Starting phenix.real_space_refine on Sat Apr 6 21:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjo_38403/04_2024/8xjo_38403_updated.pdb" } resolution = 3.11 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= 0.011 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 58 5.16 5 C 5674 2.51 5 N 1549 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1831 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 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: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2257 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 295} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 94 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'PUC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.73, per 1000 atoms: 0.53 Number of scatterers: 8950 At special positions: 0 Unit cell: (118.77, 124.12, 104.86, 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 58 16.00 O 1669 8.00 N 1549 7.00 C 5674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 102 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 183 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 34.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.503A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' 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 Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 3 through 24 removed outlier: 3.503A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.544A 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 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 30 through 55 removed outlier: 4.203A pdb=" N PHE R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N CYS R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 90 removed outlier: 3.549A pdb=" N THR R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 98 No H-bonds generated for 'chain 'R' and resid 95 through 98' Processing helix chain 'R' and resid 104 through 135 Proline residue: R 119 - end of helix removed outlier: 3.713A pdb=" N SER R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 165 removed outlier: 4.585A pdb=" N ALA R 151 " --> pdb=" O ARG R 147 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR R 152 " --> pdb=" O ARG R 148 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 153 " --> pdb=" O ALA R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 169 No H-bonds generated for 'chain 'R' and resid 167 through 169' Processing helix chain 'R' and resid 191 through 226 removed outlier: 3.737A pdb=" N HIS R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 234 Processing helix chain 'R' and resid 239 through 269 removed outlier: 4.360A pdb=" N SER R 255 " --> pdb=" O MET R 251 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 284 through 307 removed outlier: 3.768A pdb=" N TRP R 299 " --> pdb=" O ARG R 295 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN R 300 " --> pdb=" O VAL R 296 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN R 301 " --> pdb=" O ALA R 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 302 " --> pdb=" O THR R 298 " (cutoff:3.500A) Proline residue: R 305 - end of helix Processing helix chain 'R' and resid 313 through 319 removed outlier: 4.213A pdb=" N ARG R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.829A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN A 80 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU A 36 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS A 82 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU A 38 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 84 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N GLY A 40 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.843A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.892A 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: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.048A 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: 6.725A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.579A 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: 6.754A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.212A 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: 6.554A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.971A 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: 6.501A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.538A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.985A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.594A 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: 6.236A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 174 through 176 401 hydrogen bonds defined for protein. 