Starting phenix.real_space_refine on Wed Feb 14 12:24:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/02_2024/7w40_32298_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/02_2024/7w40_32298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/02_2024/7w40_32298.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/02_2024/7w40_32298.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/02_2024/7w40_32298_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w40_32298/02_2024/7w40_32298_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5882 2.51 5 N 1573 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9236 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2280 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 286} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2330 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2409 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 309} Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 365 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "H" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 81 Unusual residues: {'BAL': 1} Classifications: {'peptide': 8, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.18, per 1000 atoms: 0.56 Number of scatterers: 9236 At special positions: 0 Unit cell: (111.54, 112.554, 128.778, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1724 8.00 N 1573 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN E 1 " Input volumes are d-peptide like pdb=" CB BAL E 6 " Number of C-beta restraints generated: 2222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 35.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 38 through 68 Proline residue: A 44 - end of helix removed outlier: 4.306A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 102 removed outlier: 3.600A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 109 through 143 Proline residue: A 117 - end of helix removed outlier: 3.523A pdb=" N THR A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 177 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 220 through 243 removed outlier: 3.549A pdb=" N TYR A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 289 removed outlier: 5.329A pdb=" N LYS A 254 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 263 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 272 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 273 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS A 276 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.595A pdb=" N ILE A 283 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR A 284 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 325 removed outlier: 3.593A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix removed outlier: 3.847A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 336 Processing helix chain 'B' and resid 13 through 37 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 69 through 87 removed outlier: 4.687A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 276 through 285 removed outlier: 4.434A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 302 through 316 removed outlier: 3.973A pdb=" N LEU B 316 " --> pdb=" O MET B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 355 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.122A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.992A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 180 through 185 Processing sheet with id= B, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.882A pdb=" N VAL B 269 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N HIS B 327 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 271 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 200 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU B 42 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG B 202 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 44 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL B 204 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.947A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.606A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.895A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.636A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.658A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 317 through 320 removed outlier: 3.761A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'H' and resid 115 through 117 removed outlier: 5.889A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'H' and resid 243 through 245 removed outlier: 6.348A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1068 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: 2.77 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2015 1.33 - 1.45: 2197 1.45 - 1.57: 5142 1.57 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 9440 