Starting phenix.real_space_refine on Mon Mar 11 13:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wc9_37435/03_2024/8wc9_37435_neut_updated.pdb" } resolution = 3.2 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= 0.034 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 59 5.16 5 C 5350 2.51 5 N 1430 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 390": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "R PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R ASP 119": "OD1" <-> "OD2" Residue "R PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 220": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8394 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1801 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2521 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1932 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "S" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1737 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "Y" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 393 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.58 Number of scatterers: 8394 At special positions: 0 Unit cell: (87.55, 122.4, 121.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 59 16.00 O 1554 8.00 N 1430 7.00 C 5350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " 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=2.03 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 15 sheets defined 32.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.684A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.682A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 238' Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.199A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.566A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'R' and resid 26 through 48 removed outlier: 3.525A pdb=" N MET R 29 " --> pdb=" O TYR R 26 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 31 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR R 36 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY R 39 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN R 40 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE R 42 " --> pdb=" O GLY R 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE R 45 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE R 47 " --> pdb=" O ILE R 44 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER R 48 " --> pdb=" O ILE R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 85 removed outlier: 3.820A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Proline residue: R 77 - end of helix removed outlier: 4.087A pdb=" N GLU R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 124 removed outlier: 4.005A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 136 through 157 removed outlier: 3.882A pdb=" N LEU R 140 " --> pdb=" O ILE R 136 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 187 through 195 removed outlier: 3.754A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 Processing helix chain 'R' and resid 208 through 219 removed outlier: 3.943A pdb=" N ILE R 212 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 274 removed outlier: 4.365A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET R 253 " --> pdb=" O THR R 249 " (cutoff:3.500A) Proline residue: R 263 - end of helix Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 302 removed outlier: 3.711A pdb=" N ASN R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER R 294 " --> pdb=" O GLY R 290 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 309 No H-bonds generated for 'chain 'R' and resid 306 through 309' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 30 through 33 No H-bonds generated for 'chain 'Y' and resid 30 through 33' Processing helix chain 'Y' and resid 36 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.586A pdb=" N ALA A 243 " --> pdb=" O LEU A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.903A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.800A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.724A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.598A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.982A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.509A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.771A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.540A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= N, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.848A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR S 227 " --> pdb=" O THR S 243 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'S' and resid 174 through 176 312 hydrogen bonds defined for protein. 