Starting phenix.real_space_refine on Thu Jul 2 12:56:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gus_34278/07_2026/8gus_34278_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gus_34278/07_2026/8gus_34278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gus_34278/07_2026/8gus_34278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gus_34278/07_2026/8gus_34278.map" model { file = "/net/cci-nas-00/data/ceres_data/8gus_34278/07_2026/8gus_34278_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gus_34278/07_2026/8gus_34278_neut.cif" } resolution = 2.97 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= 0.001 sd= 0.023 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 66 5.16 5 C 5618 2.51 5 N 1495 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8805 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1733 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KO3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 0.22 Number of scatterers: 8805 At special positions: 0 Unit cell: (89.44, 117.52, 131.04, 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 66 16.00 O 1626 8.00 N 1495 7.00 C 5618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.77 Conformation dependent library (CDL) restraints added in 386.1 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 39.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.614A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.552A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.147A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.848A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.044A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.662A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.514A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 30 through 61 Processing helix chain 'R' and resid 67 through 95 removed outlier: 3.595A pdb=" N LEU R 71 " --> pdb=" O LYS R 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE R 72 " --> pdb=" O PRO R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.698A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 187 through 227 removed outlier: 3.523A pdb=" N GLY R 210 " --> pdb=" O ILE R 206 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS R 226 " --> pdb=" O SER R 222 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 271 Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 276 through 285 removed outlier: 3.675A pdb=" N ALA R 280 " --> pdb=" O GLN R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 300 removed outlier: 3.886A pdb=" N LEU R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 319 removed outlier: 3.511A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS R 319 " --> pdb=" O ALA R 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.010A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.570A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.210A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.040A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.135A 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 105 removed outlier: 6.609A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.147A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.846A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.182A 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: 3.662A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.934A 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: 6.474A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.618A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.771A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.076A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.624A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.732A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1311 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: 1.41 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1414 1.32 - 1.44: 2484 1.44 - 1.57: 4997 1.57 - 1.69: 2 1.69 - 1.82: 95 Bond restraints: 8992 Sorted by residual: bond pdb=" CG PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 1.503 1.194 0.309 3.40e-02 8.65e+02 8.26e+01 bond pdb=" N PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 1.473 1.541 -0.068 1.40e-02 5.10e+03 2.38e+01 bond pdb=" CB PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.28e+00 