Starting phenix.real_space_refine on Mon Mar 11 16:12:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/03_2024/8j24_35944_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/03_2024/8j24_35944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/03_2024/8j24_35944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/03_2024/8j24_35944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/03_2024/8j24_35944_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j24_35944/03_2024/8j24_35944_updated.pdb" } resolution = 2.6 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5509 2.51 5 N 1464 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 229": "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: 8626 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2084 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "G" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1805 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'ACT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.59 Number of scatterers: 8626 At special positions: 0 Unit cell: (117.52, 106.08, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1596 8.00 N 1464 7.00 C 5509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'B' and resid 3 through 22 removed outlier: 3.633A pdb=" N GLN B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 4.737A pdb=" N ASN B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 32 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 227 through 231 removed outlier: 4.050A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 231' Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 257 through 259 No H-bonds generated for 'chain 'C' and resid 257 through 259' Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.693A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 308 Processing helix chain 'C' and resid 331 through 350 removed outlier: 3.879A pdb=" N ASP C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 37 removed outlier: 3.518A pdb=" N TYR D 14 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Proline residue: D 23 - end of helix Processing helix chain 'D' and resid 43 through 60 Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 79 through 112 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 123 through 147 removed outlier: 5.104A pdb=" N ILE D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL D 144 " --> pdb=" O HIS D 140 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 145 " --> pdb=" O CYS D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.525A pdb=" N LEU D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 189 through 208 Processing helix chain 'D' and resid 214 through 248 removed outlier: 3.560A pdb=" N ARG D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) Proline residue: D 237 - end of helix removed outlier: 3.856A pdb=" N HIS D 242 " --> pdb=" O TYR D 238 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 243 " --> pdb=" O ASN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 272 removed outlier: 4.201A pdb=" N SER D 256 " --> pdb=" O TRP D 253 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 257 " --> pdb=" O TRP D 254 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP D 269 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Proline residue: D 270 - end of helix Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing sheet with id= A, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.418A pdb=" N ASP B 81 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 87 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 98 through 103 removed outlier: 7.089A pdb=" N GLY B 113 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 101 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 111 " --> pdb=" O CYS B 101 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 103 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR B 109 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN B 123 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 133 