Starting phenix.real_space_refine on Fri Aug 22 23:04:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdp_34677/08_2025/8hdp_34677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdp_34677/08_2025/8hdp_34677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2025/8hdp_34677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2025/8hdp_34677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2025/8hdp_34677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdp_34677/08_2025/8hdp_34677.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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 53 5.16 5 C 5280 2.51 5 N 1430 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8282 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1985 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" 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: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "R" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2166 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {'ADN%rna3p': 1, 'CLR': 4} Classifications: {'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 1.74, per 1000 atoms: 0.21 Number of scatterers: 8282 At special positions: 0 Unit cell: (95.68, 76.96, 130, 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 53 16.00 O 1519 8.00 N 1430 7.00 C 5280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.47 Conformation dependent library (CDL) restraints added in 412.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 42.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.267A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 114 through 130 removed outlier: 3.636A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.511A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.243A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.537A pdb=" N TYR A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.556A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.777A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.702A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 35 Processing helix chain 'R' and resid 40 through 59 Processing helix chain 'R' and resid 59 through 69 Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.583A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.814A pdb=" N LEU R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 184 Processing helix chain 'R' and resid 186 through 191 Processing helix chain 'R' and resid 191 through 214 Processing helix chain 'R' and resid 225 through 260 removed outlier: 3.572A pdb=" N PHE R 243 " --> pdb=" O ILE R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 267 through 291 removed outlier: 4.472A pdb=" N ASN R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER R 283 " --> pdb=" O SER R 279 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 309 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.317A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.605A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.891A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 5.651A pdb=" N CYS B 149 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER B 160 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE B 151 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 158 " --> pdb=" O PHE B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.613A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.809A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.625A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.784A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 436 hydrogen bonds defined for protein. 1236 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: 0.90 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1448 1.33 - 1.45: 2236 1.45 - 1.57: 4701 1.57 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 8458 Sorted by residual: bond pdb=" C4 ADN R 401 " pdb=" C5 ADN R 401 " ideal model delta sigma weight residual 1.385 1.467 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C5 ADN R 401 " pdb=" C6 ADN R 401 " ideal model delta sigma weight residual 1.408 1.482 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C MET R 238 " pdb=" O MET R 238 " ideal model delta sigma weight residual 1.236 1.202 0.033 1.17e-02 7.31e+03 8.14e+00 bond pdb=" N TRP R 