Starting phenix.real_space_refine on Wed Feb 12 15:59:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmt_33304/02_2025/7xmt_33304.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmt_33304/02_2025/7xmt_33304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xmt_33304/02_2025/7xmt_33304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmt_33304/02_2025/7xmt_33304.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmt_33304/02_2025/7xmt_33304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmt_33304/02_2025/7xmt_33304.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5187 2.51 5 N 1381 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8137 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1955 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1723 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "S" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 265 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain: "B" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2370 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 305} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'I8B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU A 234 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU A 234 " occ=0.00 residue: pdb=" N ALA A 235 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 235 " occ=0.00 residue: pdb=" N GLU A 236 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 236 " occ=0.00 residue: pdb=" N ASP A 237 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 237 " occ=0.00 residue: pdb=" N GLU A 238 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 238 " occ=0.00 residue: pdb=" N GLU A 239 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLU A 239 " occ=0.00 residue: pdb=" N MET A 240 " occ=0.00 ... (3 atoms not shown) pdb=" CB MET A 240 " occ=0.00 Time building chain proxies: 5.20, per 1000 atoms: 0.64 Number of scatterers: 8137 At special positions: 0 Unit cell: (111.815, 108.68, 109.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1516 8.00 N 1381 7.00 C 5187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1994 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.1% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'R' and resid 46 through 74 removed outlier: 4.198A pdb=" N ILE R 50 " --> pdb=" O GLY R 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 55 " --> pdb=" O GLN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 97 Processing helix chain 'R' and resid 99 through 109 removed outlier: 3.590A pdb=" N SER R 105 " --> pdb=" O PRO R 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 150 removed outlier: 3.553A pdb=" N VAL R 148 " --> pdb=" O ARG R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 159 through 179 removed outlier: 3.586A pdb=" N TRP R 171 " --> pdb=" O ASN R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 184 removed outlier: 3.618A pdb=" N PHE R 184 " --> pdb=" O PRO R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 218 Processing helix chain 'R' and resid 220 through 245 Processing helix chain 'R' and resid 251 through 284 removed outlier: 3.657A pdb=" N VAL R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Proline residue: R 274 - end of helix removed outlier: 3.740A pdb=" N GLN R 279 " --> pdb=" O PHE R 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU R 280 " --> pdb=" O TYR R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 307 removed outlier: 4.077A pdb=" N SER R 304 " --> pdb=" O SER R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 312 Processing helix chain 'R' and resid 315 through 320 removed outlier: 3.996A pdb=" N ARG R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG R 320 " --> pdb=" O ASP R 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 315 through 320' Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.593A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.682A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.924A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.543A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.521A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.782A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 37 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.734A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.472A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.516A pdb=" N CYS S 159 " --> pdb=" O PHE S 212 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.599A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AA7, first strand: chain 'S' and resid 189 through 190 Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 51 removed outlier: 4.864A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.794A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.732A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.443A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 202 Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.652A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.974A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2625 1.34 - 1.46: 2034 1.46 - 1.58: 3573 1.58 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 8307 Sorted by residual: bond pdb=" C I8B R 401 " pdb=" O3 I8B R 401 " ideal model delta sigma weight residual 1.331 1.233 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" N I8B R 401 " pdb=" C I8B R 401 " ideal model delta sigma weight residual 1.263 1.324 -0.061 2.00e-02 2.50e+03 9.25e+00 bond pdb=" N3 I8B R 401 " pdb=" S I8B R 401 " ideal model delta sigma weight residual 1.656 1.615 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C7 I8B R 401 " pdb=" C8 I8B R 401 " ideal model delta sigma weight residual 1.403 1.381 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" O1 I8B R 401 " pdb=" S I8B R 401 " ideal model delta sigma weight residual 1.453 1.432 0.021 2.00e-02 2.50e+03 1.15e+00 ... (remaining 8302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 11180 1.74 - 3.49: 92 3.49 - 5.23: 17 5.23 - 6.97: 3 6.97 - 8.71: 2 Bond angle restraints: 11294 Sorted by residual: angle pdb=" N I8B R 401 " pdb=" C I8B R 401 " pdb=" C1 I8B R 401 " ideal model delta sigma weight residual 125.42 116.71 8.71 3.00e+00 1.11e-01 8.44e+00 angle pdb=" N LEU A 283 " pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " ideal model delta sigma weight residual 113.65 110.15 3.50 1.47e+00 4.63e-01 5.66e+00 angle pdb=" C1 I8B R 401 " pdb=" C I8B R 401 " pdb=" O3 I8B R 401 " ideal model delta sigma weight residual 113.39 120.07 -6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" N LEU R 179 " pdb=" CA LEU R 179 " pdb=" C LEU R 179 " ideal model delta sigma weight residual 109.81 114.68 -4.87 2.21e+00 2.05e-01 4.86e+00 angle pdb=" CA VAL R 100 " pdb=" C VAL R 100 " pdb=" N PRO R 101 " ideal model delta sigma weight residual 118.88 121.97 -3.09 1.54e+00 4.22e-01 4.03e+00 ... (remaining 11289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4664 16.61 - 33.23: 195 33.23 - 49.84: 36 49.84 - 66.45: 1 66.45 - 83.07: 3 Dihedral angle restraints: 4899 sinusoidal: 1808 harmonic: 3091 Sorted by residual: dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 198 " pdb=" CB CYS R 198 " ideal model delta sinusoidal sigma weight residual -86.00 -123.08 37.08 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -82.34 52.34 1 2.00e+01 2.50e-03 9.34e+00 dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 69.30 23.70 1 1.00e+01 1.00e-02 8.09e+00 ... (remaining 4896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 917 0.034 - 0.068: 282 0.068 - 0.102: 78 0.102 - 0.137: 29 0.137 - 0.171: 2 Chirality restraints: 1308 Sorted by residual: chirality pdb=" C1 I8B R 401 " pdb=" C I8B R 401 " pdb=" C17 I8B R 401 " pdb=" N1 I8B R 401 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ILE B 33 " pdb=" N ILE B 33 " pdb=" C ILE B 33 " pdb=" CB ILE B 33 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1305 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 179 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO R 180 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 180 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 307 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 308 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 308 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 308 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO S 75 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.016 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2081 2.79 - 3.32: 7584 3.32 - 3.85: 13581 3.85 - 4.37: 16272 4.37 - 4.90: 27589 Nonbonded interactions: 67107 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 326 " pdb=" OG1 THR A 329 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.299 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.306 3.120 nonbonded pdb=" OG SER S 106 " pdb=" OD1 ASP S 109 " model vdw 2.310 3.040 ... (remaining 67102 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=0.00 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.098 8307 Z= 0.149 Angle : 0.470 8.714 11294 Z= 0.252 Chirality : 0.038 0.171 1308 Planarity : 0.003 0.043 1427 Dihedral : 9.399 83.066 2899 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.22), residues: 1050 helix: -3.42 (0.19), residues: 311 sheet: -1.91 (0.30), residues: 250 loop : -2.22 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 171 HIS 0.002 0.000 HIS R 111 PHE 0.005 0.001 PHE B 151 TYR 0.005 0.001 TYR S 102 ARG 0.001 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.918 Fit side-chains REVERT: B 111 TYR cc_start: 0.6384 (m-80) cc_final: 0.6070 (m-80) REVERT: B 289 TYR cc_start: 0.6451 (m-10) cc_final: 0.6184 (m-10) REVERT: B 335 PHE cc_start: 0.6095 (m-10) cc_final: 0.5845 (m-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.9586 time to fit residues: 188.4665 Evaluate side-chains 116 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 88 ASN R 167 ASN R 248 GLN A 269 ASN A 294 ASN B 