bond pdb=" N PRO R 184 " pdb=" CA PRO R 184 " ideal model delta sigma weight residual 1.466 1.437 0.030 1.17e-02 7.31e+03 6.37e+00 bond pdb=" C17 KO3 R 401 " pdb=" C22 KO3 R 401 " ideal model delta sigma weight residual 1.555 1.520 0.035 2.00e-02 2.50e+03 3.11e+00 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 12126 3.62 - 7.24: 49 7.24 - 10.85: 7 10.85 - 14.47: 1 14.47 - 18.09: 2 Bond angle restraints: 12185 Sorted by residual: angle pdb=" CA PRO R 184 " pdb=" N PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 112.00 93.91 18.09 1.40e+00 5.10e-01 1.67e+02 angle pdb=" N PRO R 184 " pdb=" CD PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 103.20 85.39 17.81 1.50e+00 4.44e-01 1.41e+02 angle pdb=" CA PRO R 184 " pdb=" CB PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 104.50 90.81 13.69 1.90e+00 2.77e-01 5.20e+01 angle pdb=" CA PRO R 168 " pdb=" N PRO R 168 " pdb=" CD PRO R 168 " ideal model delta sigma weight residual 112.00 103.76 8.24 1.40e+00 5.10e-01 3.47e+01 angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 124.27 -9.87 2.30e+00 1.89e-01 1.84e+01 ... (remaining 12180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 4649 15.33 - 30.66: 489 30.66 - 46.00: 186 46.00 - 61.33: 36 61.33 - 76.66: 4 Dihedral angle restraints: 5364 sinusoidal: 2080 harmonic: 3284 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 141.50 38.50 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 179 " pdb=" CB CYS R 179 " ideal model delta sinusoidal sigma weight residual -86.00 -150.83 64.83 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 124.03 -31.03 1 1.00e+01 1.00e-02 1.37e+01 ... (remaining 5361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1069 0.047 - 0.095: 258 0.095 - 0.142: 57 0.142 - 0.190: 3 0.190 - 0.237: 4 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C22 KO3 R 401 " pdb=" C17 KO3 R 401 " pdb=" C21 KO3 R 401 " pdb=" C23 KO3 R 401 " both_signs ideal model delta sigma weight residual False 3.40 3.17 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA PRO R 168 " pdb=" N PRO R 168 " pdb=" C PRO R 168 " pdb=" CB PRO R 168 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU R 196 " pdb=" CB LEU R 196 " pdb=" CD1 LEU R 196 " pdb=" CD2 LEU R 196 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1388 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 183 " 0.112 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO R 184 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO R 184 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO R 184 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 194 " 0.035 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP R 194 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP R 194 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP R 194 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 194 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 194 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 194 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 194 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 194 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP R 194 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.077 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO R 168 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.062 5.00e-02 4.00e+02 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1150 2.75 - 3.28: 8839 3.28 - 3.82: 15242 3.82 - 4.36: 18107 4.36 - 4.90: 31313 Nonbonded interactions: 74651 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 6 " pdb=" OD2 ASP A 9 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 161 " pdb=" O THR B 165 " model vdw 2.266 3.040 nonbonded pdb=" O LYS B 280 " pdb=" OG SER B 281 " model vdw 2.310 3.040 ... (remaining 74646 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.090 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.309 8996 Z= 0.245 Angle : 0.702 18.088 12193 Z= 0.378 Chirality : 0.044 0.237 1391 Planarity : 0.007 0.151 1525 Dihedral : 14.659 76.662 3234 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.44 (0.26), residues: 1117 helix: 1.67 (0.26), residues: 412 sheet: 0.03 (0.32), residues: 290 loop : -0.87 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.013 0.001 TYR S 50 PHE 0.041 0.002 PHE R 281 TRP 0.082 0.003 