247 " pdb=" CA TRP R 247 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.84e+00 bond pdb=" N GLU R 174 " pdb=" CA GLU R 174 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.27e-02 6.20e+03 6.58e+00 ... (remaining 8453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.13: 11482 6.13 - 12.26: 12 12.26 - 18.38: 1 18.38 - 24.51: 1 24.51 - 30.64: 2 Bond angle restraints: 11498 Sorted by residual: angle pdb=" C17 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 110.18 79.54 30.64 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C12 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 111.01 81.73 29.28 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sigma weight residual 112.24 90.75 21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C12 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " ideal model delta sigma weight residual 116.52 130.09 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C LEU R 248 " pdb=" N PRO R 249 " pdb=" CA PRO R 249 " ideal model delta sigma weight residual 119.84 115.03 4.81 1.25e+00 6.40e-01 1.48e+01 ... (remaining 11493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 5158 34.51 - 69.01: 71 69.01 - 103.52: 5 103.52 - 138.02: 1 138.02 - 172.53: 5 Dihedral angle restraints: 5240 sinusoidal: 2209 harmonic: 3031 Sorted by residual: dihedral pdb=" C16 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sinusoidal sigma weight residual -78.02 94.51 -172.53 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C18 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C17 CLR R 404 " pdb=" C20 CLR R 404 " ideal model delta sinusoidal sigma weight residual 312.73 144.58 168.15 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C15 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C18 CLR R 404 " ideal model delta sinusoidal sigma weight residual 69.18 -96.05 165.23 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 1317 0.383 - 0.766: 1 0.766 - 1.149: 0 1.149 - 1.532: 0 1.532 - 1.914: 2 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -1.02 -1.91 2.00e-01 2.50e+01 9.16e+01 chirality pdb=" CG LEU R 3 " pdb=" CB LEU R 3 " pdb=" CD1 LEU R 3 " pdb=" CD2 LEU R 3 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 chirality pdb=" CA GLN R 6 " pdb=" N GLN R 6 " pdb=" C GLN R 6 " pdb=" CB GLN R 6 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 1317 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 237 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ALA R 237 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA R 237 " -0.018 2.00e-02 2.50e+03 pdb=" N MET R 238 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 173 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C PHE R 173 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE R 173 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU R 174 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 178 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C PRO R 178 " -0.036 2.00e-02 2.50e+03 pdb=" O PRO R 178 " 0.014 2.00e-02 2.50e+03 pdb=" N MET R 179 " 0.012 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 108 2.58 - 3.16: 7464 3.16 - 3.74: 13104 3.74 - 4.32: 18541 4.32 - 4.90: 30724 Nonbonded interactions: 69941 Sorted by model distance: nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.006 3.040 nonbonded pdb=" OG SER R 235 " pdb=" NH2 ARG R 293 " model vdw 2.022 3.120 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.080 3.120 nonbonded pdb=" OD1 ASP A 111 " pdb=" OG SER A 113 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THR R 40 " pdb=" OD1 ASN R 43 " model vdw 2.136 3.040 ... (remaining 69936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.003 0.082 8461 Z= 0.194 Angle : 0.754 30.642 11504 Z= 0.337 Chirality : 0.085 1.914 1320 Planarity : 0.003 0.041 1446 Dihedral : 12.507 172.528 3271 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.57 % Allowed : 6.04 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.25), residues: 1027 helix: 0.17 (0.25), residues: 401 sheet: -2.09 (0.31), residues: 207 loop : -1.98 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.005 0.001 TYR R 10 PHE 0.014 0.001 PHE R 173 TRP 0.009 0.001 TRP R 247 HIS 0.005 0.001 HIS R 251 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8458) covalent geometry : angle 