882 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: 2.14 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 1698 1.33 - 1.48: 3286 1.48 - 1.63: 3505 1.63 - 1.79: 14 1.79 - 1.94: 72 Bond restraints: 8575 Sorted by residual: bond pdb=" CA ALA R 302 " pdb=" C ALA R 302 " ideal model delta sigma weight residual 1.525 1.449 0.076 1.11e-02 8.12e+03 4.67e+01 bond pdb=" C ASP R 126 " pdb=" O ASP R 126 " ideal model delta sigma weight residual 1.249 1.204 0.045 8.50e-03 1.38e+04 2.84e+01 bond pdb=" C ALA B 113 " pdb=" O ALA B 113 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.26e-02 6.30e+03 2.11e+01 bond pdb=" C VAL R 208 " pdb=" O VAL R 208 " ideal model delta sigma weight residual 1.238 1.177 0.060 1.32e-02 5.74e+03 2.09e+01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.35e-02 5.49e+03 2.02e+01 ... (remaining 8570 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.80: 236 106.80 - 114.36: 4878 114.36 - 121.92: 4722 121.92 - 129.48: 1749 129.48 - 137.05: 68 Bond angle restraints: 11653 Sorted by residual: angle pdb=" N SER B 334 " pdb=" CA SER B 334 " pdb=" C SER B 334 " ideal model delta sigma weight residual 112.58 124.09 -11.51 1.22e+00 6.72e-01 8.91e+01 angle pdb=" N SER R 46 " pdb=" CA SER R 46 " pdb=" C SER R 46 " ideal model delta sigma weight residual 112.89 104.68 8.21 1.24e+00 6.50e-01 4.38e+01 angle pdb=" N ILE R 200 " pdb=" CA ILE R 200 " pdb=" CB ILE R 200 " ideal model delta sigma weight residual 110.50 114.57 -4.07 6.30e-01 2.52e+00 4.18e+01 angle pdb=" C ILE R 32 " pdb=" CA ILE R 32 " pdb=" CB ILE R 32 " ideal model delta sigma weight residual 111.88 104.01 7.87 1.28e+00 6.10e-01 3.78e+01 angle pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" C ASN B 119 " ideal model delta sigma weight residual 111.74 119.77 -8.03 1.35e+00 5.49e-01 3.54e+01 ... (remaining 11648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.16: 4389 14.16 - 28.31: 441 28.31 - 42.46: 157 42.46 - 56.62: 33 56.62 - 70.77: 11 Dihedral angle restraints: 5031 sinusoidal: 1822 harmonic: 3209 Sorted by residual: dihedral pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual 122.80 136.44 -13.64 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" C SER B 334 " pdb=" N SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta harmonic sigma weight residual -122.60 -135.71 13.11 0 2.50e+00 1.60e-01 2.75e+01 dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.43 35.57 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 5028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1273 0.121 - 0.241: 47 0.241 - 0.362: 9 0.362 - 0.482: 2 0.482 - 0.603: 1 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" CA PRO R 298 " pdb=" N PRO R 298 " pdb=" C PRO R 298 " pdb=" CB PRO R 298 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA ASN R 40 " pdb=" N ASN R 40 " pdb=" C ASN R 40 " pdb=" CB ASN R 40 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 1329 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 200 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO R 201 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO R 201 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 201 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C TYR R 301 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 193 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ALA R 193 " -0.043 2.00e-02 2.50e+03 pdb=" O ALA R 193 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE R 194 " 0.015 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1017 2.74 - 3.28: 7925 3.28 - 3.82: 12879 3.82 - 4.36: 15107 4.36 - 4.90: 26939 Nonbonded interactions: 63867 Sorted by model distance: nonbonded pdb=" OG1 THR R 55 " pdb=" OD1 ASN R 58 " model vdw 2.205 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.217 2.440 nonbonded pdb=" ND2 ASN B 119 " pdb=" O THR B 143 " model vdw 2.281 2.520 nonbonded pdb=" NH1 ARG S 180 " pdb=" OE1 GLN S 186 " model vdw 2.286 2.520 nonbonded pdb=" NE2 GLN S 3 " pdb=" OG SER S 25 " model vdw 2.289 2.520 ... (remaining 63862 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: 0.730 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: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.730 Find NCS groups from input model: 0.310 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.007 0.076 8575 Z= 0.487 Angle : 0.906 12.047 11653 Z= 0.575 Chirality : 0.064 0.603 1332 Planarity : 0.006 0.104 1480 Dihedral : 13.761 70.775 2948 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.16 % Allowed : 2.43 % Favored : 96.41 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1079 helix: 0.73 (0.28), residues: 369 sheet: -0.03 (0.33), residues: 257 loop : -1.73 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 307 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE R 198 TYR 0.023 0.002 TYR R 287 ARG 0.006 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7817 (ptmt) cc_final: 0.7296 (pttp) REVERT: A 390 GLU cc_start: 0.7904 (tp30) cc_final: 0.7703 (tp30) REVERT: B 301 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8262 (mtmm) REVERT: R 50 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5807 (t80) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 0.2343 time to fit residues: 49.4271 Evaluate side-chains 133 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN B 340 ASN R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8575 Z= 0.152 Angle : 0.524 6.640 