Starting phenix.real_space_refine on Tue Jun 25 22:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/06_2024/8xjl_38400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/06_2024/8xjl_38400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/06_2024/8xjl_38400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/06_2024/8xjl_38400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/06_2024/8xjl_38400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjl_38400/06_2024/8xjl_38400_updated.pdb" } resolution = 2.77 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= 0.014 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 62 5.16 5 C 5624 2.51 5 N 1513 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1821 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2171 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UGU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.55 Number of scatterers: 8846 At special positions: 0 Unit cell: (105.93, 116.63, 111.28, 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 62 16.00 O 1647 8.00 N 1513 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 36.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.521A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 184 through 203 removed outlier: 3.683A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.508A pdb=" N ASP A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.658A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'R' and resid 30 through 59 removed outlier: 3.612A pdb=" N GLN R 56 " --> pdb=" O MET R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 93 Processing helix chain 'R' and resid 98 through 101 No H-bonds generated for 'chain 'R' and resid 98 through 101' Processing helix chain 'R' and resid 106 through 138 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 149 through 167 Processing helix chain 'R' and resid 169 through 172 No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 196 through 231 removed outlier: 4.138A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 278 removed outlier: 3.679A pdb=" N TRP R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 264 - end of helix removed outlier: 3.613A pdb=" N THR R 268 " --> pdb=" O PRO R 264 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N HIS R 278 " --> pdb=" O ILE R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 304 removed outlier: 3.637A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 320 removed outlier: 3.626A pdb=" N ASN R 314 " --> pdb=" O ALA R 310 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 144 removed outlier: 3.813A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 80 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 36 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS A 82 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU A 38 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 84 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLY A 40 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N VAL A 86 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.725A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.783A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.663A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.747A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.628A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.401A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.723A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= J, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.125A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.551A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.185A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1218 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: 2.72 Time building geometry restraints manager: 3.66 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: 2875 1.34 - 1.46: 2140 1.46 - 1.58: 3915 1.58 - 1.69: 3 1.69 - 1.81: 90 Bond restraints: 9023 Sorted by residual: bond pdb=" C11 UGU R 601 " pdb=" C12 UGU R 601 " ideal model delta sigma weight residual 1.530 1.316 0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C8 UGU R 601 " pdb=" C9 UGU R 601 " ideal model delta sigma weight residual 1.531 1.338 0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C12 UGU R 601 " pdb=" C8 UGU R 601 " ideal model delta sigma weight residual 1.548 1.694 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" C10 UGU R 601 " pdb=" C11 UGU R 601 " ideal model delta sigma weight residual 1.550 1.616 -0.066 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C6 UGU R 601 " pdb=" C7 UGU R 601 " ideal model delta sigma weight residual 1.502 1.561 -0.059 2.00e-02 2.50e+03 8.70e+00 ... (remaining 9018 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 200 106.90 - 113.68: 5020 113.68 - 120.45: 3335 120.45 - 127.23: 3575 127.23 - 134.01: 92 Bond angle restraints: 12222 Sorted by residual: angle pdb=" C12 UGU