1155 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: 2.43 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2936 1.34 - 1.46: 1691 1.46 - 1.57: 4420 1.57 - 1.69: 3 1.69 - 1.81: 85 Bond restraints: 9135 Sorted by residual: bond pdb=" C12 PUC R 601 " pdb=" C13 PUC R 601 " ideal model delta sigma weight residual 1.704 1.506 0.198 2.00e-02 2.50e+03 9.79e+01 bond pdb=" C21 PUC R 601 " pdb=" C9 PUC R 601 " ideal model delta sigma weight residual 1.347 1.539 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C7 PUC R 601 " pdb=" C8 PUC R 601 " ideal model delta sigma weight residual 1.707 1.540 0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C8 PUC R 601 " pdb=" C9 PUC R 601 " ideal model delta sigma weight residual 1.399 1.539 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C11 PUC R 601 " pdb=" C12 PUC R 601 " ideal model delta sigma weight residual 1.407 1.529 -0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 9130 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.42: 34 102.42 - 110.32: 2105 110.32 - 118.22: 4830 118.22 - 126.11: 5272 126.11 - 134.01: 153 Bond angle restraints: 12394 Sorted by residual: angle pdb=" C5 PUC R 601 " pdb=" C6 PUC R 601 " pdb=" C7 PUC R 601 " ideal model delta sigma weight residual 152.66 122.03 30.63 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C4 PUC R 601 " pdb=" C5 PUC R 601 " pdb=" C6 PUC R 601 " ideal model delta sigma weight residual 112.21 127.40 -15.19 3.00e+00 1.11e-01 2.56e+01 angle pdb=" C14 PUC R 601 " pdb=" C15 PUC R 601 " pdb=" O3 PUC R 601 " ideal model delta sigma weight residual 109.49 96.63 12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C14 PUC R 601 " pdb=" C15 PUC R 601 " pdb=" C16 PUC R 601 " ideal model delta sigma weight residual 109.51 121.82 -12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" C3 PUC R 601 " pdb=" C4 PUC R 601 " pdb=" C5 PUC R 601 " ideal model delta sigma weight residual 109.46 120.93 -11.47 3.00e+00 1.11e-01 1.46e+01 ... (remaining 12389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 5161 14.72 - 29.44: 196 29.44 - 44.16: 52 44.16 - 58.88: 8 58.88 - 73.60: 2 Dihedral angle restraints: 5419 sinusoidal: 2071 harmonic: 3348 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+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 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.053: 1411 1.053 - 2.106: 0 2.106 - 3.159: 0 3.159 - 4.212: 0 4.212 - 5.264: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C12 PUC R 601 " pdb=" C11 PUC R 601 " pdb=" C13 PUC R 601 " pdb=" C8 PUC R 601 " both_signs ideal model delta sigma weight residual False -2.55 2.72 -5.26 2.00e-01 2.50e+01 6.93e+02 chirality pdb=" C9 PUC R 601 " pdb=" C10 PUC R 601 " pdb=" C21 PUC R 601 " pdb=" C8 PUC R 601 " both_signs ideal model delta sigma weight residual False 2.91 3.53 -0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" C11 PUC R 601 " pdb=" C10 PUC R 601 " pdb=" C12 PUC R 601 " pdb=" O5 PUC R 601 " both_signs ideal model delta sigma weight residual False 2.86 3.17 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1409 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 236 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO B 194 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 235 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.93e-01 pdb=" N PRO R 236 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " -0.013 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1156 2.75 - 3.29: 8596 3.29 - 3.83: 14872 3.83 - 4.36: 18438 4.36 - 4.90: 31777 Nonbonded interactions: 74839 Sorted by model distance: nonbonded pdb=" O SER E 105 " pdb=" NH2 ARG E 191 " model vdw 2.213 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.214 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.240 