.9134 (mtt) cc_final: 0.8153 (mtt) REVERT: Ab 238 LEU cc_start: 0.9264 (mt) cc_final: 0.9049 (mp) REVERT: Ab 240 MET cc_start: 0.7994 (pmm) cc_final: 0.7774 (pmm) REVERT: Ab 407 MET cc_start: 0.9212 (tmm) cc_final: 0.8808 (tmm) REVERT: Ac 53 MET cc_start: 0.8888 (ptm) cc_final: 0.8640 (ptm) REVERT: Ac 88 SER cc_start: 0.8540 (m) cc_final: 0.8204 (p) REVERT: Ac 110 MET cc_start: 0.8702 (mmt) cc_final: 0.8359 (mmm) REVERT: Ac 121 PHE cc_start: 0.8630 (m-80) cc_final: 0.8310 (m-80) REVERT: Ac 178 PHE cc_start: 0.9251 (m-80) cc_final: 0.8713 (m-80) REVERT: Ac 257 MET cc_start: 0.8721 (ttm) cc_final: 0.8411 (ttm) REVERT: Ac 328 LEU cc_start: 0.9085 (tp) cc_final: 0.8865 (tp) REVERT: Ad 166 MET cc_start: 0.8249 (mmp) cc_final: 0.7843 (mmm) REVERT: Af 33 MET cc_start: 0.8826 (mmp) cc_final: 0.8446 (mmm) REVERT: Aj 18 THR cc_start: 0.8571 (m) cc_final: 0.8263 (t) outliers start: 1 outliers final: 0 residues processed: 580 average time/residue: 0.4116 time to fit residues: 394.4071 Evaluate side-chains 459 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 223 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 187 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 333 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 95 HIS ** AA 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 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** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 44 GLN ** AD 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 309 HIS AE 164 ASN ** AE 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 200 HIS AE 242 HIS ** Aa 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 345 HIS Ad 189 ASN ** Ae 219 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.066671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.052244 restraints weight = 187347.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.053725 restraints weight = 116371.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054745 restraints weight = 83089.590| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.7213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.833 32231 Z= 0.188 Angle : 0.723 16.794 43741 Z= 0.352 Chirality : 0.044 0.238 4751 Planarity : 0.004 0.083 5547 Dihedral : 9.729 135.384 4562 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3844 helix: 0.88 (0.11), residues: 2128 sheet: -0.06 (0.27), residues: 341 loop : -0.34 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPAk 34 HIS 0.014 0.001 HISAa 286 PHE 0.050 0.002 PHEAB 40 TYR 0.024 0.002 TYRAa 224 ARG 0.006 0.001 ARGAA 278 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1849) hydrogen bonds : angle 4.93204 ( 5301) SS BOND : bond 0.00608 ( 7) SS BOND : angle 2.02064 ( 14) covalent geometry : bond 0.00434 (32216) covalent geometry : angle 0.72254 (43727) Misc. bond : bond 0.41956 ( 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 585 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 584 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AA 185 ASP cc_start: 0.8803 (m-30) cc_final: 0.8566 (m-30) REVERT: AA 229 MET cc_start: 0.8467 (mtm) cc_final: 0.8141 (mtm) REVERT: AA 244 ASP cc_start: 0.8528 (m-30) cc_final: 0.8194 (m-30) REVERT: AA 368 MET cc_start: 0.7790 (mmm) cc_final: 0.7398 (mtp) REVERT: AA 440 MET cc_start: 0.9235 (tmm) cc_final: 0.9024 (tmm) REVERT: AB 89 LEU cc_start: 0.9588 (mt) cc_final: 0.9359 (mp) REVERT: AB 119 MET cc_start: 0.8536 (ttm) cc_final: 0.8136 (ttm) REVERT: AB 197 MET cc_start: 0.9423 (mpp) cc_final: 0.8904 (mpp) REVERT: AB 384 MET cc_start: 0.9084 (mtm) cc_final: 0.8776 (ptm) REVERT: AB 438 MET cc_start: 0.7019 (ptt) cc_final: 0.6811 (ptt) REVERT: AC 111 GLU cc_start: 0.8804 (pp20) cc_final: 0.8316 (tm-30) REVERT: AC 113 TRP cc_start: 0.9244 (t-100) cc_final: 0.8866 (t-100) REVERT: AC 178 PHE cc_start: 0.8959 (m-10) cc_final: 0.8599 (m-80) REVERT: AC 271 GLU cc_start: 0.8972 (tp30) cc_final: 0.8018 (tp30) REVERT: AC 272 TRP cc_start: 0.9359 (p-90) cc_final: 0.9041 (p-90) REVERT: AD 214 LEU cc_start: 0.9418 (tp) cc_final: 0.9149 (tp) REVERT: AD 237 PHE cc_start: 0.9065 (t80) cc_final: 0.8826 (t80) REVERT: AF 62 ARG cc_start: 0.8889 (mtm110) cc_final: 0.8608 (mtm180) REVERT: AF 101 GLU cc_start: 0.9066 (pt0) cc_final: 0.8825 (pt0) REVERT: AF 108 TRP cc_start: 0.9142 (t-100) cc_final: 0.8545 (t-100) REVERT: AG 19 LEU cc_start: 0.8929 (tp) cc_final: 0.8440 (tp) REVERT: AG 33 LYS cc_start: 0.9180 (mttp) cc_final: 0.8860 (mmmm) REVERT: AH 32 ARG cc_start: 0.9339 (tmt-80) cc_final: 0.9039 (ttm-80) REVERT: AH 47 ARG cc_start: 0.9219 (tmt-80) cc_final: 0.8937 (tpt90) REVERT: AH 68 GLU cc_start: 0.8677 (mp0) cc_final: 0.8179 (mp0) REVERT: AI 20 ARG cc_start: 0.7304 (ttt-90) cc_final: 0.6489 (mtm-85) REVERT: AI 67 THR cc_start: 0.8408 (m) cc_final: 0.7903 (p) REVERT: AK 39 ARG cc_start: 0.6991 (mtt90) cc_final: 0.6607 (pmt170) REVERT: Aa 179 MET cc_start: 0.7827 (mtm) cc_final: 0.7624 (mtm) REVERT: Aa 185 ASP cc_start: 0.9013 (m-30) cc_final: 0.8785 (m-30) REVERT: Aa 211 LEU cc_start: 0.8348 (mt) cc_final: 0.8129 (mt) REVERT: Aa 220 LEU cc_start: 0.9282 (tp) cc_final: 0.8939 (tt) REVERT: Aa 224 TYR cc_start: 0.8326 (m-80) cc_final: 0.7816 (m-80) REVERT: Aa 243 LEU cc_start: 0.9299 (mm) cc_final: 0.9019 (mm) REVERT: Aa 354 LEU cc_start: 0.8976 (tp) cc_final: 0.8699 (tp) REVERT: Aa 368 MET cc_start: 0.6155 (mtm) cc_final: 0.5379 (mtt) REVERT: Aa 445 CYS cc_start: 0.7868 (t) cc_final: 0.7555 (t) REVERT: Aa 462 ILE cc_start: 0.9434 (pt) cc_final: 0.9106 (mm) REVERT: Aa 477 TRP cc_start: 0.8765 (m-10) cc_final: 0.8534 (m-10) REVERT: Ab 72 GLU cc_start: 0.7425 (mp0) cc_final: 0.7077 (mp0) REVERT: Ab 119 MET cc_start: 0.9139 (tpp) cc_final: 0.8847 (mmm) REVERT: Ab 218 MET cc_start: 0.9141 (mtt) cc_final: 0.8180 (mtt) REVERT: Ab 301 ARG cc_start: 0.6375 (ptt-90) cc_final: 0.6122 (ptt180) REVERT: Ab 407 MET cc_start: 0.9144 (tmm) cc_final: 0.8743 (tmm) REVERT: Ac 53 MET cc_start: 0.8760 (ptm) cc_final: 0.8514 (ptm) REVERT: Ac 88 SER cc_start: 0.8609 (m) cc_final: 0.8335 (p) REVERT: Ac 110 MET cc_start: 0.8622 (mmt) cc_final: 0.8263 (mmm) REVERT: Ac 178 PHE cc_start: 0.9231 (m-80) cc_final: 0.8708 (m-80) REVERT: Ac 300 ILE cc_start: 0.9276 (mt) cc_final: 0.9062 (tp) REVERT: Ac 328 LEU cc_start: 0.9081 (tp) cc_final: 0.8875 (tp) REVERT: Ad 166 MET cc_start: 0.8301 (mmp) cc_final: 0.7969 (mmm) REVERT: Ad 236 TYR cc_start: 0.6204 (m-80) cc_final: 0.5638 (m-80) REVERT: Ad 306 MET cc_start: 0.8522 (mmm) cc_final: 0.8254 (tpp) REVERT: Ae 175 PHE cc_start: 0.8129 (m-10) cc_final: 0.7875 (m-10) REVERT: Af 33 MET cc_start: 0.8802 (mmp) cc_final: 0.8389 (mmm) REVERT: Aj 18 THR cc_start: 0.8650 (m) cc_final: 0.8359 (t) outliers start: 1 outliers final: 0 residues processed: 585 average time/residue: 0.4023 time to fit residues: 386.7928 Evaluate side-chains 459 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 220 optimal weight: 8.9990 chunk 329 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 221 HIS AE 164 ASN AE 200 HIS AE 242 HIS ** Aa 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.066245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051866 restraints weight = 190638.