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 144 through 149 removed outlier: 6.332A pdb=" N SER B 158 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 147 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 156 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE B 149 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLN B 154 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 168 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 174 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 185 through 190 removed outlier: 7.020A pdb=" N GLY B 200 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 188 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 198 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 190 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 196 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP B 210 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS B 216 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 227 through 232 removed outlier: 6.708A pdb=" N GLY B 242 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ILE B 230 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA B 240 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE B 232 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ALA B 238 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 243 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 260 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP B 252 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B 258 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.351A pdb=" N ASP B 296 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG B 302 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 315 through 318 removed outlier: 3.665A pdb=" N CYS B 315 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 329 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 47 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 338 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR B 45 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 319 through 323 removed outlier: 6.650A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS C 195 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU C 36 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS C 197 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU C 38 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 199 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.338A pdb=" N THR G 118 " --> pdb=" O VAL G 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 115 through 117 removed outlier: 3.575A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 141 through 143 removed outlier: 3.720A pdb=" N ALA G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 147 through 150 removed outlier: 6.547A pdb=" N LYS G 245 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL G 150 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU G 247 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 226 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU G 179 " --> pdb=" O LEU G 188 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU G 188 " --> pdb=" O LEU G 179 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1092 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: 2.64 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2774 1.34 - 1.46: 2142 1.46 - 1.58: 3817 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8814 Sorted by residual: bond pdb=" CA TYR G 236 " pdb=" C TYR G 236 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.07e+00 bond pdb=" N TYR G 236 " pdb=" CA TYR G 236 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.41e-02 5.03e+03 1.81e+00 bond pdb=" C ACT D 401 " pdb=" CH3 ACT D 401 " ideal model delta sigma weight residual 1.540 1.564 -0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" CA PRO G 237 " pdb=" C PRO G 237 " ideal model delta sigma weight residual 1.520 1.535 -0.016 1.42e-02 4.96e+03 1.21e+00 bond pdb=" CG ARG D 219 " pdb=" CD ARG D 219 