R 601 " pdb=" C13 UGU R 601 " pdb=" C14 UGU R 601 " ideal model delta sigma weight residual 127.73 112.98 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" C5 UGU R 601 " pdb=" C6 UGU R 601 " pdb=" C7 UGU R 601 " ideal model delta sigma weight residual 128.14 113.61 14.53 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C13 UGU R 601 " pdb=" C14 UGU R 601 " pdb=" C15 UGU R 601 " ideal model delta sigma weight residual 126.10 112.83 13.27 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C4 UGU R 601 " pdb=" C5 UGU R 601 " pdb=" C6 UGU R 601 " ideal model delta sigma weight residual 128.19 116.86 11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C11 UGU R 601 " pdb=" C12 UGU R 601 " pdb=" C13 UGU R 601 " ideal model delta sigma weight residual 117.79 110.36 7.43 3.00e+00 1.11e-01 6.13e+00 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 5316 33.54 - 67.07: 47 67.07 - 100.61: 4 100.61 - 134.15: 0 134.15 - 167.68: 1 Dihedral angle restraints: 5368 sinusoidal: 2073 harmonic: 3295 Sorted by residual: dihedral pdb=" C16 UGU R 601 " pdb=" C17 UGU R 601 " pdb=" C18 UGU R 601 " pdb=" C19 UGU R 601 " ideal model delta sinusoidal sigma weight residual 297.02 129.34 167.68 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PHE E 31 " pdb=" C PHE E 31 " pdb=" N GLY E 32 " pdb=" CA GLY E 32 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1276 0.068 - 0.136: 118 0.136 - 0.204: 2 0.204 - 0.272: 1 0.272 - 0.340: 1 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C12 UGU R 601 " pdb=" C11 UGU R 601 " pdb=" C13 UGU R 601 " pdb=" C8 UGU R 601 " both_signs ideal model delta sigma weight residual False 2.42 2.76 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C9 UGU R 601 " pdb=" C10 UGU R 601 " pdb=" C8 UGU R 601 " pdb=" O3 UGU R 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.46 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C8 UGU R 601 " pdb=" C12 UGU R 601 " pdb=" C7 UGU R 601 " pdb=" C9 UGU R 601 " both_signs ideal model delta sigma weight residual False -2.54 -2.73 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1395 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 194 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 59 " 0.017 5.00e-02 4.00e+02 2.53e-02 1.03e+00 pdb=" N PRO C 60 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.014 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1386 2.76 - 3.30: 8420 3.30 - 3.83: 14873 3.83 - 4.37: 18629 4.37 - 4.90: 31755 Nonbonded interactions: 75063 Sorted by model distance: nonbonded pdb=" O ARG R 291 " pdb=" CG2 THR R 294 " model vdw 2.225 3.460 nonbonded pdb=" O VAL R 303 " pdb=" NH2 ARG R 308 " model vdw 2.270 2.520 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.280 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.283 2.440 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.286 2.520 ... (remaining 75058 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: 0.300 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: 1.750 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.800 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: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 9023 Z= 0.272 Angle : 0.477 14.755 12222 Z= 0.223 Chirality : 0.041 0.340 1398 Planarity : 0.003 0.043 1548 Dihedral : 10.361 167.683 3231 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.05 % Allowed : 3.38 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.28 (0.25), residues: 1122 helix: 1.35 (0.25), residues: 414 sheet: 1.07 (0.33), residues: 267 loop : 0.37 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR E 190 ARG 0.003 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 1.056 Fit side-chains REVERT: E 42 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7808 (mmtp) REVERT: E 140 MET cc_start: 0.8395 (mmm) cc_final: 0.8174 (mmp) REVERT: E 210 THR cc_start: 0.8082 (p) cc_final: 0.7849 (p) REVERT: R 57 ARG cc_start: 0.7428 (ttm170) cc_final: 0.7096 (mtm-85) REVERT: R 198 ASP cc_start: 0.8000 (t0) cc_final: 0.7693 (t0) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.1997 time to fit residues: 277.9298 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain R residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 244 ASN B 88 ASN B 259 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9023 Z= 0.242 Angle : 0.522 6.469 12222 Z= 0.281 Chirality : 0.042 0.145 1398 Planarity : 0.004 0.043 1548 Dihedral : 6.676 123.706 1270 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.95 % Allowed : 11.39 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.83 (0.25), residues: 1122 helix: 2.39 (0.24), residues: 413 sheet: 1.04 (0.33), residues: 255 loop : 0.29 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 295 HIS 0.006 0.001 HIS R 81 PHE 0.014 0.002 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 0.926 Fit side-chains REVERT: E 42 LYS cc_start: 0.8073 (mmtm) cc_final: 0.7808 (mmtp) REVERT: E 64 