TRP R 194 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.24 ( 8992) covalent geometry : angle 0.70181 / 0.38 (12185) SS BOND : bond 0.01069 / 0.56 ( 4) SS BOND : angle 0.85729 / 0.42 ( 8) hydrogen bonds : bond 0.15641 / 10.84 ( 453) hydrogen bonds : angle 6.68107 / 4.82 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 277 LYS cc_start: 0.7554 (ttmm) cc_final: 0.7061 (tppp) REVERT: B 197 ARG cc_start: 0.7341 (ttm110) cc_final: 0.6980 (ttm110) REVERT: B 277 SER cc_start: 0.8413 (t) cc_final: 0.8005 (p) REVERT: B 304 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.8034 (ttp-110) REVERT: S 59 TYR cc_start: 0.8077 (m-10) cc_final: 0.7854 (m-10) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.4808 time to fit residues: 109.0396 Evaluate side-chains 215 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN B 62 HIS B 110 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.119571 restraints weight = 13398.479| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.14 r_work: 0.3472 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8996 Z= 0.191 Angle : 0.611 9.233 12193 Z= 0.310 Chirality : 0.042 0.192 1391 Planarity : 0.004 0.069 1525 Dihedral : 4.933 39.675 1268 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.01 % Allowed : 19.20 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.50 (0.25), residues: 1117 helix: 1.71 (0.26), residues: 416 sheet: 0.13 (0.32), residues: 270 loop : -0.86 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.016 0.001 TYR S 50 PHE 0.014 0.001 PHE R 183 TRP 0.039 0.002 TRP R 194 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 8992) covalent geometry : angle 0.61118 / 0.31 (12185) SS BOND : bond 0.01003 / 0.52 ( 4) SS BOND : angle 0.79352 / 0.41 ( 8) hydrogen bonds : bond 0.04195 / 2.89 ( 453) hydrogen bonds : angle 5.15990 / 3.73 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.339 Fit side-chains REVERT: A 32 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7519 (mtm-85) REVERT: A 46 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.7013 (mttp) REVERT: A 227 LEU cc_start: 0.8297 (mp) cc_final: 0.8055 (mt) REVERT: A 251 ASP cc_start: 0.7946 (m-30) cc_final: 0.7746 (m-30) REVERT: A 277 LYS cc_start: 0.7703 (ttmm) cc_final: 0.7250 (tppp) REVERT: A 295 THR cc_start: 0.7827 (p) cc_final: 0.7588 (p) REVERT: B 68 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8213 (ttt180) REVERT: B 160 SER cc_start: 0.7972 (p) cc_final: 0.7685 (p) REVERT: B 197 ARG cc_start: 0.7701 (ttm110) cc_final: 0.7343 (ttm110) REVERT: B 256 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8231 (mtm180) REVERT: B 289 TYR cc_start: 0.8540 (m-80) cc_final: 0.8294 (m-80) REVERT: S 59 TYR cc_start: 0.8286 (m-80) cc_final: 0.8017 (m-10) REVERT: S 183 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8487 (mt) REVERT: S 208 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7936 (mt-10) outliers start: 38 outliers final: 12 residues processed: 240 average time/residue: 0.3899 time to fit residues: 100.8481 Evaluate side-chains 225 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 62 HIS B 110 ASN B 176 GLN B 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120505 restraints weight = 13264.672| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.16 r_work: 0.3480 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8996 Z= 0.148 Angle : 0.568 8.764 12193 Z= 0.287 Chirality : 0.041 0.248 1391 Planarity : 0.004 0.049 1525 Dihedral : 5.400 65.372 1268 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.69 % Allowed : 21.20 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.60 (0.25), residues: 1117 helix: 1.86 (0.26), residues: 416 sheet: 0.05 (0.31), residues: 273 loop : -0.79 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 219 TYR 0.016 0.001 TYR S 50 PHE 0.025 0.001 PHE R 94 TRP 0.029 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 8992) covalent geometry : angle 0.56780 / 0.29 (12185) SS BOND : bond 0.00916 / 0.48 ( 4) SS BOND : angle 0.74014 / 0.37 ( 8) hydrogen bonds : bond 0.03819 / 2.62 ( 453) hydrogen bonds : angle 4.85499 / 3.49 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7350 (mtm-85) REVERT: A 227 LEU cc_start: 0.8289 (mp) cc_final: 0.8038 (mt) REVERT: A 249 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7603 (tt) REVERT: A 