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 8809 not shown) Histogram of bond angle deviations from ideal: 99.80 - 106.68: 204 106.68 - 113.56: 4804 113.56 - 120.44: 3250 120.44 - 127.32: 3591 127.32 - 134.20: 101 Bond angle restraints: 11950 Sorted by residual: angle pdb=" N TYR G 236 " pdb=" CA TYR G 236 " pdb=" C TYR G 236 " ideal model delta sigma weight residual 109.81 131.36 -21.55 2.21e+00 2.05e-01 9.51e+01 angle pdb=" C PRO G 237 " pdb=" CA PRO G 237 " pdb=" CB PRO G 237 " ideal model delta sigma weight residual 111.56 125.26 -13.70 1.65e+00 3.67e-01 6.90e+01 angle pdb=" C TYR G 236 " pdb=" N PRO G 237 " pdb=" CA PRO G 237 " ideal model delta sigma weight residual 119.84 129.57 -9.73 1.25e+00 6.40e-01 6.05e+01 angle pdb=" N ILE B 268 " pdb=" CA ILE B 268 " pdb=" C ILE B 268 " ideal model delta sigma weight residual 113.71 108.76 4.95 9.50e-01 1.11e+00 2.71e+01 angle pdb=" C GLU G 235 " pdb=" N TYR G 236 " pdb=" CA TYR G 236 " ideal model delta sigma weight residual 121.80 134.20 -12.40 2.44e+00 1.68e-01 2.58e+01 ... (remaining 11945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 4629 23.06 - 46.12: 479 46.12 - 69.18: 82 69.18 - 92.24: 11 92.24 - 115.29: 1 Dihedral angle restraints: 5202 sinusoidal: 2003 harmonic: 3199 Sorted by residual: dihedral pdb=" CA TYR G 236 " pdb=" C TYR G 236 " pdb=" N PRO G 237 " pdb=" CA PRO G 237 " ideal model delta harmonic sigma weight residual 180.00 64.71 115.29 0 5.00e+00 4.00e-02 5.32e+02 dihedral pdb=" C TYR G 236 " pdb=" N TYR G 236 " pdb=" CA TYR G 236 " pdb=" CB TYR G 236 " ideal model delta harmonic sigma weight residual -122.60 -155.16 32.56 0 2.50e+00 1.60e-01 1.70e+02 dihedral pdb=" N TYR G 236 " pdb=" C TYR G 236 " pdb=" CA TYR G 236 " pdb=" CB TYR G 236 " ideal model delta harmonic sigma weight residual 122.80 155.21 -32.41 0 2.50e+00 1.60e-01 1.68e+02 ... (remaining 5199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 1351 0.299 - 0.598: 0 0.598 - 0.896: 1 0.896 - 1.195: 0 1.195 - 1.494: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA TYR G 236 " pdb=" N TYR G 236 " pdb=" C TYR G 236 " pdb=" CB TYR G 236 " both_signs ideal model delta sigma weight residual False 2.51 1.02 1.49 2.00e-01 2.50e+01 5.58e+01 chirality pdb=" CA PRO G 237 " pdb=" N PRO G 237 " pdb=" C PRO G 237 " pdb=" CB PRO G 237 " both_signs ideal model delta sigma weight residual False 2.72 1.90 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA ILE G 58 " pdb=" N ILE G 58 " pdb=" C ILE G 58 " pdb=" CB ILE G 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1350 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 236 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO G 237 " 0.183 5.00e-02 4.00e+02 pdb=" CA PRO G 237 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 237 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 162 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C THR B 162 " 0.031 2.00e-02 2.50e+03 pdb=" O THR B 162 " -0.012 2.00e-02 2.50e+03 pdb=" N THR B 163 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 59 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C MET B 59 " 0.028 2.00e-02 2.50e+03 pdb=" O MET B 59 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS B 60 " -0.010 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 171 2.68 - 3.24: 7891 3.24 - 3.79: 13761 3.79 - 4.35: 18747 4.35 - 4.90: 31271 Nonbonded interactions: 71841 Sorted by model distance: nonbonded pdb=" O ILE D 16 " pdb=" OG1 THR D 20 " model vdw 2.131 2.440 nonbonded pdb=" O PHE D 87 " pdb=" OG SER D 91 " model vdw 2.215 2.440 nonbonded pdb=" O MET B 323 " pdb=" ND2 ASN B 338 " model vdw 2.278 2.520 nonbonded pdb=" OG SER G 162 " pdb=" O LYS G 164 " model vdw 2.293 2.440 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.305 2.440 ... (remaining 71836 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=0.01 max=1.00 mean=0.98 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.950 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.710 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.002 