Sorted by residual: bond pdb=" CG TRP E 3 " pdb=" CD2 TRP E 3 " ideal model delta sigma weight residual 1.433 1.333 0.100 1.80e-02 3.09e+03 3.07e+01 bond pdb=" CB PHE E 8 " pdb=" CG PHE E 8 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.57e+01 bond pdb=" CG HIS E 7 " pdb=" ND1 HIS E 7 " ideal model delta sigma weight residual 1.378 1.324 0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CB DPN E 1 " pdb=" CG DPN E 1 " ideal model delta sigma weight residual 1.502 1.391 0.111 2.30e-02 1.89e+03 2.34e+01 bond pdb=" C VAL A 266 " pdb=" O VAL A 266 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.19e+01 ... (remaining 9435 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.44: 181 105.44 - 112.66: 4739 112.66 - 119.88: 3741 119.88 - 127.10: 4039 127.10 - 134.32: 99 Bond angle restraints: 12799 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 110.35 102.15 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 113.97 106.80 7.17 1.28e+00 6.10e-01 3.14e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.88 117.85 4.03 7.80e-01 1.64e+00 2.67e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.55 107.06 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N ARG C 48 " pdb=" CA ARG C 48 " pdb=" C ARG C 48 " ideal model delta sigma weight residual 113.23 106.84 6.39 1.24e+00 6.50e-01 2.65e+01 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5102 16.73 - 33.46: 405 33.46 - 50.20: 78 50.20 - 66.93: 15 66.93 - 83.66: 2 Dihedral angle restraints: 5602 sinusoidal: 2154 harmonic: 3448 Sorted by residual: dihedral pdb=" C TYR H 235 " pdb=" N TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual -122.60 -140.20 17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.36 56.64 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 5599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1285 0.135 - 0.270: 145 0.270 - 0.405: 8 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LEU H 4 " pdb=" N LEU H 4 " pdb=" C LEU H 4 " pdb=" CB LEU H 4 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1436 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 175 " 0.016 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR H 175 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR H 175 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 175 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR H 175 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LYS C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 128 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 315 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C VAL C 315 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 316 " -0.017 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2005 2.79 - 3.32: 8691 3.32 - 3.85: 14869 3.85 - 4.37: 18594 4.37 - 4.90: 31109 Nonbonded interactions: 75268 Sorted by model distance: nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.266 2.440 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.290 2.440 nonbonded pdb=" NE ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.309 2.520 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.322 2.440 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.341 2.440 ... (remaining 75263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.250 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 : 0.011 0.117 9440 Z= 0.692 Angle : 1.288 8.202 12799 Z= 0.929 Chirality : 0.085 0.675 1439 Planarity : 0.006 0.053 1630 Dihedral : 12.467 83.658 3371 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 3.84 % Favored : 94.24 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.42 (0.23), residues: 1162 helix: 0.42 (0.25), residues: 411 sheet: 0.10 (0.31), residues: 286 loop : -1.08 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 82 HIS 0.009 0.002 HIS C 311 PHE 0.030 0.003 PHE C 199 TYR 0.056 0.003 TYR H 175 ARG 0.011 0.001 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 SER cc_start: 0.5579 (t) cc_final: 0.5323 (m) REVERT: B 26 ASP cc_start: 0.7878 (m-30) cc_final: 0.7571 (m-30) REVERT: B 60 ARG cc_start: 0.6721 (ttp80) cc_final: 0.6093 (mmm160) REVERT: B 83 ILE cc_start: 0.6982 (mp) cc_final: 0.6749 (mp) REVERT: B 259 ILE cc_start: 0.7714 (pt) cc_final: 0.7487 (pt) REVERT: B 322 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6755 (tptt) REVERT: B 332 THR cc_start: 0.7611 (t) cc_final: 0.7183 (m) REVERT: B 348 ILE cc_start: 0.6745 (mm) cc_final: 0.6509 (mt) outliers start: 19 outliers final: 3 residues processed: 246 average time/residue: 1.1352 time to fit residues: 298.2542 Evaluate side-chains 146 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 296 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 HIS B 336 ASN C 75 GLN C 88 ASN C 142 HIS H 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9440 Z= 0.390 Angle : 0.760 9.793 12799 Z= 