Starting phenix.real_space_refine on Fri Jul 19 17:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/07_2024/8jpn_36484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/07_2024/8jpn_36484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/07_2024/8jpn_36484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/07_2024/8jpn_36484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/07_2024/8jpn_36484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpn_36484/07_2024/8jpn_36484.cif" } resolution = 2.9 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= -0.001 sd= 0.049 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 52 5.16 5 C 5469 2.51 5 N 1447 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 276": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "R GLU 18": "OE1" <-> "OE2" Residue "R TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 119": "OD1" <-> "OD2" Residue "S ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8557 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 33} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2528 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 336} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 397 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2187 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "S" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1723 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'U9S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.52 Number of scatterers: 8557 At special positions: 0 Unit cell: (90.316, 124.69, 130.756, 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 52 16.00 O 1589 8.00 N 1447 7.00 C 5469 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 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: 3.33 Conformation dependent library (CDL) restraints added in 3.3 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.632A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.338A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.508A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.790A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.597A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 11 through 51 removed outlier: 4.827A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 74 Processing helix chain 'R' and resid 76 through 86 Processing helix chain 'R' and resid 91 through 126 removed outlier: 3.897A pdb=" N TYR R 100 " --> pdb=" O ILE R 96 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL R 101 " --> pdb=" O SER R 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU R 102 " --> pdb=" O ASN R 98 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS R 103 " --> pdb=" O ARG R 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 134 Processing helix chain 'R' and resid 135 through 155 Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 174 through 178 Processing helix chain 'R' and resid 180 through 196 Processing helix chain 'R' and resid 196 through 220 Processing helix chain 'R' and resid 227 through 259 removed outlier: 3.725A pdb=" N LEU R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.607A pdb=" N ARG R 259 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 285 removed outlier: 3.669A pdb=" N ASN R 274 " --> pdb=" O GLN R 270 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR R 280 " --> pdb=" O PHE R 276 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) Proline residue: R 282 - end of helix removed outlier: 3.841A pdb=" N PHE R 285 " --> pdb=" O ARG R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 296 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 312 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.525A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.639A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.702A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.934A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.006A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.691A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.979A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.582A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.694A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.016A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.016A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.562A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1299 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: 2.68 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2763 1.34 - 1.46: 2216 1.46 - 1.58: 3690 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 8743 Sorted by residual: bond pdb=" N VAL R 289 " pdb=" CA VAL R 289 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.04e+00 bond pdb=" N SER R 288 " pdb=" CA SER R 288 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.33e-02 5.65e+03 5.63e+00 bond pdb=" C04 U9S R 501 " pdb=" C05 U9S R 501 " ideal model delta sigma weight residual 1.466 1.504 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" N LEU S 219 " pdb=" CA LEU S 219 " ideal model delta sigma weight residual 1.456 1.480 -0.024 1.27e-02 6.20e+03 3.52e+00 bond pdb=" N ARG S 218 " pdb=" CA ARG S 218 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.33e+00 ... (remaining 8738 not shown) Histogram of bond angle deviations from ideal: 57.86 - 73.09: 3 73.09 - 88.32: 0 88.32 - 103.55: 84 103.55 - 118.78: 6888 118.78 - 134.01: 4940 Bond angle restraints: 11915 Sorted by residual: angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N ALA A 41 " ideal model delta sigma weight residual 114.58 117.46 -2.88 8.60e-01 1.35e+00 