0.032 8814 Z= 0.116 Angle : 0.551 21.547 11950 Z= 0.284 Chirality : 0.060 1.494 1353 Planarity : 0.004 0.106 1510 Dihedral : 18.152 115.295 3134 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.93 % Favored : 97.88 % Rotamer: Outliers : 3.11 % Allowed : 29.29 % Favored : 67.60 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1087 helix: 1.51 (0.26), residues: 386 sheet: 1.35 (0.32), residues: 268 loop : -0.19 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 61 HIS 0.001 0.000 HIS F 40 PHE 0.022 0.001 PHE D 246 TYR 0.007 0.001 TYR G 59 ARG 0.010 0.000 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 223 time to evaluate : 0.984 Fit side-chains REVERT: B 100 THR cc_start: 0.7162 (p) cc_final: 0.6654 (t) REVERT: B 132 ARG cc_start: 0.7111 (ptp-170) cc_final: 0.6903 (ptp-170) REVERT: C 231 ASP cc_start: 0.6889 (t0) cc_final: 0.6575 (t0) REVERT: D 30 ARG cc_start: 0.7360 (ptm160) cc_final: 0.7134 (ptm160) REVERT: D 56 LEU cc_start: 0.8412 (tp) cc_final: 0.8126 (tp) REVERT: G 196 LEU cc_start: 0.8188 (mt) cc_final: 0.7969 (mm) REVERT: G 205 SER cc_start: 0.8449 (t) cc_final: 0.8245 (p) outliers start: 29 outliers final: 17 residues processed: 247 average time/residue: 1.0901 time to fit residues: 288.1133 Evaluate side-chains 231 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain G residue 207 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN C 241 ASN C 255 ASN G 172 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8814 Z= 0.299 Angle : 0.600 10.654 11950 Z= 0.312 Chirality : 0.046 0.313 1353 Planarity : 0.004 0.050 1510 Dihedral : 6.415 50.606 1222 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 5.47 % Allowed : 26.61 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 1.35 (0.25), residues: 1087 helix: 2.03 (0.26), residues: 391 sheet: 0.98 (0.31), residues: 286 loop : -0.23 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 47 HIS 0.005 0.001 HIS D 140 PHE 0.017 0.002 PHE D 89 TYR 0.016 0.002 TYR G 101 ARG 0.006 0.000 ARG D 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 202 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7870 (p) cc_final: 0.7474 (t) REVERT: B 132 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.7039 (ptp-170) REVERT: B 215 MET cc_start: 0.6954 (ppp) cc_final: 0.6350 (ppp) REVERT: B 232 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8022 (t80) REVERT: B 254 ARG cc_start: 0.7281 (mpp80) cc_final: 0.6932 (mtm180) REVERT: B 256 ASP cc_start: 0.6927 (t0) cc_final: 0.6659 (t0) REVERT: C 28 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7227 (mt-10) REVERT: C 269 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7968 (p0) REVERT: C 345 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7980 (mtpt) REVERT: D 30 ARG cc_start: 0.7286 (ptm160) cc_final: 0.7008 (ptm160) REVERT: D 52 THR cc_start: 0.8659 (m) cc_final: 0.8449 (m) REVERT: D 127 VAL cc_start: 0.8090 (t) cc_final: 0.7616 (m) REVERT: D 140 HIS cc_start: 0.8064 (m90) cc_final: 0.7668 (m-70) REVERT: D 173 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7319 (mp) REVERT: G 18 ARG cc_start: 0.7696 (ttt180) cc_final: 0.7413 (mmt180) REVERT: G 106 SER cc_start: 0.3088 (OUTLIER) cc_final: 0.2091 (t) outliers start: 51 outliers final: 22 residues processed: 234 average time/residue: 1.1633 time to fit residues: 290.1073 Evaluate side-chains 216 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.0050 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.0470 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 235 ASN B 237 ASN B 291 ASN C 241 ASN C 255 ASN D 248 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8814 Z= 0.204 Angle : 0.525 9.883 11950 Z= 0.273 Chirality : 0.043 0.281 1353 Planarity : 0.004 0.044 1510 Dihedral : 5.705 56.543 1211 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.58 % Favored : 97.24 % Rotamer: Outliers : 5.36 % Allowed : 27.04 % Favored : 67.60 % 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: 1.35 (0.25), residues: 1087 helix: 2.24 (0.26), residues: 385 sheet: 0.89 (0.30), residues: 286 loop : -0.36 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 209 HIS 0.003 0.001 HIS G 35 PHE 0.019 0.001 PHE D 246 TYR 0.012 0.001 TYR G 101 ARG 0.005 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.8010 (mtm) REVERT: B 100 THR cc_start: 0.7827 (p) cc_final: 0.7443 (t) REVERT: B 132 ARG cc_start: 0.7210 (ptp-170) cc_final: 0.6994 (ptp-170) REVERT: B 215 MET cc_start: 0.6943 (ppp) cc_final: 0.6481 (ppp) REVERT: B 232 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8083 (t80) REVERT: B 254 ARG cc_start: 0.7338 (mpp80) cc_final: 0.6911 (mtm180) REVERT: B 256 ASP cc_start: 0.6982 (t0) cc_final: 0.6776 (t0) REVERT: C 28 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7229 (mt-10) REVERT: C 231 ASP cc_start: 0.6974 (t0) cc_final: 0.6704 (t0) REVERT: C 345 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7860 (mtpt) REVERT: D 30 ARG cc_start: 0.7270 (ptm160) cc_final: 0.7012 (ptm160) REVERT: D 127 VAL cc_start: 0.8060 (t) cc_final: 0.7588 (m) REVERT: D 140 HIS cc_start: 0.7958 (m90) cc_final: 0.7584 (m-70) REVERT: D 146 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7320 (mm) REVERT: D 216 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.6402 (mtm-85) REVERT: G 18 ARG cc_start: 0.7757 (ttt180) cc_final: 0.7447 (mmt180) REVERT: G 106 SER cc_start: 0.3132 (OUTLIER) cc_final: 0.2187 (t) REVERT: G 228 TYR cc_start: 0.8651 (m-80) cc_final: 0.8412 (m-80) outliers start: 50 outliers final: 20 residues processed: 224 average time/residue: 1.2133 time to fit residues: 289.1965 Evaluate side-chains 212 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 0.0070 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 291 ASN C 241 ASN C 255 ASN C 322 HIS D 248 GLN G 172 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8814 Z= 0.210 Angle : 0.517 9.536 11950 Z= 0.270 Chirality : 0.043 0.302 1353 Planarity : 0.004 0.060 1510 Dihedral : 5.346 58.579 1205 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 5.69 % Allowed : 26.07 % Favored : 68.24 % 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: 1.37 (0.25), residues: 1087 helix: 2.36 (0.26), residues: 383 sheet: 0.80 (0.30), residues: 292 loop : -0.38 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 167 HIS 0.003 0.001 HIS G 35 PHE 0.012 0.001 PHE D 18 TYR 0.013 0.001 TYR G 101 ARG 0.006 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.7860 (p) cc_final: 0.7494 (t) REVERT: B 132 ARG cc_start: 0.7220 (ptp-170) cc_final: 0.6996 (ptp-170) REVERT: B 215 MET cc_start: 0.6945 (ppp) cc_final: 0.6252 (ppp) REVERT: B 232 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 254 ARG cc_start: 0.7386 (mpp80) cc_final: 0.6903 (mtm180) REVERT: B 256 ASP cc_start: 0.7017 (t0) cc_final: 0.6816 (t0) REVERT: C 28 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7222 (mt-10) REVERT: C 231 ASP cc_start: 0.6934 (t0) cc_final: 0.6637 (t0) REVERT: C 345 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7848 (mtpt) REVERT: D 30 ARG cc_start: 0.7262 (ptm160) cc_final: 0.6998 (ptm160) REVERT: D 52 THR cc_start: 0.8668 (m) cc_final: 0.8456 (m) REVERT: D 127 VAL cc_start: 0.8107 (t) cc_final: 0.7636 (m) REVERT: D 140 HIS cc_start: 0.7917 (m90) cc_final: 0.7559 (m-70) REVERT: D 173 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7350 (mp) REVERT: D 216 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.6444 (mtm-85) REVERT: G 18 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7500 (mmt180) REVERT: G 106 SER cc_start: 0.3009 (OUTLIER) cc_final: 0.2054 (t) outliers start: 53 outliers final: 30 residues processed: 225 average time/residue: 1.2385 time to fit residues: 296.1336 Evaluate side-chains 219 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN B 291 ASN B 338 ASN C 241 ASN C 255 ASN D 248 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8814 Z= 0.240 Angle : 0.533 10.649 11950 Z= 0.277 Chirality : 0.043 0.263 1353 Planarity : 0.004 0.060 1510 Dihedral : 5.406 59.562 1204 