0.399 Chirality : 0.049 0.289 1439 Planarity : 0.006 0.045 1630 Dihedral : 5.788 47.932 1303 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.17 % Allowed : 13.25 % Favored : 80.59 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.24 (0.23), residues: 1162 helix: 0.74 (0.24), residues: 410 sheet: 0.03 (0.30), residues: 292 loop : -1.03 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 82 HIS 0.008 0.003 HIS C 91 PHE 0.029 0.003 PHE C 253 TYR 0.040 0.003 TYR H 235 ARG 0.008 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 145 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7165 (tt) REVERT: A 278 LEU cc_start: 0.6886 (tp) cc_final: 0.6579 (tp) REVERT: B 15 ASP cc_start: 0.7217 (m-30) cc_final: 0.6937 (m-30) REVERT: B 60 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6296 (mmp-170) REVERT: B 202 ARG cc_start: 0.6853 (mtp85) cc_final: 0.6482 (mtm180) REVERT: B 214 ARG cc_start: 0.7430 (ptt180) cc_final: 0.6953 (ptt180) REVERT: B 322 LYS cc_start: 0.7376 (mtpp) cc_final: 0.6669 (tptt) REVERT: C 68 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7253 (ttt180) REVERT: C 269 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6623 (mm) REVERT: C 322 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: H 6 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6824 (pm20) REVERT: H 235 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.4109 (t80) outliers start: 61 outliers final: 30 residues processed: 188 average time/residue: 1.3769 time to fit residues: 275.0754 Evaluate side-chains 154 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 71 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN B 327 HIS C 142 HIS H 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9440 Z= 0.184 Angle : 0.599 7.748 12799 Z= 0.312 Chirality : 0.042 0.232 1439 Planarity : 0.004 0.045 1630 Dihedral : 5.356 53.839 1303 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.16 % Allowed : 16.99 % Favored : 77.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.28 (0.24), residues: 1162 helix: 1.37 (0.25), residues: 410 sheet: 0.23 (0.30), residues: 291 loop : -0.88 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.003 0.001 HIS H 35 PHE 0.015 0.001 PHE B 201 TYR 0.030 0.001 TYR H 235 ARG 0.007 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7146 (tt) REVERT: B 38 ARG cc_start: 0.6931 (mtp-110) cc_final: 0.6703 (mtp85) REVERT: B 60 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6009 (mmm160) REVERT: B 322 LYS cc_start: 0.7439 (mtpp) cc_final: 0.6748 (tptt) REVERT: B 335 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6845 (tp30) REVERT: C 269 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6675 (mm) REVERT: H 6 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6276 (pm20) REVERT: H 235 TYR cc_start: 0.4015 (OUTLIER) cc_final: 0.3732 (t80) outliers start: 51 outliers final: 20 residues processed: 164 average time/residue: 1.4926 time to fit residues: 258.8716 Evaluate side-chains 141 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9440 Z= 0.171 Angle : 0.569 7.105 12799 Z= 0.295 Chirality : 0.041 0.207 1439 Planarity : 0.004 0.042 1630 Dihedral : 5.036 54.077 1302 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.75 % Allowed : 18.81 % Favored : 76.44 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.48 (0.24), residues: 1162 helix: 1.59 (0.26), residues: 411 sheet: 0.33 (0.29), residues: 290 loop : -0.81 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.013 0.001 PHE C 199 TYR 0.026 0.001 TYR H 235 ARG 0.005 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7155 (tt) REVERT: A 298 MET cc_start: 0.5581 (tpp) cc_final: 0.5265 (tpt) REVERT: B 60 ARG cc_start: 0.6848 (ttp80) cc_final: 0.5978 (mmp-170) REVERT: B 335 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: C 101 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7164 (mtp) REVERT: C 269 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6802 (mm) REVERT: C 322 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6071 (m-30) outliers start: 47 outliers final: 24 residues processed: 154 average time/residue: 1.4379 time to fit residues: 234.6385 Evaluate side-chains 141 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9440 Z= 0.194 Angle : 0.579 7.238 12799 Z= 0.300 Chirality : 0.042 0.196 1439 Planarity : 0.004 0.051 1630 Dihedral : 5.026 53.589 1302 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.16 % Allowed : 19.21 % Favored : 75.