0.75377 (11498) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.35947 ( 6) hydrogen bonds : bond 0.12068 ( 436) hydrogen bonds : angle 6.25935 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8121 (tt) cc_final: 0.7907 (pt) REVERT: A 212 TYR cc_start: 0.8614 (m-80) cc_final: 0.7916 (m-80) REVERT: B 9 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8591 (pp30) REVERT: B 10 GLU cc_start: 0.8695 (tp30) cc_final: 0.8449 (tp30) REVERT: B 63 TRP cc_start: 0.8484 (m100) cc_final: 0.8247 (m100) REVERT: B 171 ILE cc_start: 0.6986 (mp) cc_final: 0.6612 (mm) REVERT: B 280 LYS cc_start: 0.8845 (tttm) cc_final: 0.8560 (ttpp) REVERT: B 289 TYR cc_start: 0.8423 (m-80) cc_final: 0.7747 (m-80) REVERT: B 297 TRP cc_start: 0.7497 (m100) cc_final: 0.7256 (m100) REVERT: N 60 TYR cc_start: 0.8323 (m-80) cc_final: 0.7396 (m-80) REVERT: N 87 LYS cc_start: 0.8319 (mtpt) cc_final: 0.8048 (mtmm) REVERT: R 227 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7691 (pt0) outliers start: 5 outliers final: 1 residues processed: 293 average time/residue: 0.0939 time to fit residues: 35.9121 Evaluate side-chains 179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 239 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 75 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 GLN A 123 ASN ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS B 62 HIS B 88 ASN B 91 HIS B 119 ASN B 156 GLN B 230 ASN B 295 ASN R 175 ASN R 280 HIS ** R 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.104585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079380 restraints weight = 17021.107| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.17 r_work: 0.3159 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8461 Z= 0.198 Angle : 0.801 31.321 11504 Z= 0.363 Chirality : 0.067 1.882 1320 Planarity : 0.004 0.057 1446 Dihedral : 12.111 167.215 1421 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.31 % Allowed : 11.06 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1027 helix: 1.10 (0.26), residues: 392 sheet: -1.60 (0.31), residues: 224 loop : -1.00 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.014 0.001 TYR B 59 PHE 0.017 0.002 PHE R 173 TRP 0.014 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8458) covalent geometry : angle 0.80038 (11498) SS BOND : bond 0.00493 ( 3) SS BOND : angle 1.56925 ( 6) hydrogen bonds : bond 0.03527 ( 436) hydrogen bonds : angle 5.07410 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ARG cc_start: 0.8570 (ptp90) cc_final: 0.8186 (ptp90) REVERT: A 230 ASP cc_start: 0.8382 (m-30) cc_final: 0.8152 (m-30) REVERT: B 9 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8843 (pp30) REVERT: B 10 GLU cc_start: 0.8941 (tp30) cc_final: 0.8654 (tp30) REVERT: B 15 LYS cc_start: 0.9261 (ptpt) cc_final: 0.8997 (ptpp) REVERT: B 138 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 280 LYS cc_start: 0.9054 (tttm) cc_final: 0.8803 (ttpp) REVERT: N 32 TYR cc_start: 0.8467 (m-80) cc_final: 0.7962 (m-80) REVERT: N 36 TRP cc_start: 0.8658 (m100) cc_final: 0.8406 (m100) REVERT: N 38 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7891 (ptt90) REVERT: N 60 TYR cc_start: 0.8473 (m-80) cc_final: 0.7098 (m-80) REVERT: N 80 TYR cc_start: 0.7964 (m-80) cc_final: 0.7540 (m-80) REVERT: N 105 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7985 (mtp180) REVERT: N 115 TYR cc_start: 0.8664 (t80) cc_final: 0.8336 (t80) REVERT: R 170 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7199 (mptt) REVERT: R 227 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7963 (pt0) REVERT: R 229 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7270 (tm-30) outliers start: 29 outliers final: 21 residues processed: 188 average time/residue: 0.1031 time to fit residues: 25.3212 Evaluate side-chains 159 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 303 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 88 optimal weight: 0.0370 chunk 100 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.107440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.083247 restraints weight = 16720.625| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.06 r_work: 0.3257 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8461 Z= 0.112 Angle : 0.742 30.410 11504 Z= 0.327 Chirality : 0.066 1.869 1320 Planarity : 0.004 0.058 1446 Dihedral : 11.522 169.760 1419 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.62 % Allowed : 13.23 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1027 helix: 1.50 (0.26), residues: 394 sheet: -1.10 (0.31), residues: 222 loop : -0.99 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 13 TYR 0.010 0.001 TYR N 60 PHE 0.013 0.001 PHE A 74 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8458) covalent geometry : angle 0.74228 (11498) SS BOND : bond 0.00471 ( 3) SS BOND : angle 0.97683 ( 6) hydrogen bonds : bond 0.03152 ( 436) hydrogen bonds : angle 4.75048 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6155 (tpp) cc_final: 0.5781 (tpp) REVERT: A 62 ILE cc_start: 0.8010 (tt) cc_final: 0.7711 (pt) REVERT: A 169 ARG cc_start: 0.8565 (ptp90) cc_final: 0.8172 (ptp90) REVERT: B 9 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8805 (pp30) REVERT: B 10 GLU cc_start: 0.8908 (tp30) cc_final: 0.8549 (tp30) REVERT: B 15 LYS cc_start: 0.9224 (ptpt) cc_final: 0.8980 (ptpp) REVERT: B 23 LYS cc_start: 0.9211 (pttt) cc_final: 0.8966 (pttp) REVERT: B 138 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 280 LYS cc_start: 0.8984 (tttm) cc_final: 0.8743 (tttm) REVERT: B 336 LEU cc_start: 0.8747 (tt) cc_final: 0.8455 (tt) REVERT: G 29 LYS cc_start: 0.8872 (tppt) cc_final: 0.8613 (tppt) REVERT: G 46 LYS cc_start: 0.9389 (tppt) cc_final: 0.9138 (tppt) REVERT: N 38 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7937 (ptt90) REVERT: N 53 GLN cc_start: 0.8763 (mp10) cc_final: 0.8497 (mp10) REVERT: N 60 TYR cc_start: 0.8587 (m-80) cc_final: 0.8280 (m-80) REVERT: R 227 GLN cc_start: 0.8480 (mm-40) cc_final: 0.7990 (pt0) REVERT: R 229 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7210 (tm-30) outliers start: 23 outliers final: 16 residues processed: 171 average time/residue: 0.1146 time to fit residues: 25.1287 Evaluate side-chains 144 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 303 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 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 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.101471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076944 restraints weight = 16820.440| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.95 r_work: 0.3137 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8461 Z= 0.178 Angle : 0.763 31.306 11504 Z= 0.340 Chirality : 0.066 1.848 1320 Planarity : 0.004 0.059 1446 Dihedral : 11.400 167.863 1419 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.99 % Allowed : 13.80 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.26), residues: 1027 helix: 1.55 (0.26), residues: 391 sheet: -0.95 (0.31), residues: 221 loop : -0.69 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 13 TYR 0.013 0.001 TYR N 115 PHE 0.015 0.001 PHE A 74 TRP 0.011 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8458) covalent geometry : angle 0.76316 (11498) SS BOND : bond 0.00193 ( 3) SS BOND : angle 1.11091 ( 6) hydrogen bonds : bond 0.03490 ( 436) hydrogen bonds : angle 4.77661 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6311 (tpp) cc_final: 0.6083 (tpp) REVERT: A 62 ILE cc_start: 0.8077 (tt) cc_final: 0.7763 (pt) REVERT: A 169 ARG cc_start: 0.8539 (ptp90) cc_final: 0.8311 (ptp90) REVERT: B 8 ARG cc_start: 0.9104 (mmt90) cc_final: 0.8874 (mmt90) REVERT: B 9 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8777 (pp30) REVERT: B 10 GLU cc_start: 0.8932 (tp30) cc_final: 0.8594 (tp30) REVERT: B 15 LYS cc_start: 0.9228 (ptpt) cc_final: 0.9000 (ptpp) REVERT: B 127 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8164 (mmtm) REVERT: B 129 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7678 (mmm160) REVERT: B 138 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7836 (mm-30) REVERT: B 280 LYS cc_start: 0.9090 (tttm) cc_final: 0.8327 (ttmm) REVERT: G 22 GLU cc_start: 0.9014 (tp30) cc_final: 0.8695 (tp30) REVERT: G 29 LYS cc_start: 0.8882 (tppt) cc_final: 0.8603 (tppt) REVERT: N 38 ARG cc_start: 0.8469 (ptt-90) cc_final: 0.8207 (ptt90) REVERT: N 53 GLN cc_start: 0.8941 (mp10) cc_final: 0.8312 (mp10) REVERT: N 60 TYR cc_start: 0.8641 (m-80) cc_final: 0.8227 (m-80) REVERT: R 170 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7402 (mptt) REVERT: R 227 