1.12e+01 angle pdb=" N SER R 288 " pdb=" CA SER R 288 " pdb=" C SER R 288 " ideal model delta sigma weight residual 113.28 109.26 4.02 1.22e+00 6.72e-01 1.09e+01 angle pdb=" CB MET R 251 " pdb=" CG MET R 251 " pdb=" SD MET R 251 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C SER S 217 " pdb=" N ARG S 218 " pdb=" CA ARG S 218 " ideal model delta sigma weight residual 121.54 115.82 5.72 1.91e+00 2.74e-01 8.97e+00 angle pdb=" CA CYS S 96 " pdb=" CB CYS S 96 " pdb=" SG CYS S 96 " ideal model delta sigma weight residual 114.40 120.79 -6.39 2.30e+00 1.89e-01 7.73e+00 ... (remaining 11910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4490 17.06 - 34.13: 454 34.13 - 51.19: 133 51.19 - 68.25: 21 68.25 - 85.32: 9 Dihedral angle restraints: 5107 sinusoidal: 1746 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 268 " pdb=" CB CYS R 268 " ideal model delta sinusoidal sigma weight residual -86.00 -47.23 -38.77 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 808 0.030 - 0.059: 360 0.059 - 0.089: 131 0.089 - 0.118: 73 0.118 - 0.148: 16 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA VAL R 289 " pdb=" N VAL R 289 " pdb=" C VAL R 289 " pdb=" CB VAL R 289 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA PRO S 236 " pdb=" N PRO S 236 " pdb=" C PRO S 236 " pdb=" CB PRO S 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1385 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO S 75 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 236 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 119 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" CG ASP R 119 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP R 119 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP R 119 " -0.010 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2107 2.79 - 3.32: 7395 3.32 - 3.85: 13568 3.85 - 4.37: 16028 4.37 - 4.90: 28748 Nonbonded interactions: 67846 Sorted by model distance: nonbonded pdb=" O ALA R 104 " pdb=" OG1 THR R 108 " model vdw 2.268 2.440 nonbonded pdb=" O VAL R 272 " pdb=" OG SER R 275 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.298 2.440 nonbonded pdb=" OE1 GLU S 6 " pdb=" N GLY S 114 " model vdw 2.328 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.333 2.520 ... (remaining 67841 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: 23.080 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.160 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.004 0.039 8743 Z= 0.243 Angle : 0.608 9.704 11915 Z= 0.335 Chirality : 0.043 0.148 1388 Planarity : 0.004 0.067 1514 Dihedral : 15.560 85.318 2929 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.36 % Allowed : 20.90 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.11 (0.25), residues: 1141 helix: 2.43 (0.27), residues: 389 sheet: 1.04 (0.30), residues: 277 loop : -0.94 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.028 0.002 PHE R 34 TYR 0.014 0.001 TYR R 25 ARG 0.009 0.000 ARG R 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 0.930 Fit side-chains REVERT: A 293 SER cc_start: 0.7508 (m) cc_final: 0.7123 (m) REVERT: B 212 ASP cc_start: 0.5923 (t0) cc_final: 0.5644 (t70) REVERT: R 151 THR cc_start: 0.7725 (m) cc_final: 0.7501 (p) REVERT: R 204 CYS cc_start: 0.7966 (m) cc_final: 0.7513 (m) REVERT: R 208 TYR cc_start: 0.7321 (t80) cc_final: 0.7010 (t80) outliers start: 3 outliers final: 3 residues processed: 194 average time/residue: 0.9999 time to fit residues: 208.3367 Evaluate side-chains 117 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain S residue 73 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 269 ASN B 259 GLN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 ASN S 113 GLN S 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8743 Z= 0.267 Angle : 0.637 6.993 11915 Z= 0.343 Chirality : 0.045 0.213 1388 Planarity : 0.005 0.050 1514 Dihedral : 4.569 28.222 1246 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.11 % Allowed : 20.67 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.07 (0.25), residues: 1141 helix: 2.56 (0.26), residues: 390 sheet: 1.11 (0.31), residues: 271 loop : -1.17 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.005 0.002 HIS R 131 PHE 0.017 0.002 PHE R 34 TYR 0.025 0.002 TYR R 277 ARG 0.010 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 126 time to evaluate : 0.869 Fit side-chains REVERT: B 258 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.6984 (t70) REVERT: R 111 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7838 (mm) REVERT: R 151 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7742 (p) REVERT: R 204 CYS cc_start: 0.8101 (m) cc_final: 0.7474 (m) REVERT: R 208 TYR cc_start: 0.7541 (t80) cc_final: 0.7159 (t80) REVERT: S 183 GLN cc_start: 0.8749 (mt0) cc_final: 0.8420 (mt0) REVERT: S 202 ARG cc_start: 0.7390 (mtp180) cc_final: 0.6851 (mtp180) outliers start: 43 outliers final: 13 residues processed: 155 average time/residue: 1.0565 time to fit residues: 175.7783 Evaluate side-chains 118 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 235 ILE Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 259 GLN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 134 GLN R 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8743 Z= 0.229 Angle : 0.576 7.358 11915 Z= 0.309 Chirality : 0.043 0.142 1388 Planarity : 0.004 0.049 1514 Dihedral : 4.388 29.934 1242 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.56 % Allowed : 22.80 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1141 helix: 2.80 (0.26), residues: 391 sheet: 0.85 (0.30), residues: 280 loop : -1.10 