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.47 (0.24), residues: 1162 helix: 1.50 (0.26), residues: 410 sheet: 0.39 (0.29), residues: 287 loop : -0.77 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 PHE 0.015 0.002 PHE B 201 TYR 0.030 0.002 TYR H 235 ARG 0.007 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7252 (tt) REVERT: B 60 ARG cc_start: 0.6896 (ttp80) cc_final: 0.6027 (mmm160) REVERT: B 335 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6777 (tp30) REVERT: C 101 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7153 (mtp) REVERT: C 134 ARG cc_start: 0.5226 (OUTLIER) cc_final: 0.4770 (ptm160) REVERT: C 269 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6827 (mm) REVERT: C 322 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6163 (m-30) outliers start: 51 outliers final: 30 residues processed: 152 average time/residue: 1.3891 time to fit residues: 223.8193 Evaluate side-chains 146 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9440 Z= 0.345 Angle : 0.692 7.721 12799 Z= 0.362 Chirality : 0.046 0.232 1439 Planarity : 0.005 0.057 1630 Dihedral : 5.489 53.419 1302 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.66 % Allowed : 19.41 % Favored : 74.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.03 (0.24), residues: 1162 helix: 0.86 (0.25), residues: 411 sheet: 0.30 (0.30), residues: 282 loop : -0.84 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.007 0.002 HIS C 142 PHE 0.020 0.003 PHE B 201 TYR 0.026 0.002 TYR H 235 ARG 0.009 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 120 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6901 (mtp-110) cc_final: 0.6626 (mtp85) REVERT: B 60 ARG cc_start: 0.6954 (ttp80) cc_final: 0.6303 (mmp-170) REVERT: B 335 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6874 (tp30) REVERT: C 134 ARG cc_start: 0.5315 (OUTLIER) cc_final: 0.4899 (ptm160) REVERT: C 234 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: C 269 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6871 (mm) REVERT: C 322 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: H 192 MET cc_start: 0.7030 (ttp) cc_final: 0.6708 (ttt) outliers start: 56 outliers final: 35 residues processed: 159 average time/residue: 1.3804 time to fit residues: 232.7050 Evaluate side-chains 154 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 0.0020 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.0170 chunk 66 optimal weight: 0.5980 overall best weight: 0.5026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9440 Z= 0.178 Angle : 0.600 8.604 12799 Z= 0.308 Chirality : 0.042 0.219 1439 Planarity : 0.004 0.055 1630 Dihedral : 5.143 51.837 1302 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.15 % Allowed : 21.84 % Favored : 74.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.32 (0.24), residues: 1162 helix: 1.34 (0.26), residues: 410 sheet: 0.26 (0.29), residues: 289 loop : -0.78 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.007 0.001 HIS C 183 PHE 0.014 0.001 PHE B 201 TYR 0.026 0.001 TYR B 285 ARG 0.012 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.5805 (tpp) cc_final: 0.5554 (tpt) REVERT: B 38 ARG cc_start: 0.6871 (mtp-110) cc_final: 0.6633 (mtp85) REVERT: B 60 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6202 (mmp-170) REVERT: B 78 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6551 (mt) REVERT: B 202 ARG cc_start: 0.6882 (mtp85) cc_final: 0.6495 (ptm160) REVERT: B 335 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6835 (tp30) REVERT: C 52 ARG cc_start: 0.7712 (ptp-110) cc_final: 0.7399 (ptm160) REVERT: C 101 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: C 134 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.4995 (ptm160) REVERT: C 175 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7718 (mm110) REVERT: C 234 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7101 (m-80) outliers start: 41 outliers final: 28 residues processed: 146 average time/residue: 1.4080 time to fit residues: 217.9284 Evaluate side-chains 149 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 176 GLN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9440 Z= 0.244 Angle : 0.630 8.412 12799 Z= 0.325 Chirality : 0.043 0.237 1439 Planarity : 0.005 0.046 1630 Dihedral : 5.182 51.467 1302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.85 % Allowed : 21.74 % Favored : 73.41 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.24 (0.24), residues: 1162 helix: 1.19 (0.26), residues: 410 sheet: 0.30 (0.30), residues: 285 loop : -0.80 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS C 183 PHE 0.015 0.002 PHE C 199 TYR 0.025 0.001 TYR H 235 ARG 0.009 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.5854 (tpp) cc_final: 0.5613 (tpt) REVERT: B 38 ARG cc_start: 0.6841 (mtp-110) cc_final: 0.6596 (mtp85) REVERT: B 60 ARG cc_start: 0.6994 (ttp80) cc_final: 0.6317 (mmp-170) REVERT: B 78 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6591 (mt) REVERT: B 87 MET cc_start: 0.6967 (mmm) cc_final: 0.6620 (mmt) REVERT: B 261 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: B 335 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6849 (tp30) REVERT: C 52 ARG cc_start: 