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.248 2.440 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.262 2.520 ... (remaining 74834 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: 0.430 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: 2.050 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.770 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.006 0.198 9135 Z= 0.416 Angle : 0.618 30.630 12394 Z= 0.277 Chirality : 0.148 5.264 1412 Planarity : 0.003 0.037 1582 Dihedral : 8.835 73.599 3251 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.06 % Allowed : 3.27 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1148 helix: 1.01 (0.26), residues: 407 sheet: 0.65 (0.30), residues: 294 loop : 0.70 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.003 0.001 HIS E 167 PHE 0.014 0.002 PHE B 199 TYR 0.012 0.001 TYR E 102 ARG 0.006 0.001 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 229 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8496 (mttt) cc_final: 0.8177 (mmtt) REVERT: A 96 TRP cc_start: 0.7611 (p-90) cc_final: 0.7338 (p-90) REVERT: A 114 ASP cc_start: 0.7937 (t0) cc_final: 0.7724 (t0) REVERT: A 120 GLU cc_start: 0.7213 (mt-10) cc_final: 0.7003 (mp0) REVERT: A 233 ASP cc_start: 0.8206 (t0) cc_final: 0.7996 (m-30) REVERT: A 238 MET cc_start: 0.8331 (mtt) cc_final: 0.8096 (mtp) REVERT: B 78 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8098 (tptt) REVERT: B 156 GLN cc_start: 0.8151 (mt0) cc_final: 0.7920 (mt0) REVERT: B 219 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7772 (mtp85) REVERT: B 301 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8717 (mtpp) REVERT: E 206 SER cc_start: 0.6907 (p) cc_final: 0.6430 (p) REVERT: E 219 LEU cc_start: 0.8331 (tt) cc_final: 0.8079 (tt) REVERT: R 30 PHE cc_start: 0.7620 (t80) cc_final: 0.7079 (t80) REVERT: R 243 MET cc_start: 0.7637 (tpp) cc_final: 0.7201 (tpp) REVERT: R 300 ASN cc_start: 0.7933 (t0) cc_final: 0.7643 (t0) outliers start: 10 outliers final: 6 residues processed: 235 average time/residue: 0.2797 time to fit residues: 84.3796 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 ARG Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 88 ASN B 156 GLN E 113 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9135 Z= 0.206 Angle : 0.518 5.853 12394 Z= 0.273 Chirality : 0.043 0.187 1412 Planarity : 0.004 0.041 1582 Dihedral : 5.839 58.293 1294 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.53 % Allowed : 8.87 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.56 (0.25), residues: 1148 helix: 1.82 (0.26), residues: 406 sheet: 0.68 (0.30), residues: 295 loop : 0.71 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR A 115 ARG 0.004 0.000 ARG R 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 96 TRP cc_start: 0.7586 (p-90) cc_final: 0.7316 (p-90) REVERT: A 148 LEU cc_start: 0.8153 (tp) cc_final: 0.7908 (tp) REVERT: A 225 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7160 (tpp-160) REVERT: A 233 ASP cc_start: 0.8167 (t0) cc_final: 0.7776 (m-30) REVERT: B 118 ASP cc_start: 0.8121 (p0) cc_final: 0.7914 (p0) REVERT: B 130 GLU cc_start: 0.8349 (mp0) cc_final: 0.8098 (mp0) REVERT: B 262 MET cc_start: 0.8081 (ttm) cc_final: 0.7572 (ttm) REVERT: B 301 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8731 (mtpp) REVERT: C 21 MET cc_start: 0.7373 (mtm) cc_final: 0.7169 (mtm) REVERT: E 195 LEU cc_start: 0.8778 (tp) cc_final: 0.8426 (mp) REVERT: E 219 LEU cc_start: 0.8160 (tt) cc_final: 0.7950 (tt) REVERT: R 235 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6891 (ptt90) outliers start: 24 outliers final: 15 residues processed: 184 average time/residue: 0.2566 time to fit residues: 62.3251 Evaluate side-chains 154 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 235 ARG Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 298 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9135 Z= 0.162 Angle : 0.485 7.342 12394 Z= 0.251 Chirality : 0.041 0.140 1412 Planarity : 0.003 0.035 1582 Dihedral : 5.367 56.200 1291 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.17 % Allowed : 11.51 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.62 (0.25), residues: 1148 helix: 2.12 (0.26), residues: 