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.012 0.001 TYR R 277 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.863 Fit side-chains REVERT: A 9 ASP cc_start: 0.8510 (m-30) cc_final: 0.8289 (m-30) REVERT: A 20 ASP cc_start: 0.8617 (m-30) cc_final: 0.8253 (m-30) REVERT: A 186 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: B 217 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8210 (pmt) REVERT: B 234 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8667 (t80) REVERT: B 258 ASP cc_start: 0.7894 (t70) cc_final: 0.7663 (t0) REVERT: R 151 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7820 (p) REVERT: R 209 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7708 (mttt) REVERT: S 3 GLN cc_start: 0.8125 (mt0) cc_final: 0.7804 (mm-40) REVERT: S 11 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7247 (mp) REVERT: S 183 GLN cc_start: 0.8609 (mt0) cc_final: 0.8344 (mt0) outliers start: 30 outliers final: 9 residues processed: 133 average time/residue: 1.1166 time to fit residues: 158.7360 Evaluate side-chains 120 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8743 Z= 0.160 Angle : 0.500 5.551 11915 Z= 0.269 Chirality : 0.041 0.143 1388 Planarity : 0.004 0.052 1514 Dihedral : 4.089 26.992 1242 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.97 % Allowed : 23.63 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.33 (0.25), residues: 1141 helix: 2.91 (0.26), residues: 400 sheet: 0.82 (0.30), residues: 283 loop : -0.99 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR R 25 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.934 Fit side-chains REVERT: A 186 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 22 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5034 (mpt-90) REVERT: B 234 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8789 (t80) REVERT: B 258 ASP cc_start: 0.8002 (t70) cc_final: 0.7713 (t0) REVERT: R 151 THR cc_start: 0.8106 (m) cc_final: 0.7851 (p) REVERT: R 209 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7739 (mttt) outliers start: 25 outliers final: 10 residues processed: 133 average time/residue: 1.0710 time to fit residues: 152.7138 Evaluate side-chains 125 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 269 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.0000 chunk 45 optimal weight: 0.0270 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 0.0170 chunk 36 optimal weight: 5.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8743 Z= 0.163 Angle : 0.506 5.952 11915 Z= 0.271 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.054 1514 Dihedral : 3.987 25.192 1242 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 23.87 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.42 (0.25), residues: 1141 helix: 2.99 (0.26), residues: 403 sheet: 0.82 (0.30), residues: 284 loop : -0.93 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.025 0.001 PHE R 34 TYR 0.011 0.001 TYR S 190 ARG 0.008 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.957 Fit side-chains REVERT: A 186 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: B 22 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.5040 (mpt-90) REVERT: B 217 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7978 (pmt) REVERT: B 227 SER cc_start: 0.9422 (m) cc_final: 0.9071 (t) REVERT: B 234 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8697 (t80) REVERT: B 258 ASP cc_start: 0.8018 (t70) cc_final: 0.7748 (t0) REVERT: R 151 THR cc_start: 0.8103 (m) cc_final: 0.7851 (p) outliers start: 26 outliers final: 14 residues processed: 136 average time/residue: 1.1166 time to fit residues: 162.8025 Evaluate side-chains 133 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 17 GLN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.6954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8743 Z= 0.338 Angle : 0.637 8.260 11915 Z= 0.338 Chirality : 0.046 0.166 1388 Planarity : 0.004 0.057 1514 Dihedral : 4.558 27.928 1242 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.68 % Allowed : 22.80 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.07 (0.25), residues: 1141 helix: 2.74 (0.26), residues: 398 sheet: 0.67 (0.30), residues: 286 loop : -1.16 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS S 35 PHE 0.018 0.002 PHE R 241 TYR 0.018 0.002 TYR R 25 ARG 0.006 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 0.973 Fit side-chains REVERT: A 20 ASP cc_start: 0.8621 (m-30) cc_final: 0.8295 (m-30) REVERT: A 186 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 251 ASP cc_start: 0.8451 (t70) cc_final: 0.8075 (t70) REVERT: A 285 ILE cc_start: 0.8243 (mm) cc_final: 0.7995 (mt) REVERT: B 22 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.5165 (mpt-90) REVERT: B 227 SER cc_start: 0.9445 (m) cc_final: 0.9089 (t) REVERT: B 234 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8800 (t80) REVERT: R 214 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7391 (mp) REVERT: S 179 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8798 (tt0) outliers start: 31 outliers final: 16 residues processed: 138 average time/residue: 0.9846 time to fit residues: 146.5059 Evaluate side-chains 132 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8743 Z= 0.151 Angle : 0.502 7.836 11915 Z= 0.269 Chirality : 0.041 0.145 1388 Planarity : 0.004 0.054 1514 Dihedral : 4.108 24.781 1242 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.14 % Allowed : 24.70 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.36 (0.25), residues: 1141 helix: 2.96 (0.26), residues: 402 sheet: 0.83 (0.30), residues: 278 loop : -0.98 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.013 