251 ASP cc_start: 0.7952 (m-30) cc_final: 0.7740 (m-30) REVERT: A 276 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7124 (pp20) REVERT: A 277 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7241 (tppp) REVERT: A 295 THR cc_start: 0.7851 (p) cc_final: 0.7558 (p) REVERT: A 317 LYS cc_start: 0.8055 (ptmt) cc_final: 0.7746 (ptpt) REVERT: B 160 SER cc_start: 0.7976 (p) cc_final: 0.7714 (p) REVERT: B 170 ASP cc_start: 0.7930 (t70) cc_final: 0.7499 (t0) REVERT: B 239 ASN cc_start: 0.7803 (m110) cc_final: 0.7597 (m-40) REVERT: B 277 SER cc_start: 0.8393 (t) cc_final: 0.8100 (p) REVERT: B 289 TYR cc_start: 0.8534 (m-80) cc_final: 0.8285 (m-80) REVERT: R 151 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7595 (mm) REVERT: S 146 SER cc_start: 0.8803 (p) cc_final: 0.8567 (p) REVERT: S 208 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7926 (mt-10) REVERT: S 223 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.7957 (t80) outliers start: 35 outliers final: 19 residues processed: 226 average time/residue: 0.4083 time to fit residues: 100.0925 Evaluate side-chains 229 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 110 ASN B 176 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.134499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119542 restraints weight = 13415.000| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.16 r_work: 0.3466 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8996 Z= 0.176 Angle : 0.588 8.608 12193 Z= 0.293 Chirality : 0.042 0.247 1391 Planarity : 0.004 0.050 1525 Dihedral : 5.412 70.129 1268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.22 % Allowed : 22.26 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.59 (0.25), residues: 1117 helix: 1.87 (0.26), residues: 416 sheet: -0.02 (0.31), residues: 275 loop : -0.77 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 52 TYR 0.018 0.001 TYR S 50 PHE 0.027 0.001 PHE R 94 TRP 0.029 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 8992) covalent geometry : angle 0.58812 / 0.29 (12185) SS BOND : bond 0.00972 / 0.51 ( 4) SS BOND : angle 0.81674 / 0.41 ( 8) hydrogen bonds : bond 0.03811 / 2.62 ( 453) hydrogen bonds : angle 4.79802 / 3.43 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7726 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: A 249 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 251 ASP cc_start: 0.7974 (m-30) cc_final: 0.7763 (m-30) REVERT: A 276 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7053 (pp20) REVERT: A 277 LYS cc_start: 0.7740 (ttmm) cc_final: 0.7259 (tppp) REVERT: A 295 THR cc_start: 0.7890 (p) cc_final: 0.7578 (p) REVERT: A 317 LYS cc_start: 0.8191 (ptmt) cc_final: 0.7926 (ptpt) REVERT: A 323 PHE cc_start: 0.8475 (m-80) cc_final: 0.8235 (m-80) REVERT: B 160 SER cc_start: 0.8026 (p) cc_final: 0.7781 (p) REVERT: B 170 ASP cc_start: 0.7884 (t70) cc_final: 0.7465 (t0) REVERT: B 197 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7527 (mtp85) REVERT: B 239 ASN cc_start: 0.7842 (m110) cc_final: 0.7597 (m-40) REVERT: B 258 ASP cc_start: 0.7741 (t0) cc_final: 0.7536 (t0) REVERT: B 289 TYR cc_start: 0.8526 (m-80) cc_final: 0.8248 (m-80) REVERT: S 146 SER cc_start: 0.8815 (p) cc_final: 0.8578 (p) REVERT: S 166 LEU cc_start: 0.8753 (tt) cc_final: 0.8549 (tp) REVERT: S 208 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8003 (mt-10) REVERT: S 223 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7897 (t80) outliers start: 40 outliers final: 20 residues processed: 238 average time/residue: 0.3682 time to fit residues: 95.3887 Evaluate side-chains 236 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 108 optimal weight: 0.0040 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 110 ASN B 176 GLN B 220 GLN R 227 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.119993 restraints weight = 13272.898| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.14 r_work: 0.3473 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8996 Z= 0.156 Angle : 0.577 10.872 12193 Z= 0.287 Chirality : 0.041 0.230 1391 Planarity : 0.003 0.051 1525 Dihedral : 5.348 71.115 1268 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.75 % Allowed : 21.84 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.64 (0.26), residues: 1117 helix: 1.94 (0.26), residues: 416 sheet: 0.00 (0.31), residues: 274 loop : -0.77 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.018 0.001 TYR S 50 PHE 0.031 0.001 PHE R 94 TRP 0.028 0.002 TRP R 194 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8992) covalent geometry : angle 0.57717 / 0.29 (12185) SS BOND : bond 0.00933 / 0.49 ( 4) SS BOND : angle 0.75083 / 0.39 ( 8) hydrogen bonds : bond 0.03680 / 2.53 ( 453) hydrogen bonds : angle 4.72922 / 3.38 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 218 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7300 (mtm-85) REVERT: A 249 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7630 (tt) REVERT: A 251 ASP cc_start: 0.7964 (m-30) cc_final: 0.7737 (m-30) REVERT: A 276 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7109 (pp20) REVERT: A 277 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7294 (tppp) REVERT: A 295 THR cc_start: 0.7900 (p) cc_final: 0.7553 (p) REVERT: A 317 LYS cc_start: 0.8159 (ptmt) cc_final: 0.7896 (ptpt) REVERT: B 160 SER cc_start: 0.8049 (p) cc_final: 0.7831 (p) REVERT: B 170 ASP cc_start: 0.7889 (t70) cc_final: 0.7464 (t0) REVERT: B 239 ASN cc_start: 0.7824 (m110) cc_final: 0.7576 (m-40) REVERT: B 258 ASP cc_start: 0.7683 (t0) cc_final: 0.7422 (t0) REVERT: B 289 TYR cc_start: 0.8547 (m-80) cc_final: 0.8209 (m-80) REVERT: R 26 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6458 (mpm) REVERT: R 87 PHE cc_start: 0.8487 (t80) cc_final: 0.8225 (t80) REVERT: S 119 VAL cc_start: 0.7873 (OUTLIER) cc_final: 0.7480 (t) REVERT: S 146 SER cc_start: 0.8794 (p) cc_final: 0.8553 (p) REVERT: S 166 LEU cc_start: 0.8725 (tt) cc_final: 0.8520 (tp) REVERT: S 208 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8004 (mt-10) REVERT: S 223 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7902 (t80) outliers start: 45 outliers final: 22 residues processed: 237 average time/residue: 0.3938 time to fit residues: 101.5534 Evaluate side-chains 243 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 45 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 110 ASN B 176 GLN R 95 HIS S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.121305 restraints weight = 13338.426| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.16 r_work: 0.3494 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8996 Z= 0.123 Angle : 0.554 8.913 12193 Z= 0.276 Chirality : 0.040 0.185 1391 Planarity : 0.003 0.052 1525 Dihedral : 5.282 74.138 1268 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.43 % Allowed : 23.00 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.68 (0.26), residues: 1117 helix: 2.03 (0.26), residues: 415 sheet: -0.07 (0.31), residues: 275 loop : -0.72 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.018 0.001 TYR S 50 PHE 0.024 0.001 PHE R 94 TRP 0.023 0.001 TRP R 194 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8992) covalent geometry : angle 0.55433 / 0.28 (12185) SS BOND : bond 0.00751 / 0.39 ( 4) SS BOND : angle 0.67091 / 0.34 ( 8) hydrogen bonds : bond 0.03485 / 2.39 ( 453) hydrogen bonds : angle 4.59181 / 3.28 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7319 (mtm-85) REVERT: A 249 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7634 (tt) REVERT: A 251 ASP cc_start: 0.7971 (m-30) cc_final: 0.7687 (m-30) REVERT: A 276 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7053 (pp20) REVERT: A 277 LYS cc_start: 0.7785 (ttmm) cc_final: 0.7288 (tppp) REVERT: A 295 THR cc_start: 0.7897 (p) cc_final: 0.7544 (p) REVERT: A 310 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8145 (mt) REVERT: A 317 LYS cc_start: 0.8112 (ptmt) cc_final: 0.7883 (ptpt) REVERT: B 86 THR cc_start: 0.8525 (p) cc_final: 0.8304 (p) REVERT: B 160 SER cc_start: 0.7965 (p) cc_final: 0.7754 (p) REVERT: B 170 ASP cc_start: 0.7871 (t70) cc_final: 0.7414 (t0) REVERT: B 239 ASN cc_start: 0.7782 (m110) cc_final: 0.7542 (m-40) REVERT: B 258 ASP cc_start: 0.7662 (t0) cc_final: 0.7398 (t0) REVERT: B 289 TYR cc_start: 0.8503 (m-80) cc_final: 0.8169 (m-80) REVERT: R 87 PHE cc_start: 0.8465 (t80) cc_final: 0.8224 (t80) REVERT: S 119 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7395 (t) REVERT: S 146 SER cc_start: 0.8787 (p) cc_final: 0.8544 (p) REVERT: S 208 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7912 (mt-10) REVERT: S 223 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7763 (t80) outliers start: 42 outliers final: 21 residues processed: 234 average time/residue: 0.4086 time to fit residues: 103.8424 Evaluate side-chains 237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 0.0670 chunk 100 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 94 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 176 GLN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.135564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120792 restraints weight = 13464.960| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.16 r_work: 0.3489 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8996 Z= 0.135 Angle : 0.568 12.333 12193 Z= 0.282 Chirality : 0.041 0.198 1391 Planarity : 0.003 0.052 1525 Dihedral : 5.258 74.843 1268 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.80 % Allowed : 24.16 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.76 (0.26), residues: 1117 helix: 2.15 (0.26), residues: 409 sheet: -0.07 (0.31), residues: 275 loop : -0.68 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.019 0.001 TYR S 50 PHE 0.025 0.001 PHE R 281 TRP 0.016 0.001 TRP R 194 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8992) covalent geometry : angle 0.56815 / 0.28 (12185) SS BOND : bond 0.00850 / 0.44 ( 4) SS BOND : angle 0.72357 / 0.37 ( 8) hydrogen bonds : bond 0.03531 / 2.41 ( 453) hydrogen bonds : angle 4.58350 / 3.27 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.323 Fit side-chains REVERT: A 32 ARG cc_start: 0.7674 (mtm-85) cc_final: 0.7323 (mtm-85) REVERT: A 249 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 251 ASP cc_start: 0.7935 (m-30) cc_final: 0.7631 (m-30) REVERT: A 276 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: A 277 LYS cc_start: 0.7837 (ttmm) cc_final: 0.7330 (tppp) REVERT: A 295 THR cc_start: 0.7901 (p) cc_final: 0.7552 (p) REVERT: A 310 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8174 (mt) REVERT: A 317 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7904 (ptpt) REVERT: B 86 THR cc_start: 0.8540 (p) cc_final: 0.8317 (p) REVERT: B 160 SER cc_start: 0.7983 (p) cc_final: 0.7767 (p) REVERT: B 170 ASP cc_start: 0.7893 (t70) cc_final: 0.7437 (t0) REVERT: B 197 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7338 (ttm110) REVERT: B 239 ASN cc_start: 0.7796 (m110) cc_final: 0.7554 (m-40) REVERT: B 258 ASP cc_start: 0.7621 (t0) cc_final: 0.7341 (t0) REVERT: B 289 TYR cc_start: 0.8517 (m-80) cc_final: 0.8232 (m-80) REVERT: R 129 ILE cc_start: 0.8527 (mm) cc_final: 0.8305 (mp) REVERT: S 119 VAL cc_start: 0.7738 (m) cc_final: 0.7361 (t) REVERT: S 146 SER cc_start: 0.8792 (p) cc_final: 0.8547 (p) REVERT: S 208 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7942 (mt-10) REVERT: S 223 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7767 (t80) outliers start: 36 outliers final: 22 residues processed: 232 average time/residue: 0.4129 time to fit residues: 104.1355 Evaluate side-chains 237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 91 PHE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 267 HIS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 100 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 5 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 110 ASN B 176 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120809 restraints weight = 13320.131| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.15 r_work: 0.3493 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8996 Z= 0.135 Angle : 0.576 11.492 12193 Z= 0.284 Chirality : 0.041 0.199 1391 Planarity : 0.003 0.053 1525 Dihedral : 5.272 73.907 1268 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.90 % Allowed : 23.63 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.78 (0.26), residues: 1117 helix: 2.14 (0.26), residues: 409 sheet: -0.02 (0.31), residues: 275 loop : -0.66 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.001 TYR S 50 PHE 0.027 0.001 PHE R 94 TRP 0.014 0.001 TRP R 194 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 8992) covalent geometry : angle 0.57550 / 0.28 (12185) SS BOND : bond 0.00825 / 0.43 ( 4) SS BOND : angle 0.96793 / 0.44 ( 8) hydrogen bonds : bond 0.03492 / 2.40 ( 453) hydrogen bonds : angle 4.52756 / 3.22 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7318 (mtm-85) REVERT: A 249 