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 6.12 % Allowed : 26.29 % Favored : 67.60 % 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: 1.26 (0.25), residues: 1087 helix: 2.31 (0.26), residues: 384 sheet: 0.70 (0.29), residues: 292 loop : -0.47 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 167 HIS 0.004 0.001 HIS D 211 PHE 0.013 0.002 PHE D 18 TYR 0.017 0.002 TYR G 174 ARG 0.006 0.000 ARG C 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: B 100 THR cc_start: 0.8005 (p) cc_final: 0.7636 (t) REVERT: B 132 ARG cc_start: 0.7194 (ptp-170) cc_final: 0.6970 (ptp-170) REVERT: B 215 MET cc_start: 0.6880 (ppp) cc_final: 0.6190 (ppp) REVERT: B 232 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8087 (t80) REVERT: B 254 ARG cc_start: 0.7459 (mpp80) cc_final: 0.6966 (mtm180) REVERT: C 231 ASP cc_start: 0.6914 (t0) cc_final: 0.6659 (t0) REVERT: C 345 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7934 (mtpt) REVERT: D 30 ARG cc_start: 0.7289 (ptm160) cc_final: 0.7022 (ptm160) REVERT: D 127 VAL cc_start: 0.8104 (t) cc_final: 0.7667 (m) REVERT: D 140 HIS cc_start: 0.7849 (m90) cc_final: 0.7403 (m-70) REVERT: D 173 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7373 (mp) REVERT: G 106 SER cc_start: 0.3051 (OUTLIER) cc_final: 0.1991 (t) REVERT: G 228 TYR cc_start: 0.8700 (m-80) cc_final: 0.8395 (m-80) outliers start: 57 outliers final: 33 residues processed: 227 average time/residue: 1.1676 time to fit residues: 282.0513 Evaluate side-chains 224 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 345 LYS Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN B 228 ASN B 291 ASN C 241 ASN C 255 ASN D 248 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8814 Z= 0.217 Angle : 0.515 8.720 11950 Z= 0.269 Chirality : 0.042 0.188 1353 Planarity : 0.004 0.049 1510 Dihedral : 5.248 54.975 1204 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.94 % Allowed : 27.47 % Favored : 67.60 % 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: 1.24 (0.25), residues: 1087 helix: 2.31 (0.26), residues: 384 sheet: 0.66 (0.30), residues: 292 loop : -0.48 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 167 HIS 0.003 0.001 HIS G 35 PHE 0.013 0.001 PHE D 18 TYR 0.021 0.002 TYR G 236 ARG 0.007 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 193 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: B 99 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: B 100 THR cc_start: 0.7911 (p) cc_final: 0.7587 (t) REVERT: B 132 ARG cc_start: 0.7187 (ptp-170) cc_final: 0.6957 (ptp-170) REVERT: B 215 MET cc_start: 0.6708 (ppp) cc_final: 0.6274 (ppp) REVERT: B 232 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8166 (t80) REVERT: B 254 ARG cc_start: 0.7467 (mpp80) cc_final: 0.6965 (mtm180) REVERT: C 231 ASP cc_start: 0.6915 (t0) cc_final: 0.6651 (t0) REVERT: C 269 ASN cc_start: 0.8218 (p0) cc_final: 0.8002 (p0) REVERT: D 30 ARG cc_start: 0.7293 (ptm160) cc_final: 0.7029 (ptm160) REVERT: D 52 THR cc_start: 0.8660 (m) cc_final: 0.8437 (m) REVERT: D 127 VAL cc_start: 0.8100 (t) cc_final: 0.7630 (m) REVERT: D 131 LEU cc_start: 0.8224 (mt) cc_final: 0.8006 (mm) REVERT: D 140 HIS cc_start: 0.7844 (m90) cc_final: 0.7435 (m-70) REVERT: D 173 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7322 (mp) REVERT: G 106 SER cc_start: 0.3057 (OUTLIER) cc_final: 0.2072 (t) REVERT: G 228 TYR cc_start: 0.8661 (m-80) cc_final: 0.8348 (m-80) outliers start: 46 outliers final: 29 residues processed: 223 average time/residue: 1.1918 time to fit residues: 282.7849 Evaluate side-chains 231 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN C 241 ASN C 255 ASN C 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8814 Z= 0.299 Angle : 0.562 7.943 11950 Z= 0.294 Chirality : 0.044 0.213 1353 Planarity : 0.004 0.053 1510 Dihedral : 5.379 57.916 1202 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.04 % Allowed : 27.58 % Favored : 67.38 % 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: 1.11 (0.25), residues: 1087 helix: 2.20 (0.26), residues: 