44 GLN B 110 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.198322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160134 restraints weight = 8155.320| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.65 r_work: 0.3887 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8307 Z= 0.293 Angle : 0.697 13.812 11294 Z= 0.353 Chirality : 0.046 0.185 1308 Planarity : 0.005 0.054 1427 Dihedral : 4.596 25.673 1175 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.70 % Allowed : 12.19 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.24), residues: 1050 helix: -1.05 (0.27), residues: 327 sheet: -1.44 (0.31), residues: 263 loop : -1.60 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.007 0.002 HIS A 188 PHE 0.015 0.002 PHE R 184 TYR 0.018 0.002 TYR R 85 ARG 0.004 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: R 110 ARG cc_start: 0.6707 (ttt-90) cc_final: 0.5861 (tpp80) REVERT: A 221 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.6785 (tt) REVERT: B 111 TYR cc_start: 0.7696 (m-80) cc_final: 0.7424 (m-80) REVERT: B 221 THR cc_start: 0.7663 (t) cc_final: 0.7413 (m) REVERT: B 268 ASN cc_start: 0.7460 (t0) cc_final: 0.6932 (t0) outliers start: 23 outliers final: 6 residues processed: 142 average time/residue: 1.0685 time to fit residues: 162.7801 Evaluate side-chains 110 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN R 282 ASN A 269 ASN A 294 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.195900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158024 restraints weight = 8282.541| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.67 r_work: 0.3864 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8307 Z= 0.229 Angle : 0.623 10.433 11294 Z= 0.311 Chirality : 0.043 0.211 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.304 15.583 1175 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.81 % Allowed : 16.88 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1050 helix: 0.04 (0.29), residues: 325 sheet: -1.20 (0.32), residues: 258 loop : -1.40 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.004 0.001 HIS A 322 PHE 0.014 0.001 PHE B 222 TYR 0.018 0.002 TYR R 85 ARG 0.006 0.001 ARG R 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.936 Fit side-chains REVERT: B 111 TYR cc_start: 0.7657 (m-80) cc_final: 0.7417 (m-80) REVERT: B 217 MET cc_start: 0.6579 (pp-130) cc_final: 0.5642 (tpp) REVERT: B 268 ASN cc_start: 0.7672 (t0) cc_final: 0.7168 (t0) REVERT: B 315 VAL cc_start: 0.6076 (OUTLIER) cc_final: 0.5842 (m) outliers start: 24 outliers final: 9 residues processed: 133 average time/residue: 1.0573 time to fit residues: 150.5536 Evaluate side-chains 115 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 5 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN A 294 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.190840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151973 restraints weight = 8162.584| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.69 r_work: 0.3782 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8307 Z= 0.248 Angle : 0.646 11.157 11294 Z= 0.322 Chirality : 0.044 0.296 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.497 16.247 1175 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.52 % Allowed : 18.64 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.26), residues: 1050 helix: 0.44 (0.30), residues: 323 sheet: -1.23 (0.31), residues: 265 loop : -1.21 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 99 HIS 0.005 0.001 HIS B 183 PHE 0.015 0.002 PHE R 184 TYR 0.018 0.002 TYR R 85 ARG 0.005 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.862 Fit side-chains REVERT: R 88 ASN cc_start: 0.6980 (t0) cc_final: 0.6599 (t0) REVERT: R 243 LEU cc_start: 0.7625 (tt) cc_final: 0.7404 (tp) REVERT: R 263 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.7030 (ttm) REVERT: A 29 LYS cc_start: 0.8177 (mmtm) cc_final: 0.7881 (tppp) REVERT: A 256 ASN cc_start: 0.7606 (p0) cc_final: 0.7370 (p0) REVERT: B 111 TYR cc_start: 0.7743 (m-80) cc_final: 0.7539 (m-80) REVERT: B 221 THR cc_start: 0.7920 (t) cc_final: 0.7639 (m) outliers start: 30 outliers final: 16 residues processed: 151 average time/residue: 1.0766 time to fit residues: 173.8833 Evaluate side-chains 136 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 130 MET Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain R residue 263 MET Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 199 ASN R 248 GLN R 282 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.193889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154725 restraints weight = 8111.211| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.69 r_work: 0.3831 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8307 Z= 0.187 Angle : 0.618 9.903 11294 Z= 0.304 Chirality : 0.042 0.270 1308 Planarity : 0.004 0.047 1427 Dihedral : 4.309 15.849 1175 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.70 % Allowed : 21.34 