11653 Z= 0.278 Chirality : 0.042 0.162 1332 Planarity : 0.004 0.042 1480 Dihedral : 5.332 65.194 1198 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 8.46 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1079 helix: 1.27 (0.29), residues: 360 sheet: 0.11 (0.34), residues: 264 loop : -1.62 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS A 362 PHE 0.014 0.001 PHE R 303 TYR 0.022 0.001 TYR R 287 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7851 (ptmt) cc_final: 0.7339 (pttp) REVERT: R 50 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5807 (t80) REVERT: R 119 ASP cc_start: 0.8462 (t0) cc_final: 0.8209 (t0) outliers start: 10 outliers final: 4 residues processed: 140 average time/residue: 0.2062 time to fit residues: 40.2244 Evaluate side-chains 126 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 126 ASP Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 75 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8575 Z= 0.205 Angle : 0.523 6.489 11653 Z= 0.277 Chirality : 0.042 0.180 1332 Planarity : 0.004 0.040 1480 Dihedral : 5.025 63.900 1194 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.39 % Allowed : 12.98 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1079 helix: 1.36 (0.29), residues: 361 sheet: 0.08 (0.33), residues: 269 loop : -1.66 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR R 287 ARG 0.004 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7880 (ptmt) cc_final: 0.7364 (pttp) REVERT: R 50 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.5889 (t80) REVERT: R 119 ASP cc_start: 0.8485 (t0) cc_final: 0.8223 (t0) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 0.2058 time to fit residues: 38.2768 Evaluate side-chains 130 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8575 Z= 0.199 Angle : 0.512 6.364 11653 Z= 0.271 Chirality : 0.042 0.190 1332 Planarity : 0.004 0.039 1480 Dihedral : 4.523 49.547 1191 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.85 % Allowed : 14.60 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1079 helix: 1.41 (0.29), residues: 359 sheet: 0.05 (0.33), residues: 268 loop : -1.60 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 PHE 0.011 0.001 PHE B 199 TYR 0.020 0.001 TYR R 287 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7903 (ptmt) cc_final: 0.7415 (pttp) REVERT: A 307 LYS cc_start: 0.5584 (mmtt) cc_final: 0.5291 (mmtm) REVERT: R 50 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.5631 (t80) REVERT: R 119 ASP cc_start: 0.8454 (t0) cc_final: 0.8175 (t0) outliers start: 16 outliers final: 10 residues processed: 133 average time/residue: 0.2212 time to fit residues: 39.5820 Evaluate side-chains 129 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.0070 chunk 94 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.0770 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8575 Z= 0.118 Angle : 0.463 6.200 11653 Z= 0.244 Chirality : 0.040 0.203 1332 Planarity : 0.003 0.039 1480 Dihedral : 4.215 49.258 1191 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.27 % Allowed : 15.41 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1079 helix: 1.63 (0.29), residues: 359 sheet: 0.12 (0.32), residues: 278 loop : -1.51 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS A 362 PHE 0.009 0.001 PHE B 199 TYR 0.023 0.001 TYR R 287 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7878 (ptmt) cc_final: 0.7410 (pttp) REVERT: B 325 MET cc_start: 0.6581 (mtt) cc_final: 0.6218 (mtm) REVERT: R 50 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.5703 (t80) REVERT: R 119 ASP cc_start: 0.8374 (t0) cc_final: 0.8108 (t0) outliers start: 11 outliers final: 5 residues processed: 140 average time/residue: 0.2808 time to fit residues: 52.8863 Evaluate side-chains 129 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 26 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.0060 chunk 101 optimal weight: 4.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 239 ASN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8575 Z= 0.199 Angle : 0.507 6.683 11653 Z= 0.267 Chirality : 0.042 0.180 1332 Planarity : 0.003 0.037 1480 Dihedral : 4.349 48.664 1191 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.09 % Allowed : 16.11 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1079 helix: 1.53 (0.29), residues: 360 sheet: 0.10 (0.33), residues: 268 loop : -1.51 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE A 376 TYR 0.012 0.001 TYR A 37 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7489 (pttp) REVERT: B 325 MET cc_start: 0.6567 (mtt) cc_final: 0.6263 (mtm) REVERT: R 50 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.5631 (t80) REVERT: R 119 ASP cc_start: 0.8467 (t0) cc_final: 0.8182 (t0) outliers start: 18 outliers final: 11 residues processed: 133 average time/residue: 0.2117 time to fit residues: 38.7138 Evaluate side-chains 132 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8575 Z= 0.128 Angle : 0.470 6.312 11653 Z= 0.245 Chirality : 0.041 0.209 1332 Planarity : 0.003 0.037 1480 Dihedral : 4.105 