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7664 (tt) REVERT: A 251 ASP cc_start: 0.7973 (m-30) cc_final: 0.7693 (m-30) REVERT: A 277 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7315 (tppp) REVERT: A 295 THR cc_start: 0.7894 (p) cc_final: 0.7540 (p) REVERT: A 314 LYS cc_start: 0.8400 (tppp) cc_final: 0.8116 (mmmm) REVERT: B 86 THR cc_start: 0.8550 (p) cc_final: 0.8330 (p) REVERT: B 160 SER cc_start: 0.7985 (p) cc_final: 0.7767 (p) REVERT: B 170 ASP cc_start: 0.7897 (t70) cc_final: 0.7444 (t0) REVERT: B 197 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7327 (ttm110) REVERT: B 239 ASN cc_start: 0.7809 (m110) cc_final: 0.7560 (m-40) REVERT: B 258 ASP cc_start: 0.7597 (t0) cc_final: 0.7340 (t0) REVERT: B 277 SER cc_start: 0.8388 (t) cc_final: 0.8078 (p) REVERT: B 289 TYR cc_start: 0.8507 (m-80) cc_final: 0.8155 (m-80) REVERT: R 22 MET cc_start: 0.7330 (mmt) cc_final: 0.6961 (mmt) REVERT: R 26 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5248 (mmp) REVERT: S 119 VAL cc_start: 0.7700 (m) cc_final: 0.7321 (t) REVERT: S 146 SER cc_start: 0.8784 (p) cc_final: 0.8532 (p) REVERT: S 208 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7918 (mt-10) REVERT: S 223 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7771 (t80) outliers start: 37 outliers final: 24 residues processed: 227 average time/residue: 0.3821 time to fit residues: 94.5192 Evaluate side-chains 234 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 91 PHE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN B 32 GLN B 62 HIS B 110 ASN B 176 GLN B 293 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120079 restraints weight = 13364.812| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.15 r_work: 0.3476 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8996 Z= 0.172 Angle : 0.618 13.424 12193 Z= 0.300 Chirality : 0.042 0.218 1391 Planarity : 0.003 0.053 1525 Dihedral : 5.378 73.142 1268 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.38 % Allowed : 24.05 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.74 (0.25), residues: 1117 helix: 2.08 (0.26), residues: 409 sheet: -0.03 (0.31), residues: 276 loop : -0.67 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.020 0.001 TYR S 50 PHE 0.030 0.002 PHE R 94 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8992) covalent geometry : angle 0.61787 / 0.30 (12185) SS BOND : bond 0.00980 / 0.51 ( 4) SS BOND : angle 1.00219 / 0.48 ( 8) hydrogen bonds : bond 0.03666 / 2.52 ( 453) hydrogen bonds : angle 4.60151 / 3.26 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: A 249 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 251 ASP cc_start: 0.7963 (m-30) cc_final: 0.7763 (m-30) REVERT: A 276 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7001 (pp20) REVERT: A 277 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7263 (tppp) REVERT: A 295 THR cc_start: 0.7898 (p) cc_final: 0.7543 (p) REVERT: A 309 ASP cc_start: 0.7421 (m-30) cc_final: 0.7084 (m-30) REVERT: A 316 THR cc_start: 0.8061 (m) cc_final: 0.7816 (m) REVERT: A 323 PHE cc_start: 0.8458 (m-80) cc_final: 0.8251 (m-80) REVERT: B 68 ARG cc_start: 0.8475 (ttt180) cc_final: 0.8221 (tmt90) REVERT: B 86 THR cc_start: 0.8548 (p) cc_final: 0.8328 (p) REVERT: B 160 SER cc_start: 0.8046 (p) cc_final: 0.7821 (p) REVERT: B 170 ASP cc_start: 0.7849 (t70) cc_final: 0.7402 (t0) REVERT: B 197 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7343 (ttm110) REVERT: B 239 ASN cc_start: 0.7836 (m110) cc_final: 0.7540 (m-40) REVERT: B 251 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8011 (ttm170) REVERT: B 258 ASP cc_start: 0.7603 (t0) cc_final: 0.7313 (t0) REVERT: B 275 SER cc_start: 0.8247 (t) cc_final: 0.7950 (p) REVERT: B 289 TYR cc_start: 0.8513 (m-80) cc_final: 0.8238 (m-80) REVERT: R 22 MET cc_start: 0.7411 (mmt) cc_final: 0.7045 (mmt) REVERT: R 26 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5065 (mmp) REVERT: S 119 VAL cc_start: 0.7742 (m) cc_final: 0.7365 (t) REVERT: S 146 SER cc_start: 0.8771 (p) cc_final: 0.8529 (p) REVERT: S 208 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7885 (mt-10) REVERT: S 223 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7833 (t80) outliers start: 32 outliers final: 22 residues processed: 238 average time/residue: 0.4191 time to fit residues: 107.6770 Evaluate