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1050 helix: 0.72 (0.30), residues: 323 sheet: -1.16 (0.31), residues: 262 loop : -1.17 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE B 222 TYR 0.017 0.001 TYR R 85 ARG 0.004 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.970 Fit side-chains REVERT: R 88 ASN cc_start: 0.7324 (t0) cc_final: 0.7039 (t0) REVERT: R 243 LEU cc_start: 0.7609 (tt) cc_final: 0.7388 (tp) REVERT: A 29 LYS cc_start: 0.8077 (mmtm) cc_final: 0.7829 (tppp) REVERT: A 349 LYS cc_start: 0.7216 (mttm) cc_final: 0.6950 (mtmm) REVERT: B 111 TYR cc_start: 0.7691 (m-80) cc_final: 0.7428 (m-80) REVERT: B 318 LEU cc_start: 0.7992 (tt) cc_final: 0.7599 (tp) outliers start: 23 outliers final: 11 residues processed: 141 average time/residue: 1.0332 time to fit residues: 156.3075 Evaluate side-chains 128 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN R 282 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.195101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.155839 restraints weight = 8129.335| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.61 r_work: 0.3857 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8307 Z= 0.176 Angle : 0.611 9.464 11294 Z= 0.299 Chirality : 0.042 0.279 1308 Planarity : 0.003 0.046 1427 Dihedral : 4.250 16.566 1175 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.58 % Allowed : 21.10 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1050 helix: 0.91 (0.31), residues: 323 sheet: -1.07 (0.32), residues: 255 loop : -1.07 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS S 167 PHE 0.013 0.001 PHE R 184 TYR 0.015 0.001 TYR R 85 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.875 Fit side-chains REVERT: R 88 ASN cc_start: 0.7327 (t0) cc_final: 0.7097 (t0) REVERT: R 97 MET cc_start: 0.3764 (mtt) cc_final: 0.3182 (mmp) REVERT: A 33 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6220 (pp20) REVERT: A 256 ASN cc_start: 0.7169 (p0) cc_final: 0.6918 (p0) REVERT: A 349 LYS cc_start: 0.7252 (mttm) cc_final: 0.7019 (mtmm) REVERT: B 46 ARG cc_start: 0.8238 (mmm160) cc_final: 0.7977 (tpt170) REVERT: B 111 TYR cc_start: 0.7651 (m-80) cc_final: 0.7371 (m-80) REVERT: B 217 MET cc_start: 0.6573 (pp-130) cc_final: 0.5575 (tpp) REVERT: B 318 LEU cc_start: 0.7989 (tt) cc_final: 0.7615 (tp) outliers start: 22 outliers final: 12 residues processed: 137 average time/residue: 1.0944 time to fit residues: 160.6049 Evaluate side-chains 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN R 282 ASN A 294 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.192974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.153570 restraints weight = 8216.844| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.68 r_work: 0.3807 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8307 Z= 0.205 Angle : 0.631 11.720 11294 Z= 0.309 Chirality : 0.043 0.288 1308 Planarity : 0.003 0.046 1427 Dihedral : 4.340 17.690 1175 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.81 % Allowed : 21.22 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1050 helix: 0.86 (0.30), residues: 329 sheet: -1.05 (0.31), residues: 263 loop : -1.04 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS S 167 PHE 0.010 0.001 PHE A 189 TYR 0.015 0.001 TYR R 85 ARG 0.005 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.893 Fit side-chains REVERT: R 97 MET cc_start: 0.3861 (mtt) cc_final: 0.3275 (mmp) REVERT: A 29 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7910 (tppp) REVERT: A 33 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.5799 (pp20) REVERT: B 46 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8025 (tpt170) REVERT: B 111 TYR cc_start: 0.7696 (m-80) cc_final: 0.7442 (m-80) REVERT: B 172 GLU cc_start: 0.7385 (pm20) cc_final: 0.7173 (pm20) REVERT: B 318 LEU cc_start: 0.7983 (tt) cc_final: 0.7628 (tp) outliers start: 24 outliers final: 14 residues processed: 137 average time/residue: 1.1561 time to fit residues: 169.9535 Evaluate side-chains 131 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.195046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.157196 restraints weight = 8229.811| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.70 r_work: 0.3849 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3719 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8307 Z= 0.176 Angle : 0.623 10.319 11294 Z= 0.304 Chirality : 0.042 0.286 1308 Planarity : 0.003 0.045 1427 Dihedral : 4.260 18.818 1175 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.58 % Allowed : 22.98 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1050 helix: 0.96 (0.30), residues: 333 sheet: -1.01 (0.31), residues: 258 loop : -1.02 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE R 184 TYR 0.012 0.001 TYR R 85 ARG 0.004 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.920 Fit side-chains REVERT: R 97 MET cc_start: 0.3787 (mtt) cc_final: 0.3291 (mmp) REVERT: R 159 ARG cc_start: 0.6850 (mtt-85) cc_final: 0.6584 (mpt-90) REVERT: B 46 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7911 (tpt170) REVERT: B 111 TYR cc_start: 0.7641 (m-80) cc_final: 0.7330 (m-80) REVERT: B 217 MET cc_start: 0.6573 (pp-130) cc_final: 0.5570 (tpp) REVERT: B 318 LEU cc_start: 0.8075 (tt) cc_final: 0.7696 (tp) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 1.0545 time to fit residues: 152.7701 Evaluate side-chains 130 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 129 ASN Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.194183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.156263 restraints weight = 8359.261| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.69 r_work: 0.3838 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3710 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8307 Z= 0.194 Angle : 0.639 13.308 11294 Z= 0.310 Chirality : 0.043 0.276 1308 Planarity : 0.003 0.045 1427 Dihedral : 4.288 17.745 1175 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.11 % Allowed : 23.56 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1050 helix: 0.98 (0.31), residues: 331 sheet: -0.95 (0.31), residues: 257 loop : -1.03 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.003 0.001 HIS S 167 PHE 0.011 0.001 PHE A 191 TYR 0.018 0.001 TYR B 264 ARG 0.005 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.899 Fit side-chains REVERT: R 97 MET cc_start: 0.3785 (mtt) cc_final: 0.3291 (mmp) REVERT: A 29 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7795 (tppp) REVERT: S 220 GLU cc_start: 0.7590 (mp0) cc_final: 0.6662 (mp0) REVERT: B 46 ARG cc_start: 0.8322 (mmm160) cc_final: 0.7960 (tpt170) REVERT: B 111 TYR cc_start: 0.7675 (m-80) cc_final: 0.7412 (m-80) REVERT: B 135 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 217 MET cc_start: 0.6605 (pp-130) cc_final: 0.5638 (tpp) REVERT: B 318 LEU cc_start: 0.8066 (tt) cc_final: 0.7669 (tp) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 1.1102 time to fit residues: 160.6560 Evaluate side-chains 131 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 256 ASN Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 0.0030 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN R 199 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.193749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.155911 restraints weight = 8249.659| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 1.70 r_work: 0.3836 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8307 Z= 0.189 Angle : 0.630 10.435 11294 Z= 0.307 Chirality : 0.043 0.263 1308 Planarity : 0.003 0.045 1427 Dihedral : 4.347 18.001 1175 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.88 % Allowed : 24.62 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1050 helix: 0.89 (0.31), residues: 335 sheet: -0.79 (0.32), residues: 247 loop : -1.03 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS S 167 PHE 0.026 0.001 PHE B 335 TYR 0.016 0.001 TYR B 264 ARG 0.005 0.000 ARG R 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.704 Fit side-chains REVERT: R 97 MET cc_start: 0.3577 (mtt) cc_final: 0.3108 (mmp) REVERT: A 198 MET cc_start: 0.7627 (ttp) cc_final: 0.7393 (mtp) REVERT: S 140 MET cc_start: 0.7533 (mmm) cc_final: 0.7318 (mmm) REVERT: S 220 GLU cc_start: 0.7627 (mp0) cc_final: 0.6674 (mp0) REVERT: B 46 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7913 (tpt170) REVERT: B 111 TYR cc_start: 0.7678 (m-80) cc_final: 0.7410 (m-80) REVERT: B 135 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8309 (p) REVERT: B 197 ARG cc_start: 0.7978 (ptp-110) cc_final: 0.7501 (ptm160) REVERT: B 217 MET cc_start: 0.6572 (pp-130) cc_final: 0.5621 (tpp) REVERT: B 318 LEU cc_start: 0.8129 (tt) cc_final: 0.7722 (tp) outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 0.9400 time to fit residues: 132.2724 Evaluate side-chains 127 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.0470 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 14 optimal weight: 50.0000 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 65 ASN ** R 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 ASN ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.192577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154675 restraints weight = 8359.320| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.79 r_work: 0.3805 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8307 Z= 0.205 Angle : 0.646 13.514 11294 Z= 0.317 Chirality : 0.043 0.259 1308 Planarity : 0.004 0.045 1427 Dihedral : 4.482 20.135 1175 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.88 % Allowed : 24.97 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1050 helix: 0.93 (0.31), residues: 334 sheet: -0.84 (0.31), residues: 253 loop : -0.98 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS S 167 PHE 0.028 0.001 PHE B 335 TYR 0.025 0.001 TYR B 264 ARG 0.005 0.000 ARG R 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12610.60 seconds wall clock time: 221 minutes 42.17 seconds (13302.17 seconds total)