48.191 1191 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.39 % Allowed : 17.38 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1079 helix: 1.64 (0.29), residues: 361 sheet: 0.12 (0.33), residues: 271 loop : -1.43 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE A 376 TYR 0.009 0.001 TYR A 37 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7454 (pttp) REVERT: B 325 MET cc_start: 0.6428 (mtt) cc_final: 0.6097 (mtm) REVERT: R 50 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.5615 (t80) REVERT: R 119 ASP cc_start: 0.8353 (t0) cc_final: 0.8121 (t0) outliers start: 12 outliers final: 9 residues processed: 135 average time/residue: 0.2156 time to fit residues: 39.9899 Evaluate side-chains 135 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 297 ASN S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8575 Z= 0.223 Angle : 0.531 8.019 11653 Z= 0.278 Chirality : 0.042 0.202 1332 Planarity : 0.003 0.037 1480 Dihedral : 4.405 47.681 1191 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.74 % Allowed : 17.73 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1079 helix: 1.45 (0.29), residues: 361 sheet: 0.18 (0.33), residues: 263 loop : -1.57 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.005 0.001 HIS A 362 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR S 190 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.8042 (ptmt) cc_final: 0.7570 (pttp) REVERT: A 392 ASN cc_start: 0.8510 (p0) cc_final: 0.8242 (p0) REVERT: B 325 MET cc_start: 0.6557 (mtt) cc_final: 0.6265 (mtm) REVERT: R 50 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.5625 (t80) REVERT: R 119 ASP cc_start: 0.8461 (t0) cc_final: 0.8181 (t0) REVERT: S 18 ARG cc_start: 0.7628 (mmm160) cc_final: 0.6786 (mmm-85) outliers start: 15 outliers final: 12 residues processed: 133 average time/residue: 0.2129 time to fit residues: 38.8922 Evaluate side-chains 135 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 0.0870 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8575 Z= 0.127 Angle : 0.479 7.296 11653 Z= 0.250 Chirality : 0.041 0.230 1332 Planarity : 0.003 0.037 1480 Dihedral : 4.127 47.562 1191 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.27 % Allowed : 17.84 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1079 helix: 1.63 (0.29), residues: 359 sheet: 0.20 (0.33), residues: 268 loop : -1.49 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 PHE 0.009 0.001 PHE B 199 TYR 0.022 0.001 TYR R 287 ARG 0.008 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7934 (ptmt) cc_final: 0.7510 (pttp) REVERT: B 325 MET cc_start: 0.6455 (mtt) cc_final: 0.6128 (mtm) REVERT: R 50 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.5582 (t80) REVERT: R 119 ASP cc_start: 0.8343 (t0) cc_final: 0.8083 (t0) REVERT: S 18 ARG cc_start: 0.7617 (mmm160) cc_final: 0.6812 (mmm-85) outliers start: 11 outliers final: 9 residues processed: 134 average time/residue: 0.2176 time to fit residues: 39.8423 Evaluate side-chains 135 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN B 75 GLN B 183 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8575 Z= 0.228 Angle : 0.532 7.372 11653 Z= 0.280 Chirality : 0.042 0.211 1332 Planarity : 0.003 0.037 1480 Dihedral : 4.399 47.078 1191 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.62 % Allowed : 17.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1079 helix: 1.51 (0.29), residues: 358 sheet: 0.20 (0.33), residues: 264 loop : -1.62 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR S 190 ARG 0.008 0.000 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 274 LYS cc_start: 0.7965 (ptmt) cc_final: 0.7536 (pttp) REVERT: A 392 ASN cc_start: 0.8501 (p0) cc_final: 0.8270 (p0) REVERT: B 301 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8080 (mtmm) REVERT: B 325 MET cc_start: 0.6515 (mtt) cc_final: 0.6222 (mtm) REVERT: R 50 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.5531 (t80) REVERT: R 119 ASP cc_start: 0.8466 (t0) cc_final: 0.8180 (t0) REVERT: S 18 ARG cc_start: 0.7657 (mmm160) cc_final: 0.6887 (mmm160) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.2123 time to fit residues: 38.1299 Evaluate side-chains 137 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 167 VAL Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122815 restraints weight = 10127.532| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.72 r_work: 0.3304 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8575 Z= 0.130 Angle : 0.481 7.242 11653 Z= 0.251 Chirality : 0.040 0.227 1332 Planarity : 0.003 0.036 1480 Dihedral : 4.096 46.808 1191 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.16 % Allowed : 18.19 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1079 helix: 1.63 (0.29), residues: 360 sheet: 0.17 (0.33), residues: 268 loop : -1.49 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 PHE 0.009 0.001 PHE A 376 TYR 0.020 0.001 TYR R 287 ARG 0.007 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.48 seconds wall clock time: 39 minutes 9.58 seconds (2349.58 seconds total)