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.053308 restraints weight = 117520.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054346 restraints weight = 83871.107| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.7386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.843 32231 Z= 0.207 Angle : 0.742 16.485 43741 Z= 0.363 Chirality : 0.044 0.246 4751 Planarity : 0.005 0.122 5547 Dihedral : 9.716 145.052 4562 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3844 helix: 0.88 (0.11), residues: 2127 sheet: -0.19 (0.27), residues: 344 loop : -0.32 (0.18), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPAd 276 HIS 0.020 0.002 HISAA 66 PHE 0.039 0.002 PHEAB 40 TYR 0.021 0.002 TYRAd 236 ARG 0.007 0.001 ARGAa 170 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 1849) hydrogen bonds : angle 4.97557 ( 5301) SS BOND : bond 0.00626 ( 7) SS BOND : angle 1.88688 ( 14) covalent geometry : bond 0.00475 (32216) covalent geometry : angle 0.74162 (43727) Misc. bond : bond 0.42711 ( 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 570 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 569 time to evaluate : 3.396 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: 0.8805 (m-30) cc_final: 0.8571 (m-30) REVERT: AA 229 MET cc_start: 0.8487 (mtm) cc_final: 0.8155 (mtm) REVERT: AA 244 ASP cc_start: 0.8516 (m-30) cc_final: 0.8184 (m-30) REVERT: AA 354 LEU cc_start: 0.8958 (tp) cc_final: 0.8711 (tp) REVERT: AA 440 MET cc_start: 0.9242 (tmm) cc_final: 0.9032 (tmm) REVERT: AB 89 LEU cc_start: 0.9590 (mt) cc_final: 0.9369 (mp) REVERT: AB 119 MET cc_start: 0.8615 (ttm) cc_final: 0.8287 (ttm) REVERT: AB 177 LEU cc_start: 0.9442 (tp) cc_final: 0.9213 (tp) REVERT: AB 384 MET cc_start: 0.9070 (mtm) cc_final: 0.8659 (ptm) REVERT: AB 438 MET cc_start: 0.6969 (ptt) cc_final: 0.6725 (ptt) REVERT: AC 111 GLU cc_start: 0.8909 (pp20) cc_final: 0.8518 (tm-30) REVERT: AC 113 TRP cc_start: 0.9257 (t-100) cc_final: 0.8898 (t-100) REVERT: AC 181 PHE cc_start: 0.8850 (m-80) cc_final: 0.8351 (m-80) REVERT: AC 375 LYS cc_start: 0.8887 (tptt) cc_final: 0.8686 (tppt) REVERT: AD 214 LEU cc_start: 0.9432 (tp) cc_final: 0.9174 (tp) REVERT: AD 237 PHE cc_start: 0.9054 (t80) cc_final: 0.8805 (t80) REVERT: AD 288 MET cc_start: 0.8207 (mpp) cc_final: 0.7994 (mtm) REVERT: AE 151 LYS cc_start: 0.7663 (mmpt) cc_final: 0.7417 (mmpt) REVERT: AF 62 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8610 (mtm180) REVERT: AF 101 GLU cc_start: 0.9070 (pt0) cc_final: 0.8835 (pt0) REVERT: AF 108 TRP cc_start: 0.9150 (t-100) cc_final: 0.8568 (t-100) REVERT: AG 19 LEU cc_start: 0.8783 (tp) cc_final: 0.8367 (tp) REVERT: AG 33 LYS cc_start: 0.9161 (mttp) cc_final: 0.8849 (mmmm) REVERT: AH 47 ARG cc_start: 0.9220 (tmt-80) cc_final: 0.8938 (tpt90) REVERT: AH 68 GLU cc_start: 0.8732 (mp0) cc_final: 0.8244 (mp0) REVERT: AH 84 LEU cc_start: 0.9493 (mt) cc_final: 0.9279 (mt) REVERT: AI 20 ARG cc_start: 0.7288 (ttt-90) cc_final: 0.6485 (mtm-85) REVERT: AK 39 ARG cc_start: 0.6949 (mtt90) cc_final: 0.6601 (pmt170) REVERT: Aa 179 MET cc_start: 0.7870 (mtm) cc_final: 0.7626 (mtm) REVERT: Aa 185 ASP cc_start: 0.9044 (m-30) cc_final: 0.8824 (m-30) REVERT: Aa 220 LEU cc_start: 0.9270 (tp) cc_final: 0.8934 (tp) REVERT: Aa 243 LEU cc_start: 0.9288 (mm) cc_final: 0.9021 (mm) REVERT: Aa 354 LEU cc_start: 0.8989 (tp) cc_final: 0.8707 (tp) REVERT: Aa 368 MET cc_start: 0.6344 (mtm) cc_final: 0.5655 (mtt) REVERT: Aa 445 CYS cc_start: 0.7779 (t) cc_final: 0.7497 (t) REVERT: Aa 477 TRP cc_start: 