0.001 TYR S 190 ARG 0.007 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.043 Fit side-chains REVERT: A 285 ILE cc_start: 0.8282 (mm) cc_final: 0.8031 (mt) REVERT: B 22 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.5144 (mpt-90) REVERT: B 217 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7977 (pmt) REVERT: B 227 SER cc_start: 0.9407 (m) cc_final: 0.9085 (t) REVERT: B 234 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8770 (t80) REVERT: R 214 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7236 (mp) outliers start: 18 outliers final: 6 residues processed: 133 average time/residue: 1.1335 time to fit residues: 161.3662 Evaluate side-chains 126 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 0.0020 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.7113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8743 Z= 0.156 Angle : 0.518 12.201 11915 Z= 0.272 Chirality : 0.041 0.141 1388 Planarity : 0.004 0.054 1514 Dihedral : 3.985 23.653 1242 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.26 % Allowed : 25.06 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.43 (0.25), residues: 1141 helix: 3.00 (0.26), residues: 405 sheet: 0.85 (0.30), residues: 278 loop : -0.94 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.020 0.001 TYR R 25 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.899 Fit side-chains REVERT: A 229 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 285 ILE cc_start: 0.8306 (mm) cc_final: 0.8051 (mt) REVERT: B 22 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.5121 (mpt-90) REVERT: B 217 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.7987 (pmt) REVERT: B 227 SER cc_start: 0.9406 (m) cc_final: 0.9087 (t) REVERT: B 234 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8710 (t80) REVERT: R 214 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7193 (mp) outliers start: 19 outliers final: 10 residues processed: 129 average time/residue: 1.0757 time to fit residues: 148.9751 Evaluate side-chains 130 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 255 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8743 Z= 0.163 Angle : 0.522 13.759 11915 Z= 0.274 Chirality : 0.041 0.141 1388 Planarity : 0.004 0.055 1514 Dihedral : 3.947 23.123 1242 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.26 % Allowed : 25.42 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.48 (0.25), residues: 1141 helix: 3.04 (0.26), residues: 404 sheet: 0.88 (0.30), residues: 278 loop : -0.91 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR S 190 ARG 0.005 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.975 Fit side-chains REVERT: A 35 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8817 (mtmt) REVERT: A 229 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 285 ILE cc_start: 0.8321 (mm) cc_final: 0.8058 (mt) REVERT: B 217 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8003 (pmt) REVERT: B 227 SER cc_start: 0.9397 (m) cc_final: 0.9090 (t) REVERT: B 234 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8709 (t80) REVERT: R 214 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7188 (mp) outliers start: 19 outliers final: 10 residues processed: 133 average time/residue: 1.0742 time to fit residues: 153.4892 Evaluate side-chains 129 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.7239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8743 Z= 0.158 Angle : 0.523 14.024 11915 Z= 0.273 Chirality : 0.041 0.141 1388 Planarity : 0.004 0.055 1514 Dihedral : 3.923 22.671 1242 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.90 % Allowed : 25.65 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.48 (0.25), residues: 1141 helix: 3.05 (0.26), residues: 404 sheet: 0.83 (0.30), residues: 282 loop : -0.90 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.016 0.001 TYR R 126 ARG 0.005 0.000 ARG C 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.910 Fit side-chains REVERT: A 35 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8802 (mtmt) REVERT: A 229 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8238 (t0) REVERT: A 285 ILE cc_start: 0.8321 (mm) cc_final: 0.8063 (mt) REVERT: B 217 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8013 (pmt) REVERT: B 227 SER cc_start: 0.9381 (m) cc_final: 0.9073 (t) REVERT: B 234 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8699 (t80) REVERT: R 214 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7185 (mp) outliers start: 16 outliers final: 10 residues processed: 126 average time/residue: 1.1258 time to fit residues: 152.1650 Evaluate side-chains 128 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0980 chunk 13 optimal weight: 0.0870 chunk 24 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** R 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111679 restraints weight = 10698.261| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.03 r_work: 0.2957 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8743 Z= 0.140 Angle : 0.507 14.070 11915 Z= 0.264 Chirality : 0.041 0.143 1388 Planarity : 0.004 0.054 1514 Dihedral : 3.818 21.477 1242 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.14 % Allowed : 25.65 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.52 (0.25), residues: 1141 helix: 3.07 (0.26), residues: 404 sheet: 0.85 (0.30), residues: 282 loop : -0.86 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 199 TYR 0.016 0.001 TYR R 126 ARG 0.005 0.000 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.74 seconds wall clock time: 62 minutes 3.89 seconds (3723.89 seconds total)