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7692 (tttm) REVERT: E 140 MET cc_start: 0.8405 (mmm) cc_final: 0.8087 (mmp) outliers start: 28 outliers final: 12 residues processed: 159 average time/residue: 1.1566 time to fit residues: 196.6080 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 237 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 HIS R 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9023 Z= 0.383 Angle : 0.601 7.615 12222 Z= 0.319 Chirality : 0.045 0.149 1398 Planarity : 0.004 0.042 1548 Dihedral : 6.928 117.550 1270 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.90 % Allowed : 11.81 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1122 helix: 2.15 (0.24), residues: 413 sheet: 0.76 (0.32), residues: 258 loop : 0.17 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 63 HIS 0.006 0.001 HIS A 82 PHE 0.017 0.002 PHE B 199 TYR 0.021 0.002 TYR R 188 ARG 0.007 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.019 Fit side-chains REVERT: A 75 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: B 219 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6894 (mtp180) REVERT: C 28 ILE cc_start: 0.8508 (pt) cc_final: 0.8146 (tt) REVERT: E 42 LYS cc_start: 0.8265 (mmtm) cc_final: 0.8033 (mmtp) REVERT: E 64 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (tttm) REVERT: E 140 MET cc_start: 0.8407 (mmm) cc_final: 0.8117 (mmp) REVERT: R 57 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6503 (ttp80) outliers start: 37 outliers final: 15 residues processed: 156 average time/residue: 1.2198 time to fit residues: 202.6252 Evaluate side-chains 146 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 57 ARG Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9023 Z= 0.227 Angle : 0.516 7.498 12222 Z= 0.272 Chirality : 0.041 0.139 1398 Planarity : 0.004 0.046 1548 Dihedral : 5.986 79.398 1270 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.59 % Allowed : 13.71 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.69 (0.25), residues: 1122 helix: 2.45 (0.24), residues: 420 sheet: 0.67 (0.31), residues: 258 loop : 0.18 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS R 81 PHE 0.022 0.001 PHE R 90 TYR 0.017 0.001 TYR R 188 ARG 0.005 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 115 TYR cc_start: 0.8559 (m-80) cc_final: 0.8327 (m-80) REVERT: B 175 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: C 28 ILE cc_start: 0.8486 (pt) cc_final: 0.8118 (tt) REVERT: E 42 LYS cc_start: 0.8275 (mmtm) cc_final: 0.8039 (mmtp) REVERT: E 140 MET cc_start: 0.8406 (mmm) cc_final: 0.8065 (mmp) outliers start: 34 outliers final: 16 residues processed: 153 average time/residue: 1.2316 time to fit residues: 200.4401 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 209 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9023 Z= 0.155 Angle : 0.470 7.336 12222 Z= 0.248 Chirality : 0.040 0.134 1398 Planarity : 0.003 0.048 1548 Dihedral : 5.435 74.715 1270 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.06 % Allowed : 14.87 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.92 (0.25), residues: 1122 helix: 2.74 (0.25), residues: 416 sheet: 0.69 (0.31), residues: 256 loop : 0.28 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 81 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR E 190 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.052 Fit side-chains REVERT: A 75 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7634 (pm20) REVERT: C 28 ILE cc_start: 0.8355 (pt) cc_final: 0.8041 (tt) REVERT: E 42 LYS cc_start: 0.8264 (mmtm) cc_final: 0.8031 (mmtp) REVERT: E 140 MET cc_start: 0.8398 (mmm) cc_final: 0.8123 (mmp) outliers start: 29 outliers final: 17 residues processed: 149 average time/residue: 1.2157 time to fit residues: 192.9268 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 213 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 119 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9023 Z= 0.276 Angle : 0.535 7.578 12222 Z= 0.283 Chirality : 0.042 0.140 1398 Planarity : 0.004 0.045 1548 Dihedral : 5.649 72.492 1268 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.27 % Allowed : 15.61 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.69 (0.25), residues: 1122 helix: 2.50 (0.24), residues: 419 sheet: 0.60 (0.31), residues: 258 loop : 0.17 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS A 209 PHE 0.015 0.002 PHE B 199 TYR 0.020 0.002 TYR B 59 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8422 (pt) cc_final: 0.8080 (tt) REVERT: E 42 LYS cc_start: 0.8293 (mmtm) cc_final: 0.8051 (mmtp) REVERT: E 140 MET cc_start: 0.8430 (mmm) cc_final: 0.8055 (mmp) REVERT: R 207 PHE cc_start: 0.7572 (t80) cc_final: 0.7350 (t80) outliers start: 31 outliers final: 16 residues processed: 149 average time/residue: 1.3268 time to fit residues: 210.3240 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 119 GLN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9023 