side-chains 246 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 91 PHE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 62 HIS B 110 ASN B 176 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.121539 restraints weight = 13241.452| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.16 r_work: 0.3492 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8996 Z= 0.152 Angle : 0.616 11.489 12193 Z= 0.298 Chirality : 0.042 0.222 1391 Planarity : 0.003 0.052 1525 Dihedral : 5.336 74.327 1268 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.38 % Allowed : 24.37 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.74 (0.25), residues: 1117 helix: 2.07 (0.26), residues: 409 sheet: -0.05 (0.31), residues: 275 loop : -0.64 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.021 0.001 TYR S 50 PHE 0.033 0.001 PHE R 94 TRP 0.011 0.002 TRP B 339 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8992) covalent geometry : angle 0.61600 / 0.30 (12185) SS BOND : bond 0.00892 / 0.46 ( 4) SS BOND : angle 0.86349 / 0.41 ( 8) hydrogen bonds : bond 0.03648 / 2.49 ( 453) hydrogen bonds : angle 4.57342 / 3.24 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7261 (mtm-85) REVERT: A 249 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7654 (tt) REVERT: A 251 ASP cc_start: 0.7972 (m-30) cc_final: 0.7769 (m-30) REVERT: A 276 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: A 277 LYS cc_start: 0.7762 (ttmm) cc_final: 0.7264 (tppp) REVERT: A 295 THR cc_start: 0.7871 (p) cc_final: 0.7504 (p) REVERT: A 309 ASP cc_start: 0.7480 (m-30) cc_final: 0.7198 (m-30) REVERT: A 314 LYS cc_start: 0.8378 (tppp) cc_final: 0.8097 (mmmm) REVERT: A 316 THR cc_start: 0.8024 (m) cc_final: 0.7791 (m) REVERT: B 68 ARG cc_start: 0.8478 (ttt180) cc_final: 0.8218 (tmt90) REVERT: B 160 SER cc_start: 0.8000 (p) cc_final: 0.7793 (p) REVERT: B 170 ASP cc_start: 0.7953 (t70) cc_final: 0.7478 (t0) REVERT: B 197 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7317 (ttm110) REVERT: B 239 ASN cc_start: 0.7816 (m110) cc_final: 0.7527 (m-40) REVERT: B 251 ARG cc_start: 0.8474 (mtp85) cc_final: 0.7994 (ttm170) REVERT: B 258 ASP cc_start: 0.7920 (t0) cc_final: 0.7579 (t0) REVERT: B 275 SER cc_start: 0.8252 (t) cc_final: 0.7963 (p) REVERT: C 50 LEU cc_start: 0.8814 (mm) cc_final: 0.8562 (mt) REVERT: R 22 MET cc_start: 0.7432 (mmt) cc_final: 0.7049 (mmt) REVERT: R 26 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.4845 (mmp) REVERT: S 146 SER cc_start: 0.8799 (p) cc_final: 0.8547 (p) REVERT: S 166 LEU cc_start: 0.8763 (tt) cc_final: 0.8534 (tp) REVERT: S 208 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7880 (mt-10) REVERT: S 223 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7781 (t80) outliers start: 32 outliers final: 22 residues processed: 231 average time/residue: 0.4262 time to fit residues: 106.2030 Evaluate side-chains 232 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 91 PHE Chi-restraints excluded: chain R residue 172 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.0270 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 HIS B 110 ASN B 176 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121915 restraints weight = 13147.559| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.16 r_work: 0.3499 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8996 Z= 0.137 Angle : 0.605 11.092 12193 Z= 0.294 Chirality : 0.042 0.256 1391 Planarity : 0.004 0.053 1525 Dihedral : 5.305 78.015 1268 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.95 % Allowed : 25.32 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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 are not related in a simple way. whole: 0.75 (0.26), residues: 1117 helix: 2.06 (0.26), residues: 410 sheet: -0.06 (0.31), residues: 275 loop : -0.62 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.021 0.001 TYR S 50 PHE 0.034 0.001 PHE R 94 TRP 0.019 0.002 TRP R 194 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8992) covalent geometry : angle 0.60443 / 0.29 (12185) SS BOND : bond 0.00833 / 0.43 ( 4) SS BOND : angle 0.83536 / 0.40 ( 8) hydrogen bonds : bond 0.03569 / 2.44 ( 453) hydrogen bonds : angle 4.52945 / 3.21 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.39 seconds wall clock time: 55 minutes 18.36 seconds (3318.36 seconds total)