384 sheet: 0.60 (0.30), residues: 286 loop : -0.53 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 167 HIS 0.004 0.001 HIS D 140 PHE 0.016 0.002 PHE D 18 TYR 0.018 0.002 TYR G 236 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: B 100 THR cc_start: 0.8026 (p) cc_final: 0.7680 (t) REVERT: B 132 ARG cc_start: 0.7224 (ptp-170) cc_final: 0.6968 (ptp-170) REVERT: B 215 MET cc_start: 0.6587 (ppp) cc_final: 0.6382 (ppp) REVERT: B 254 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7019 (mtm180) REVERT: C 231 ASP cc_start: 0.6994 (t0) cc_final: 0.6734 (t0) REVERT: C 269 ASN cc_start: 0.8260 (p0) cc_final: 0.7951 (p0) REVERT: D 30 ARG cc_start: 0.7291 (ptm160) cc_final: 0.7020 (ptm160) REVERT: D 52 THR cc_start: 0.8669 (m) cc_final: 0.8456 (m) REVERT: D 127 VAL cc_start: 0.8100 (t) cc_final: 0.7640 (m) REVERT: D 131 LEU cc_start: 0.8254 (mt) cc_final: 0.8014 (mm) REVERT: D 140 HIS cc_start: 0.7873 (m90) cc_final: 0.7450 (m-70) REVERT: D 173 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7362 (mp) REVERT: G 106 SER cc_start: 0.2806 (OUTLIER) cc_final: 0.1681 (t) REVERT: G 228 TYR cc_start: 0.8736 (m-80) cc_final: 0.8468 (m-80) outliers start: 47 outliers final: 30 residues processed: 227 average time/residue: 1.2210 time to fit residues: 294.7029 Evaluate side-chains 227 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN C 241 ASN C 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8814 Z= 0.266 Angle : 0.544 7.595 11950 Z= 0.286 Chirality : 0.043 0.191 1353 Planarity : 0.004 0.056 1510 Dihedral : 5.321 56.619 1202 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.29 % Allowed : 28.00 % Favored : 67.70 % 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: 1.08 (0.25), residues: 1087 helix: 2.17 (0.26), residues: 384 sheet: 0.59 (0.29), residues: 292 loop : -0.56 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 167 HIS 0.003 0.001 HIS D 140 PHE 0.015 0.002 PHE D 18 TYR 0.028 0.002 TYR G 174 ARG 0.005 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: B 100 THR cc_start: 0.7948 (p) cc_final: 0.7624 (t) REVERT: B 132 ARG cc_start: 0.7210 (ptp-170) cc_final: 0.6951 (ptp-170) REVERT: B 232 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8094 (t80) REVERT: B 254 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7025 (mtm180) REVERT: C 231 ASP cc_start: 0.7018 (t0) cc_final: 0.6768 (t0) REVERT: C 269 ASN cc_start: 0.8246 (p0) cc_final: 0.8000 (p0) REVERT: D 30 ARG cc_start: 0.7278 (ptm160) cc_final: 0.7010 (ptm160) REVERT: D 52 THR cc_start: 0.8656 (m) cc_final: 0.8439 (m) REVERT: D 127 VAL cc_start: 0.8088 (t) cc_final: 0.7637 (m) REVERT: D 131 LEU cc_start: 0.8252 (mt) cc_final: 0.8017 (mm) REVERT: D 140 HIS cc_start: 0.7854 (m90) cc_final: 0.7420 (m-70) REVERT: D 173 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7353 (mp) REVERT: G 106 SER cc_start: 0.2823 (OUTLIER) cc_final: 0.1814 (t) REVERT: G 228 TYR cc_start: 0.8669 (m-80) cc_final: 0.8386 (m-80) outliers start: 40 outliers final: 29 residues processed: 215 average time/residue: 1.2213 time to fit residues: 278.8047 Evaluate side-chains 224 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.0010 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.0470 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN B 237 ASN B 291 ASN C 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8814 Z= 0.153 Angle : 0.502 7.465 11950 Z= 0.261 Chirality : 0.041 0.142 1353 Planarity : 0.004 0.060 1510 Dihedral : 4.999 57.216 1202 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.11 % Allowed : 29.29 % Favored : 67.60 % 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: 1.24 (0.25), residues: 1087 helix: 2.34 (0.26), residues: 385 sheet: 0.64 (0.30), residues: 292 loop : -0.48 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 209 HIS 0.002 0.001 HIS G 35 PHE 0.012 0.001 PHE D 18 TYR 0.020 0.001 TYR G 174 ARG 0.004 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 THR cc_start: 0.7726 (p) cc_final: 0.7476 (t) REVERT: B 215 MET