Z= 0.189 Angle : 0.496 7.892 12222 Z= 0.262 Chirality : 0.041 0.134 1398 Planarity : 0.003 0.048 1548 Dihedral : 5.452 69.590 1268 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.95 % Allowed : 15.72 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.79 (0.25), residues: 1122 helix: 2.59 (0.24), residues: 420 sheet: 0.77 (0.31), residues: 258 loop : 0.12 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 81 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR B 59 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 130 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: C 28 ILE cc_start: 0.8401 (pt) cc_final: 0.8062 (tt) REVERT: E 42 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8119 (mmtp) REVERT: E 140 MET cc_start: 0.8407 (mmm) cc_final: 0.8116 (mmp) outliers start: 28 outliers final: 15 residues processed: 145 average time/residue: 1.2897 time to fit residues: 198.7364 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 119 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9023 Z= 0.328 Angle : 0.565 7.621 12222 Z= 0.300 Chirality : 0.043 0.143 1398 Planarity : 0.004 0.045 1548 Dihedral : 5.822 71.786 1268 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.85 % Allowed : 16.46 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.50 (0.25), residues: 1122 helix: 2.39 (0.24), residues: 412 sheet: 0.62 (0.30), residues: 261 loop : -0.04 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.004 0.001 HIS A 209 PHE 0.016 0.002 PHE B 199 TYR 0.022 0.002 TYR B 59 ARG 0.004 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.895 Fit side-chains REVERT: C 28 ILE cc_start: 0.8423 (pt) cc_final: 0.8078 (tt) REVERT: E 42 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8101 (mmtp) REVERT: E 140 MET cc_start: 0.8426 (mmm) cc_final: 0.8049 (mmp) outliers start: 27 outliers final: 18 residues processed: 148 average time/residue: 1.2715 time to fit residues: 199.9941 Evaluate side-chains 145 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN A 119 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9023 Z= 0.176 Angle : 0.504 11.084 12222 Z= 0.265 Chirality : 0.041 0.132 1398 Planarity : 0.003 0.048 1548 Dihedral : 5.476 68.155 1268 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.11 % Allowed : 17.30 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.67 (0.25), residues: 1122 helix: 2.69 (0.24), residues: 411 sheet: 0.52 (0.30), residues: 263 loop : 0.02 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE B 199 TYR 0.014 0.001 TYR E 190 ARG 0.004 0.000 ARG R 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.977 Fit side-chains REVERT: C 28 ILE cc_start: 0.8406 (pt) cc_final: 0.8082 (tt) REVERT: E 42 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8139 (mmtp) REVERT: E 140 MET cc_start: 0.8435 (mmm) cc_final: 0.8139 (mmp) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 1.3334 time to fit residues: 194.9427 Evaluate side-chains 137 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 68 optimal weight: 0.0040 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9023 Z= 0.130 Angle : 0.464 6.470 12222 Z= 0.246 Chirality : 0.040 0.133 1398 Planarity : 0.003 0.051 1548 Dihedral : 5.130 59.974 1268 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.37 % Allowed : 17.93 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.25), residues: 1122 helix: 2.90 (0.24), residues: 413 sheet: 0.55 (0.31), residues: 267 loop : 0.18 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 81 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR E 190 ARG 0.006 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.039 Fit side-chains REVERT: B 46 ARG cc_start: 0.7538 (mmm160) cc_final: 0.7286 (mmm-85) REVERT: C 28 ILE cc_start: 0.8392 (pt) cc_final: 0.8086 (tt) REVERT: E 42 LYS cc_start: 0.8361 (mmtm) cc_final: 0.8128 (mmtp) REVERT: E 140 MET cc_start: 0.8442 (mmm) cc_final: 0.8091 (mmp) outliers start: 13 outliers final: 10 residues processed: 134 average time/residue: 1.2944 time to fit residues: 184.3727 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN R 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122527 restraints weight = 10288.377| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.72 r_work: 0.3186 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9023 Z= 0.162 Angle : 0.495 9.830 12222 Z= 0.259 Chirality : 0.040 0.132 1398 Planarity : 0.003 0.050 1548 Dihedral : 5.164 58.202 1268 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.16 % Allowed : 18.67 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.82 (0.25), residues: 1122 helix: 2.80 (0.24), residues: 413 sheet: 0.49 (0.31), residues: 268 loop : 0.20 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 81 PHE 0.013 0.001 PHE B 199 TYR 0.014 0.001 TYR E 190 ARG 0.004 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3751.18 seconds wall clock time: 66 minutes 20.83 seconds (3980.83 seconds total)