401 sheet: 0.57 (0.29), residues: 286 loop : 0.62 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 224 PHE 0.022 0.001 PHE R 115 TYR 0.010 0.001 TYR A 115 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7562 (p-90) cc_final: 0.7294 (p-90) REVERT: A 225 ARG cc_start: 0.7783 (ttm-80) cc_final: 0.7135 (tpp-160) REVERT: A 233 ASP cc_start: 0.8211 (t0) cc_final: 0.7773 (m-30) REVERT: A 238 MET cc_start: 0.8125 (mtt) cc_final: 0.7732 (mtp) REVERT: B 217 MET cc_start: 0.7819 (ppp) cc_final: 0.6571 (ppp) REVERT: B 219 ARG cc_start: 0.7941 (mtp85) cc_final: 0.7429 (mmt-90) REVERT: B 262 MET cc_start: 0.8131 (ttm) cc_final: 0.7745 (ttm) REVERT: B 301 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8710 (mtpt) REVERT: C 21 MET cc_start: 0.7470 (mtm) cc_final: 0.7258 (mtm) REVERT: E 17 SER cc_start: 0.8258 (m) cc_final: 0.7908 (p) REVERT: E 195 LEU cc_start: 0.8759 (tp) cc_final: 0.8417 (mp) REVERT: E 218 ARG cc_start: 0.7575 (mpt180) cc_final: 0.7284 (mtm110) REVERT: E 219 LEU cc_start: 0.8081 (tt) cc_final: 0.7878 (tt) REVERT: R 235 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6827 (ptt90) outliers start: 30 outliers final: 19 residues processed: 171 average time/residue: 0.2758 time to fit residues: 61.7026 Evaluate side-chains 163 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 235 ARG Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 176 GLN E 171 ASN R 224 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9135 Z= 0.243 Angle : 0.515 7.293 12394 Z= 0.264 Chirality : 0.042 0.143 1412 Planarity : 0.003 0.035 1582 Dihedral : 5.397 54.969 1291 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.70 % Allowed : 12.57 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.55 (0.25), residues: 1148 helix: 2.06 (0.26), residues: 401 sheet: 0.46 (0.29), residues: 290 loop : 0.63 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS R 224 PHE 0.024 0.002 PHE A 108 TYR 0.012 0.001 TYR A 115 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7098 (tpp-160) REVERT: A 233 ASP cc_start: 0.8196 (t0) cc_final: 0.7766 (m-30) REVERT: E 17 SER cc_start: 0.8243 (m) cc_final: 0.7917 (p) REVERT: E 224 VAL cc_start: 0.8168 (t) cc_final: 0.7876 (m) REVERT: R 235 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6814 (ptt90) outliers start: 35 outliers final: 27 residues processed: 174 average time/residue: 0.2543 time to fit residues: 58.6892 Evaluate side-chains 172 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 235 ARG Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9135 Z= 0.333 Angle : 0.567 7.541 12394 Z= 0.290 Chirality : 0.044 0.146 1412 Planarity : 0.004 0.037 1582 Dihedral : 5.580 55.836 1291 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.39 % Allowed : 12.25 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.22 (0.25), residues: 1148 helix: 1.70 (0.26), residues: 407 sheet: 0.33 (0.29), residues: 289 loop : 0.49 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 96 HIS 0.005 0.001 HIS A 209 PHE 0.018 0.002 PHE A 108 TYR 0.016 0.002 TYR A 115 ARG 0.005 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 152 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8093 (mttt) cc_final: 0.7742 (mmtt) REVERT: A 233 ASP cc_start: 0.8150 (t0) cc_final: 0.7785 (m-30) REVERT: A 238 MET cc_start: 0.8177 (mtt) cc_final: 0.7909 (mtp) REVERT: B 118 ASP cc_start: 0.8352 (p0) cc_final: 0.8146 (p0) REVERT: B 234 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: B 258 ASP cc_start: 0.7199 (t70) cc_final: 0.6515 (t0) REVERT: E 17 SER cc_start: 0.8303 (m) cc_final: 0.8014 (p) REVERT: E 224 VAL cc_start: 0.8200 (t) cc_final: 0.7936 (m) REVERT: R 128 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8294 (p) outliers start: 51 outliers final: 40 residues processed: 182 average time/residue: 0.2361 time to fit residues: 58.1326 Evaluate side-chains 183 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 141 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9135 Z= 0.356 Angle : 0.581 7.907 12394 Z= 0.296 Chirality : 0.044 0.154 1412 Planarity : 0.004 0.039 1582 Dihedral : 5.558 55.907 1287 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.28 % Allowed : 12.99 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.04 (0.25), residues: 1148 helix: 1.46 (0.25), residues: 415 sheet: 0.33 (0.29), residues: 284 loop : 0.36 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.007 0.001 HIS R 224 PHE 0.018 0.002 PHE B 241 TYR 0.039 0.002 TYR E 190 ARG 0.004 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 154 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8261 (mttt) cc_final: 0.7893 (mmtt) REVERT: A 233 ASP cc_start: 0.8226 (t0) cc_final: 0.7755 (m-30) REVERT: B 59 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: B 234 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8786 (m-80) REVERT: B 262 MET cc_start: 0.8531 (tpp) cc_final: 0.8114 (ttm) REVERT: E 17 SER cc_start: 0.8312 (m) cc_final: 0.8032 (p) REVERT: E 195 LEU cc_start: 0.8873 (tp) cc_final: 0.8460 (mp) REVERT: E 224 VAL cc_start: 0.8211 (t) cc_final: 0.7959 (m) REVERT: R 235 ARG cc_start: 0.6995 (ptt90) cc_final: 0.6557 (ptt90) outliers start: 50 outliers final: 40 residues processed: 184 average time/residue: 0.2467 time to fit residues: 60.9486 Evaluate side-chains 186 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 216 THR Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9135 Z= 0.171 Angle : 0.495 9.015 12394 Z= 0.254 Chirality : 0.040 0.137 1412 Planarity : 0.003 0.037 1582 Dihedral : 5.254 55.338 1287 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.48 % Allowed : 15.42 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1148 helix: 1.83 (0.26), residues: 413 sheet: 0.40 (0.30), residues: 289 loop : 0.47 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 96 HIS 0.007 0.001 HIS R 224 PHE 0.018 0.001 PHE A 108 TYR 0.028 0.001 TYR E 190 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8175 (mttt) cc_final: 0.7859 (mmtt) REVERT: A 83 MET cc_start: 0.8938 (mtp) cc_final: 0.8737 (mtp) REVERT: A 123 ASN cc_start: 0.8324 (m-40) cc_final: 0.8108 (m-40) REVERT: A 225 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7042 (tpp-160) REVERT: A 233 ASP cc_start: 0.8286 (t0) cc_final: 0.7775 (m-30) REVERT: B 59 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: B 130 GLU cc_start: 0.8412 (mp0) cc_final: 0.8164 (mp0) REVERT: B 234 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8899 (m-80) REVERT: E 17 SER cc_start: 0.8292 (m) cc_final: 0.8055 (p) REVERT: E 195 LEU cc_start: 0.8770 (tp) cc_final: 0.8405 (mp) REVERT: E 218 ARG cc_start: 0.7446 (mpt180) cc_final: 0.7188 (mtm110) REVERT: E 224 VAL cc_start: 0.8124 (t) cc_final: 0.7849 (m) REVERT: R 108 MET cc_start: 0.7127 (tpp) cc_final: 0.6877 (tpp) outliers start: 33 outliers final: 25 residues processed: 168 average time/residue: 0.2437 time to fit residues: 54.7492 Evaluate side-chains 170 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9135 Z= 0.234 Angle : 0.525 8.601 12394 Z= 0.269 Chirality : 0.042 0.142 1412 Planarity : 0.003 0.037 1582 Dihedral : 5.303 55.055 1287 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.91 % Allowed : 15.63 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.29 (0.25), residues: 1148 helix: 1.77 (0.26), residues: 414 sheet: 0.39 (0.29), residues: 289 loop : 0.46 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.015 0.001 PHE A 108 TYR 0.026 0.001 TYR E 190 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8101 (mttt) cc_final: 0.7779 (mmtt) REVERT: A 123 ASN cc_start: 0.8331 (m-40) cc_final: 0.8117 (m-40) REVERT: A 233 ASP cc_start: 0.8311 (t0) cc_final: 0.7825 (m-30) REVERT: B 59 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: B 130 GLU cc_start: 0.8411 (mp0) cc_final: 0.8161 (mp0) REVERT: B 234 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: E 17 SER cc_start: 0.8289 (m) cc_final: 0.8027 (p) REVERT: E 195 LEU cc_start: 0.8809 (tp) cc_final: 0.8435 (mp) REVERT: E 218 ARG cc_start: 0.7426 (mpt180) cc_final: 0.7184 (mtm110) REVERT: E 224 VAL cc_start: 0.8024 (t) cc_final: 0.7747 (m) REVERT: R 128 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8178 (p) outliers start: 37 outliers final: 32 residues processed: 170 average time/residue: 0.2348 time to fit residues: 54.3055 Evaluate side-chains 177 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 296 VAL Chi-restraints excluded: chain R residue 311 