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8069 (pt0) REVERT: R 229 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7174 (tm-30) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.0927 time to fit residues: 20.2773 Evaluate side-chains 154 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.100819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076320 restraints weight = 16775.570| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.96 r_work: 0.3086 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8461 Z= 0.165 Angle : 0.753 30.925 11504 Z= 0.334 Chirality : 0.065 1.820 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.333 170.170 1419 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.42 % Allowed : 15.17 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.26), residues: 1027 helix: 1.55 (0.26), residues: 391 sheet: -0.78 (0.32), residues: 223 loop : -0.56 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 19 TYR 0.022 0.001 TYR R 308 PHE 0.015 0.001 PHE A 74 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8458) covalent geometry : angle 0.75256 (11498) SS BOND : bond 0.00136 ( 3) SS BOND : angle 0.96238 ( 6) hydrogen bonds : bond 0.03396 ( 436) hydrogen bonds : angle 4.78747 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6372 (tpp) cc_final: 0.6115 (tpp) REVERT: A 62 ILE cc_start: 0.8044 (tt) cc_final: 0.7753 (pt) REVERT: B 8 ARG cc_start: 0.9172 (mmt90) cc_final: 0.8928 (mmt90) REVERT: B 9 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8770 (pp30) REVERT: B 10 GLU cc_start: 0.8956 (tp30) cc_final: 0.8607 (tp30) REVERT: B 35 ASN cc_start: 0.8800 (m110) cc_final: 0.8446 (m-40) REVERT: B 127 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8140 (mmtt) REVERT: B 129 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7823 (mmm160) REVERT: B 280 LYS cc_start: 0.9089 (tttm) cc_final: 0.8315 (ttmm) REVERT: G 22 GLU cc_start: 0.9035 (tp30) cc_final: 0.8820 (tp30) REVERT: G 29 LYS cc_start: 0.8931 (tppt) cc_final: 0.8599 (tppt) REVERT: N 5 GLN cc_start: 0.7723 (mp10) cc_final: 0.7489 (mp10) REVERT: N 38 ARG cc_start: 0.8485 (ptt-90) cc_final: 0.8128 (ptt90) REVERT: N 46 GLU cc_start: 0.7478 (tt0) cc_final: 0.7104 (tt0) REVERT: N 53 GLN cc_start: 0.8897 (mp10) cc_final: 0.8262 (mp10) REVERT: N 60 TYR cc_start: 0.8572 (m-80) cc_final: 0.7412 (m-80) REVERT: N 80 TYR cc_start: 0.8137 (m-80) cc_final: 0.7826 (m-80) REVERT: R 170 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7405 (mptt) outliers start: 30 outliers final: 20 residues processed: 166 average time/residue: 0.0980 time to fit residues: 21.4031 Evaluate side-chains 154 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.103378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.079000 restraints weight = 16470.269| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.95 r_work: 0.3192 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8461 Z= 0.111 Angle : 0.727 30.685 11504 Z= 0.320 Chirality : 0.064 1.827 1320 Planarity : 0.004 0.062 1446 Dihedral : 11.218 170.595 1419 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.65 % Allowed : 15.28 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1027 helix: 1.73 (0.26), residues: 391 sheet: -0.50 (0.32), residues: 232 loop : -0.58 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.011 0.001 TYR N 115 PHE 0.015 0.001 PHE N 103 TRP 0.011 0.001 TRP B 297 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8458) covalent geometry : angle 0.72672 (11498) SS BOND : bond 0.00051 ( 3) SS BOND : angle 0.58878 ( 6) hydrogen bonds : bond 0.03222 ( 436) hydrogen bonds : angle 4.62213 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8039 (tt) cc_final: 0.7595 (pt) REVERT: B 8 ARG cc_start: 0.9209 (mmt90) cc_final: 0.8974 (mmt90) REVERT: B 9 GLN cc_start: 0.9196 (tm-30) cc_final: 0.8810 (pp30) REVERT: B 10 GLU cc_start: 0.8951 (tp30) cc_final: 0.8568 (tp30) REVERT: B 35 ASN cc_start: 0.8864 (m110) cc_final: 0.8393 (m-40) REVERT: B 129 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7867 (mmm160) REVERT: B 280 LYS cc_start: 0.9022 (tttm) cc_final: 0.8292 (ttmm) REVERT: B 289 TYR cc_start: 0.8971 (m-80) cc_final: 0.8391 (m-80) REVERT: B 297 TRP cc_start: 0.8440 (m100) cc_final: 0.7888 (m100) REVERT: G 22 GLU cc_start: 0.9036 (tp30) cc_final: 0.8807 (tp30) REVERT: G 29 LYS cc_start: 0.8959 (tppt) cc_final: 0.8606 (tppt) REVERT: N 5 GLN cc_start: 0.7761 (mp10) cc_final: 0.7474 (mp10) REVERT: N 38 ARG cc_start: 0.8507 (ptt-90) cc_final: 0.8107 (ptt90) REVERT: N 46 GLU cc_start: 0.7573 (tt0) cc_final: 0.7145 (tt0) REVERT: N 51 ILE cc_start: 0.7570 (pt) cc_final: 0.7369 (pt) REVERT: N 53 GLN cc_start: 0.8848 (mp10) cc_final: 0.8283 (mp10) REVERT: N 60 TYR cc_start: 0.8530 (m-80) cc_final: 0.7430 (m-80) REVERT: N 68 PHE cc_start: 0.8518 (m-10) cc_final: 0.8235 (m-10) REVERT: N 80 TYR cc_start: 0.8230 (m-80) cc_final: 0.7940 (m-80) REVERT: R 170 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7416 (mptt) REVERT: R 173 PHE cc_start: 0.8227 (t80) cc_final: 0.7921 (t80) REVERT: R 227 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7779 (tt0) outliers start: 32 outliers final: 23 residues processed: 166 average time/residue: 0.1132 time to fit residues: 24.7301 Evaluate side-chains 161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 283 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.102044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.077778 restraints weight = 16717.971| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.95 r_work: 0.3109 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8461 Z= 0.132 Angle : 0.733 30.767 11504 Z= 0.321 Chirality : 0.064 1.816 1320 Planarity : 0.004 0.059 1446 Dihedral : 11.218 171.070 1419 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.96 % Allowed : 17.10 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1027 helix: 1.76 (0.26), residues: 391 sheet: -0.43 (0.32), residues: 233 loop : -0.44 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.022 0.001 TYR R 308 PHE 0.014 0.001 PHE A 74 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8458) covalent geometry : angle 0.73266 (11498) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.61448 ( 6) hydrogen bonds : bond 0.03303 ( 436) hydrogen bonds : angle 4.60256 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8032 (tt) cc_final: 0.7594 (pt) REVERT: B 8 ARG cc_start: 0.9261 (mmt90) cc_final: 0.8993 (mmt90) REVERT: B 9 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8784 (pp30) REVERT: B 10 GLU cc_start: 0.8939 (tp30) cc_final: 0.8554 (tp30) REVERT: B 35 ASN cc_start: 0.8872 (m110) cc_final: 0.8394 (m-40) REVERT: B 280 LYS cc_start: 0.9023 (tttm) cc_final: 0.8300 (ttmm) REVERT: G 22 GLU cc_start: 0.9018 (tp30) cc_final: 0.8797 (tp30) REVERT: G 29 LYS cc_start: 0.8931 (tppt) cc_final: 0.8612 (tppt) REVERT: N 3 GLN cc_start: 0.8331 (mt0) cc_final: 0.8118 (mt0) REVERT: N 5 GLN cc_start: 0.7780 (mp10) cc_final: 0.7446 (mp10) REVERT: N 38 ARG cc_start: 0.8495 (ptt-90) cc_final: 0.8152 (ptt90) REVERT: N 46 GLU cc_start: 0.7637 (tt0) cc_final: 0.7242 (tt0) REVERT: N 51 ILE cc_start: 0.7661 (pt) cc_final: 0.7430 (pt) REVERT: N 53 GLN cc_start: 0.8821 (mp10) cc_final: 0.8175 (mp10) REVERT: N 60 TYR cc_start: 0.8599 (m-80) cc_final: 0.8161 (m-80) REVERT: N 80 TYR cc_start: 0.8261 (m-80) cc_final: 0.8031 (m-80) REVERT: R 170 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7426 (mptt) REVERT: R 173 PHE cc_start: 0.8221 (t80) cc_final: 0.7902 (t80) outliers start: 26 outliers final: 19 residues processed: 160 average time/residue: 0.1226 time to fit residues: 25.7769 Evaluate side-chains 151 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 283 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.099175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074445 restraints weight = 16896.566| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.83 r_work: 0.3107 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8461 Z= 0.217 Angle : 0.781 30.883 11504 Z= 0.351 Chirality : 0.065 1.802 1320 Planarity : 0.004 0.060 1446 Dihedral : 11.395 171.685 1419 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.08 % Allowed : 17.33 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1027 helix: 1.54 (0.26), residues: 393 sheet: -0.53 (0.33), residues: 223 loop : -0.40 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.024 0.001 TYR N 115 PHE 0.016 0.001 PHE A 74 TRP 0.010 0.002 TRP B 169 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 8458) covalent geometry : angle 0.78141 (11498) SS BOND : bond 0.00226 ( 3) SS BOND : angle 0.85763 ( 