cc_start: 0.6794 (ppp) cc_final: 0.6310 (ppp) REVERT: B 232 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 254 ARG cc_start: 0.7489 (mpp80) cc_final: 0.6964 (mtm180) REVERT: C 231 ASP cc_start: 0.6959 (t0) cc_final: 0.6698 (t0) REVERT: C 269 ASN cc_start: 0.8247 (p0) cc_final: 0.7915 (p0) REVERT: D 30 ARG cc_start: 0.7283 (ptm160) cc_final: 0.7049 (ptm160) REVERT: D 127 VAL cc_start: 0.8087 (t) cc_final: 0.7636 (m) REVERT: D 131 LEU cc_start: 0.8218 (mt) cc_final: 0.8002 (mm) REVERT: D 173 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7343 (mp) REVERT: G 18 ARG cc_start: 0.7910 (tpt170) cc_final: 0.7390 (mmt180) REVERT: G 228 TYR cc_start: 0.8661 (m-80) cc_final: 0.8314 (m-80) outliers start: 29 outliers final: 21 residues processed: 209 average time/residue: 1.2308 time to fit residues: 272.7163 Evaluate side-chains 210 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 187 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 164 CYS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 156 VAL Chi-restraints excluded: chain G residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 99 optimal weight: 0.0070 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN C 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8814 Z= 0.189 Angle : 0.522 8.360 11950 Z= 0.270 Chirality : 0.042 0.146 1353 Planarity : 0.004 0.060 1510 Dihedral : 4.752 58.119 1200 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.79 % Allowed : 30.15 % Favored : 67.06 % 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: 1.24 (0.25), residues: 1087 helix: 2.31 (0.26), residues: 385 sheet: 0.61 (0.29), residues: 292 loop : -0.44 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 209 HIS 0.003 0.001 HIS G 35 PHE 0.014 0.001 PHE D 18 TYR 0.023 0.001 TYR G 174 ARG 0.004 0.000 ARG B 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 THR cc_start: 0.7767 (p) cc_final: 0.7516 (t) REVERT: B 132 ARG cc_start: 0.7211 (ptp-170) cc_final: 0.6948 (ptp-170) REVERT: B 215 MET cc_start: 0.6807 (ppp) cc_final: 0.6171 (ppp) REVERT: B 232 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8140 (t80) REVERT: B 235 ASN cc_start: 0.7508 (t160) cc_final: 0.7293 (t0) REVERT: B 254 ARG cc_start: 0.7475 (mpp80) cc_final: 0.6975 (mtm180) REVERT: B 256 ASP cc_start: 0.6940 (t0) cc_final: 0.6690 (t70) REVERT: C 231 ASP cc_start: 0.6964 (t0) cc_final: 0.6704 (t0) REVERT: C 269 ASN cc_start: 0.8248 (p0) cc_final: 0.7908 (p0) REVERT: D 30 ARG cc_start: 0.7285 (ptm160) cc_final: 0.7046 (ptm160) REVERT: D 52 THR cc_start: 0.8646 (m) cc_final: 0.8425 (m) REVERT: D 127 VAL cc_start: 0.8100 (t) cc_final: 0.7642 (m) REVERT: D 131 LEU cc_start: 0.8223 (mt) cc_final: 0.8000 (mm) REVERT: D 173 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7330 (mp) REVERT: G 18 ARG cc_start: 0.7911 (tpt170) cc_final: 0.7437 (mmt180) REVERT: G 228 TYR cc_start: 0.8690 (m-80) cc_final: 0.8358 (m-80) outliers start: 26 outliers final: 20 residues processed: 206 average time/residue: 1.3062 time to fit residues: 284.8809 Evaluate side-chains 214 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN B 291 ASN C 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105471 restraints weight = 11798.277| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.56 r_work: 0.3299 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8814 Z= 0.263 Angle : 0.563 10.540 11950 Z= 0.291 Chirality : 0.043 0.174 1353 Planarity : 0.004 0.058 1510 Dihedral : 4.622 30.086 1197 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.33 % Allowed : 29.72 % Favored : 66.95 % 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: 1.11 (0.25), residues: 1087 helix: 2.16 (0.26), residues: 385 sheet: 0.56 (0.30), residues: 292 loop : -0.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 209 HIS 0.003 0.001 HIS G 35 PHE 0.017 0.002 PHE D 18 TYR 0.022 0.002 TYR G 174 ARG 0.004 0.000 ARG B 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.26 seconds wall clock time: 82 minutes 59.21 seconds (4979.21 seconds total)