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9135 Z= 0.164 Angle : 0.489 9.288 12394 Z= 0.251 Chirality : 0.040 0.137 1412 Planarity : 0.003 0.037 1582 Dihedral : 5.148 55.397 1287 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.17 % Allowed : 16.68 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1148 helix: 2.00 (0.26), residues: 413 sheet: 0.61 (0.30), residues: 281 loop : 0.48 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.008 0.001 HIS R 224 PHE 0.015 0.001 PHE A 108 TYR 0.024 0.001 TYR E 190 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 123 ASN cc_start: 0.8323 (m-40) cc_final: 0.8110 (m-40) REVERT: A 225 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7062 (tpp-160) REVERT: A 233 ASP cc_start: 0.8246 (t0) cc_final: 0.7746 (m-30) REVERT: A 238 MET cc_start: 0.8117 (mtt) cc_final: 0.7816 (mtt) REVERT: B 59 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 234 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: E 17 SER cc_start: 0.8289 (m) cc_final: 0.8042 (p) REVERT: E 163 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8179 (ptmm) REVERT: E 195 LEU cc_start: 0.8749 (tp) cc_final: 0.8422 (mp) REVERT: E 218 ARG cc_start: 0.7353 (mpt180) cc_final: 0.7137 (mtm110) REVERT: E 224 VAL cc_start: 0.7970 (t) cc_final: 0.7672 (m) REVERT: R 128 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8129 (p) outliers start: 30 outliers final: 24 residues processed: 171 average time/residue: 0.2470 time to fit residues: 56.6989 Evaluate side-chains 178 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 311 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9135 Z= 0.191 Angle : 0.511 10.811 12394 Z= 0.260 Chirality : 0.041 0.137 1412 Planarity : 0.003 0.037 1582 Dihedral : 5.162 55.223 1287 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.38 % Allowed : 16.90 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1148 helix: 1.98 (0.26), residues: 413 sheet: 0.54 (0.30), residues: 283 loop : 0.47 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 96 HIS 0.008 0.001 HIS R 224 PHE 0.015 0.001 PHE A 108 TYR 0.024 0.001 TYR E 190 ARG 0.008 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 123 ASN cc_start: 0.8323 (m-40) cc_final: 0.8105 (m-40) REVERT: A 152 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7772 (ttmt) REVERT: A 225 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7053 (tpp-160) REVERT: A 233 ASP cc_start: 0.8261 (t0) cc_final: 0.7759 (m-30) REVERT: B 59 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: B 219 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7521 (ttm-80) REVERT: B 234 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: E 17 SER cc_start: 0.8362 (m) cc_final: 0.8137 (p) REVERT: E 195 LEU cc_start: 0.8752 (tp) cc_final: 0.8414 (mp) REVERT: E 218 ARG cc_start: 0.7341 (mpt180) cc_final: 0.7089 (mtm110) REVERT: E 224 VAL cc_start: 0.7846 (t) cc_final: 0.7557 (m) REVERT: R 108 MET cc_start: 0.7094 (tpp) cc_final: 0.6534 (mmp) REVERT: R 128 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8133 (p) outliers start: 32 outliers final: 26 residues processed: 169 average time/residue: 0.2389 time to fit residues: 54.3049 Evaluate side-chains 178 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 95 TRP Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 311 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN R 224 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122188 restraints weight = 10236.410| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.41 r_work: 0.3291 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9135 Z= 0.245 Angle : 0.534 10.809 12394 Z= 0.271 Chirality : 0.041 0.143 1412 Planarity : 0.003 0.037 1582 Dihedral : 5.287 55.635 1287 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.70 % Allowed : 16.47 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1148 helix: 1.89 (0.26), residues: 413 sheet: 0.49 (0.30), residues: 283 loop : 0.39 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 96 HIS 0.008 0.001 HIS R 224 PHE 0.015 0.001 PHE A 108 TYR 0.024 0.001 TYR E 190 ARG 0.008 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.19 seconds wall clock time: 43 minutes 56.32 seconds (2636.32 seconds total)