6) hydrogen bonds : bond 0.03613 ( 436) hydrogen bonds : angle 4.81204 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8053 (tt) cc_final: 0.7608 (pt) REVERT: B 8 ARG cc_start: 0.9243 (mmt90) cc_final: 0.8933 (mmt90) REVERT: B 9 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8837 (pp30) REVERT: B 10 GLU cc_start: 0.8973 (tp30) cc_final: 0.8569 (tp30) REVERT: B 35 ASN cc_start: 0.8898 (m110) cc_final: 0.8481 (m-40) REVERT: G 22 GLU cc_start: 0.9016 (tp30) cc_final: 0.8743 (tp30) REVERT: G 29 LYS cc_start: 0.8941 (tppt) cc_final: 0.8621 (tppt) REVERT: G 32 LYS cc_start: 0.8970 (tptt) cc_final: 0.8721 (tppt) REVERT: N 5 GLN cc_start: 0.7880 (mp10) cc_final: 0.7516 (mp10) REVERT: N 19 ARG cc_start: 0.8408 (ttt90) cc_final: 0.8088 (ttt90) REVERT: N 38 ARG cc_start: 0.8643 (ptt-90) cc_final: 0.8327 (ptt90) REVERT: N 46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7392 (tt0) REVERT: N 53 GLN cc_start: 0.8787 (mp10) cc_final: 0.8088 (mp10) REVERT: N 60 TYR cc_start: 0.8723 (m-80) cc_final: 0.8223 (m-80) REVERT: N 78 THR cc_start: 0.9233 (m) cc_final: 0.8577 (p) REVERT: N 87 LYS cc_start: 0.8364 (mmtp) cc_final: 0.7916 (mmtp) REVERT: N 122 THR cc_start: 0.8342 (m) cc_final: 0.7902 (p) REVERT: R 170 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7434 (mptt) REVERT: R 173 PHE cc_start: 0.8233 (t80) cc_final: 0.7964 (t80) outliers start: 27 outliers final: 22 residues processed: 171 average time/residue: 0.1189 time to fit residues: 26.7689 Evaluate side-chains 163 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 283 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.101656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077106 restraints weight = 16852.967| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.86 r_work: 0.3121 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8461 Z= 0.135 Angle : 0.765 30.612 11504 Z= 0.342 Chirality : 0.065 1.813 1320 Planarity : 0.004 0.059 1446 Dihedral : 11.322 172.384 1419 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.19 % Allowed : 18.02 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.27), residues: 1027 helix: 1.59 (0.26), residues: 392 sheet: -0.48 (0.33), residues: 223 loop : -0.28 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 13 TYR 0.021 0.001 TYR N 115 PHE 0.014 0.001 PHE A 74 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8458) covalent geometry : angle 0.76532 (11498) SS BOND : bond 0.00109 ( 3) SS BOND : angle 0.69057 ( 6) hydrogen bonds : bond 0.03398 ( 436) hydrogen bonds : angle 4.72582 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8054 (tt) cc_final: 0.7605 (pt) REVERT: B 8 ARG cc_start: 0.9214 (mmt90) cc_final: 0.8899 (mmt90) REVERT: B 9 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8821 (pp30) REVERT: B 10 GLU cc_start: 0.8952 (tp30) cc_final: 0.8559 (tp30) REVERT: B 35 ASN cc_start: 0.8889 (m110) cc_final: 0.8465 (m-40) REVERT: B 280 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8487 (ttmm) REVERT: B 289 TYR cc_start: 0.8994 (m-80) cc_final: 0.8577 (m-80) REVERT: G 13 ARG cc_start: 0.9075 (ptp-110) cc_final: 0.8793 (mtm110) REVERT: G 14 LYS cc_start: 0.9510 (mmmt) cc_final: 0.9039 (tppt) REVERT: G 22 GLU cc_start: 0.8974 (tp30) cc_final: 0.8752 (tp30) REVERT: G 29 LYS cc_start: 0.8900 (tppt) cc_final: 0.8597 (tppt) REVERT: G 32 LYS cc_start: 0.9019 (tptt) cc_final: 0.8782 (tppt) REVERT: N 3 GLN cc_start: 0.8465 (mt0) cc_final: 0.8223 (mt0) REVERT: N 5 GLN cc_start: 0.7828 (mp10) cc_final: 0.7426 (mp10) REVERT: N 19 ARG cc_start: 0.8533 (ttt90) cc_final: 0.8241 (ttt90) REVERT: N 46 GLU cc_start: 0.7914 (tt0) cc_final: 0.7502 (tt0) REVERT: N 51 ILE cc_start: 0.7908 (pt) cc_final: 0.7594 (pt) REVERT: N 53 GLN cc_start: 0.8728 (mp10) cc_final: 0.8180 (mp10) REVERT: N 60 TYR cc_start: 0.8675 (m-80) cc_final: 0.8210 (m-80) REVERT: N 87 LYS cc_start: 0.8395 (mmtp) cc_final: 0.7942 (mmtp) REVERT: R 39 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: R 170 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7456 (mptt) REVERT: R 173 PHE cc_start: 0.8122 (t80) cc_final: 0.7843 (t80) outliers start: 28 outliers final: 23 residues processed: 168 average time/residue: 0.1181 time to fit residues: 26.3383 Evaluate side-chains 166 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 283 