0.8770 (m-10) cc_final: 0.8546 (m-10) REVERT: Ab 72 GLU cc_start: 0.7377 (mp0) cc_final: 0.7043 (mp0) REVERT: Ab 119 MET cc_start: 0.9128 (tpp) cc_final: 0.8849 (mmm) REVERT: Ab 218 MET cc_start: 0.9190 (mtt) cc_final: 0.8229 (mtt) REVERT: Ab 407 MET cc_start: 0.9196 (tmm) cc_final: 0.8800 (tmm) REVERT: Ac 53 MET cc_start: 0.8813 (ptm) cc_final: 0.8605 (ptm) REVERT: Ac 88 SER cc_start: 0.8758 (m) cc_final: 0.8434 (t) REVERT: Ac 110 MET cc_start: 0.8627 (mmt) cc_final: 0.8260 (mmm) REVERT: Ac 121 PHE cc_start: 0.8648 (m-80) cc_final: 0.8343 (m-80) REVERT: Ac 178 PHE cc_start: 0.9232 (m-80) cc_final: 0.8721 (m-80) REVERT: Ac 183 PHE cc_start: 0.8686 (m-80) cc_final: 0.8359 (m-80) REVERT: Ac 300 ILE cc_start: 0.9276 (mt) cc_final: 0.9072 (tp) REVERT: Ac 328 LEU cc_start: 0.9023 (tp) cc_final: 0.8797 (tp) REVERT: Ad 166 MET cc_start: 0.8316 (mmp) cc_final: 0.7969 (mmm) REVERT: Ae 175 PHE cc_start: 0.8166 (m-10) cc_final: 0.7862 (m-10) REVERT: Ae 213 LEU cc_start: 0.8033 (mm) cc_final: 0.7694 (pp) REVERT: Af 33 MET cc_start: 0.8861 (mmp) cc_final: 0.8405 (mmm) REVERT: Af 56 TYR cc_start: 0.8642 (t80) cc_final: 0.8062 (t80) REVERT: Af 60 MET cc_start: 0.9239 (mmm) cc_final: 0.9003 (mtp) REVERT: Aj 18 THR cc_start: 0.8656 (m) cc_final: 0.8385 (t) REVERT: Aj 30 LEU cc_start: 0.9432 (tt) cc_final: 0.9144 (mm) REVERT: Ak 49 ASN cc_start: 0.7615 (t0) cc_final: 0.7254 (t0) outliers start: 1 outliers final: 0 residues processed: 570 average time/residue: 0.3952 time to fit residues: 369.6119 Evaluate side-chains 449 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 283 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 364 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 348 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 282 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 241 GLN ** AA 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 342 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** ** AB 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 164 ASN AE 200 HIS AE 242 HIS ** Aa 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 128 HIS ** Aa 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ab 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 219 HIS ** 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 = 0.3581 r_free = 0.3581 target = 0.066662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052305 restraints weight = 190430.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.053806 restraints weight = 117701.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054844 restraints weight = 83593.113| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.7524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.811 32231 Z= 0.190 Angle : 0.738 15.791 43741 Z= 0.360 Chirality : 0.044 0.198 4751 Planarity : 0.005 0.111 5547 Dihedral : 9.678 145.574 4562 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3844 helix: 0.87 (0.11), residues: 2132 sheet: -0.25 (0.26), residues: 353 loop : -0.32 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPAD 96 HIS 0.015 0.001 HISAA 66 PHE 0.040 0.002 PHEAB 40 TYR 0.023 0.002 TYRAD 210 ARG 0.007 0.001 ARGAA 278 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1849) hydrogen bonds : angle 4.96829 ( 5301) SS BOND : bond 0.00606 ( 7) SS BOND : angle 1.74282 ( 14) covalent geometry : bond 0.00441 (32216) covalent geometry : angle 0.73734 (43727) Misc. bond : bond 0.41005 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14379.71 seconds wall clock time: 252 minutes 36.98 seconds (15156.98 seconds total)