0.7705 (ptp-110) cc_final: 0.7447 (ptm160) REVERT: C 101 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: C 175 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7561 (mm110) REVERT: C 234 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: C 322 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6306 (m-30) REVERT: H 235 TYR cc_start: 0.4198 (OUTLIER) cc_final: 0.3882 (t80) outliers start: 48 outliers final: 29 residues processed: 147 average time/residue: 1.4273 time to fit residues: 222.5769 Evaluate side-chains 148 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 68 optimal weight: 0.0050 chunk 110 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9440 Z= 0.167 Angle : 0.588 10.050 12799 Z= 0.300 Chirality : 0.041 0.212 1439 Planarity : 0.004 0.042 1630 Dihedral : 4.982 50.596 1302 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.94 % Allowed : 22.35 % Favored : 73.71 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.45 (0.25), residues: 1162 helix: 1.46 (0.26), residues: 410 sheet: 0.37 (0.30), residues: 288 loop : -0.76 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.005 0.001 HIS C 183 PHE 0.012 0.001 PHE C 199 TYR 0.026 0.001 TYR B 285 ARG 0.008 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 146 MET cc_start: 0.5252 (mmp) cc_final: 0.5025 (mmt) REVERT: A 298 MET cc_start: 0.5774 (tpp) cc_final: 0.5569 (tpt) REVERT: B 60 ARG cc_start: 0.6961 (ttp80) cc_final: 0.6233 (mmp-170) REVERT: B 78 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6639 (mt) REVERT: B 202 ARG cc_start: 0.6835 (mtp85) cc_final: 0.6570 (ptm160) REVERT: C 101 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7104 (mtp) REVERT: C 175 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7545 (mm-40) REVERT: C 234 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: D 52 THR cc_start: 0.6489 (t) cc_final: 0.6121 (m) REVERT: H 235 TYR cc_start: 0.3979 (OUTLIER) cc_final: 0.3694 (t80) outliers start: 39 outliers final: 26 residues processed: 148 average time/residue: 1.3488 time to fit residues: 212.0526 Evaluate side-chains 141 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 92 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9440 Z= 0.163 Angle : 0.600 11.894 12799 Z= 0.304 Chirality : 0.041 0.204 1439 Planarity : 0.004 0.049 1630 Dihedral : 4.790 51.014 1302 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.24 % Allowed : 23.36 % Favored : 73.41 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.61 (0.25), residues: 1162 helix: 1.64 (0.27), residues: 410 sheet: 0.49 (0.30), residues: 287 loop : -0.75 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.005 0.001 HIS C 183 PHE 0.011 0.001 PHE C 199 TYR 0.021 0.001 TYR H 235 ARG 0.013 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 146 MET cc_start: 0.5083 (mmp) cc_final: 0.4874 (mmt) REVERT: A 218 PHE cc_start: 0.5093 (m-80) cc_final: 0.4625 (t80) REVERT: A 298 MET cc_start: 0.5760 (tpp) cc_final: 0.5528 (tpt) REVERT: B 38 ARG cc_start: 0.6714 (mtp-110) cc_final: 0.6481 (mtp85) REVERT: B 60 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6297 (mmp-170) REVERT: B 78 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6693 (mt) REVERT: C 101 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7222 (mtp) REVERT: C 129 ARG cc_start: 0.6653 (OUTLIER) cc_final: 0.6443 (tmm-80) REVERT: C 175 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7475 (mm-40) REVERT: C 234 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: D 52 THR cc_start: 0.6564 (t) cc_final: 0.6227 (m) REVERT: H 158 SER cc_start: 0.7386 (m) cc_final: 0.6960 (p) REVERT: H 235 TYR cc_start: 0.3772 (OUTLIER) cc_final: 0.3511 (t80) outliers start: 32 outliers final: 22 residues processed: 143 average time/residue: 1.3682 time to fit residues: 207.7703 Evaluate side-chains 138 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.0040 chunk 94 optimal weight: 9.9990 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.208107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171841 restraints weight = 9591.161| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.69 r_work: 0.3978 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9440 Z= 0.163 Angle : 0.585 9.210 12799 Z= 0.297 Chirality : 0.041 0.203 1439 Planarity : 0.004 0.064 1630 Dihedral : 4.765 50.844 1302 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.13 % Allowed : 23.66 % Favored : 73.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1162 helix: 1.65 (0.26), residues: 411 sheet: 0.53 (0.30), residues: 289 loop : -0.71 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.011 0.001 HIS C 183 PHE 0.011 0.001 PHE C 199 TYR 0.026 0.001 TYR B 285 ARG 0.013 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4617.73 seconds wall clock time: 82 minutes 28.87 seconds (4948.87 seconds total)