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.101231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076690 restraints weight = 16798.949| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.85 r_work: 0.3117 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8461 Z= 0.147 Angle : 0.771 30.663 11504 Z= 0.346 Chirality : 0.064 1.806 1320 Planarity : 0.004 0.059 1446 Dihedral : 11.324 172.628 1419 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.51 % Allowed : 18.93 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.27), residues: 1027 helix: 1.60 (0.26), residues: 392 sheet: -0.44 (0.33), residues: 223 loop : -0.26 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.024 0.001 TYR N 115 PHE 0.014 0.001 PHE A 74 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8458) covalent geometry : angle 0.77064 (11498) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.79669 ( 6) hydrogen bonds : bond 0.03489 ( 436) hydrogen bonds : angle 4.72575 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2054 Ramachandran restraints generated. 1027 Oldfield, 0 Emsley, 1027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8043 (tt) cc_final: 0.7618 (pt) REVERT: B 8 ARG cc_start: 0.9219 (mmt90) cc_final: 0.8898 (mmt90) REVERT: B 9 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8811 (pp30) REVERT: B 10 GLU cc_start: 0.8947 (tp30) cc_final: 0.8549 (tp30) REVERT: B 35 ASN cc_start: 0.8833 (m110) cc_final: 0.8429 (m110) REVERT: B 262 MET cc_start: 0.8101 (tpt) cc_final: 0.7862 (tpp) REVERT: B 280 LYS cc_start: 0.9069 (ttpp) cc_final: 0.8550 (ttmm) REVERT: B 289 TYR cc_start: 0.9005 (m-80) cc_final: 0.8574 (m-80) REVERT: G 14 LYS cc_start: 0.9528 (mmmt) cc_final: 0.9076 (tppt) REVERT: G 22 GLU cc_start: 0.8976 (tp30) cc_final: 0.8723 (tp30) REVERT: G 29 LYS cc_start: 0.8894 (tppt) cc_final: 0.8620 (tppt) REVERT: G 32 LYS cc_start: 0.9021 (tptt) cc_final: 0.8785 (tppt) REVERT: N 3 GLN cc_start: 0.8463 (mt0) cc_final: 0.8223 (mt0) REVERT: N 5 GLN cc_start: 0.7769 (mp10) cc_final: 0.7386 (mp10) REVERT: N 19 ARG cc_start: 0.8550 (ttt90) cc_final: 0.8260 (ttt90) REVERT: N 38 ARG cc_start: 0.8759 (ptt-90) cc_final: 0.8188 (ptt90) REVERT: N 46 GLU cc_start: 0.7946 (tt0) cc_final: 0.7332 (tt0) REVERT: N 50 ASP cc_start: 0.7926 (p0) cc_final: 0.7722 (p0) REVERT: N 51 ILE cc_start: 0.7939 (pt) cc_final: 0.7639 (pt) REVERT: N 53 GLN cc_start: 0.8757 (mp10) cc_final: 0.8172 (mp10) REVERT: N 60 TYR cc_start: 0.8687 (m-80) cc_final: 0.8213 (m-80) REVERT: N 78 THR cc_start: 0.9224 (m) cc_final: 0.8688 (p) REVERT: N 87 LYS cc_start: 0.8418 (mmtp) cc_final: 0.7957 (mmtp) REVERT: R 39 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: R 170 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7402 (mptt) REVERT: R 173 PHE cc_start: 0.8064 (t80) cc_final: 0.7796 (t80) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.1223 time to fit residues: 25.6527 Evaluate side-chains 161 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 179 MET Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 256 VAL Chi-restraints excluded: chain R residue 283 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 94 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.102643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.078363 restraints weight = 16771.449| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.86 r_work: 0.3191 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8461 Z= 0.120 Angle : 0.765 30.536 11504 Z= 0.341 Chirality : 0.065 1.814 1320 Planarity : 0.004 0.059 1446 Dihedral : 11.280 172.772 1419 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.39 % Allowed : 19.04 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.27), residues: 1027 helix: 1.71 (0.26), residues: 392 sheet: -0.24 (0.33), residues: 230 loop : -0.28 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 13 TYR 0.021 0.001 TYR N 115 PHE 0.013 0.001 PHE A 74 TRP 0.014 0.001 TRP B 332 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8458) covalent geometry : angle 0.76517 (11498) SS BOND : bond 0.00095 ( 3) SS BOND : angle 0.69092 ( 6) hydrogen bonds : bond 0.03401 ( 436) hydrogen bonds : angle 4.68480 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.90 seconds wall clock time: 36 minutes 42.47 seconds (2202.47 seconds total)