Starting phenix.real_space_refine on Sat Dec 28 07:58:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xmt_33304/12_2024/7xmt_33304.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xmt_33304/12_2024/7xmt_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_33304/12_2024/7xmt_33304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xmt_33304/12_2024/7xmt_33304.map" model { file = "/net/cci-nas-00/data/ceres_data/7xmt_33304/12_2024/7xmt_33304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xmt_33304/12_2024/7xmt_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.85, per 1000 atoms: 0.60 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: 2.04 Conformation dependent library (CDL) restraints added in 1.0 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: 0.94 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: 2.42 Time building geometry restraints manager: 2.32 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: 0.970 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: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.090 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- 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 : 0.896 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: 0.9704 time to fit residues: 191.1322 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 : 0.871 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.901 Fit side-chains revert: symmetry clash REVERT: R 110 ARG cc_start: 0.6713 (ttt-90) cc_final: 0.5993 (tpp80) REVERT: A 221 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6678 (tt) REVERT: B 111 TYR cc_start: 0.7530 (m-80) cc_final: 0.7237 (m-80) REVERT: B 221 THR cc_start: 0.7486 (t) cc_final: 0.7276 (m) REVERT: B 268 ASN cc_start: 0.7178 (t0) cc_final: 0.6741 (t0) outliers start: 23 outliers final: 6 residues processed: 142 average time/residue: 1.0620 time to fit residues: 161.5072 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 : 0.865 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8307 Z= 0.213 Angle : 0.612 10.334 11294 Z= 0.305 Chirality : 0.043 0.200 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.239 15.295 1175 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.05 % Allowed : 16.53 % Favored : 80.42 % 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: 0.05 (0.29), residues: 325 sheet: -1.20 (0.32), residues: 258 loop : -1.41 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS S 167 PHE 0.013 0.001 PHE B 222 TYR 0.017 0.001 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 144 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.919 Fit side-chains REVERT: A 14 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: B 111 TYR cc_start: 0.7447 (m-80) cc_final: 0.7220 (m-80) REVERT: B 268 ASN cc_start: 0.7293 (t0) cc_final: 0.6919 (t0) outliers start: 26 outliers final: 9 residues processed: 133 average time/residue: 1.0895 time to fit residues: 154.9386 Evaluate side-chains 117 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain A residue 14 GLU 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 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8307 Z= 0.188 Angle : 0.599 9.941 11294 Z= 0.295 Chirality : 0.043 0.291 1308 Planarity : 0.004 0.048 1427 Dihedral : 4.175 16.173 1175 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.05 % Allowed : 18.87 % Favored : 78.08 % 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: -1.04 (0.26), residues: 1050 helix: 0.54 (0.30), residues: 324 sheet: -1.14 (0.32), residues: 258 loop : -1.21 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.001 PHE R 184 TYR 0.018 0.001 TYR R 85 ARG 0.004 0.000 ARG R 188 *********************** 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 143 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.974 Fit side-chains REVERT: R 243 LEU cc_start: 0.7601 (tt) cc_final: 0.7382 (tp) REVERT: B 111 TYR cc_start: 0.7440 (m-80) cc_final: 0.7196 (m-80) REVERT: B 325 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6729 (mmm) outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 0.9859 time to fit residues: 140.0469 Evaluate side-chains 124 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 221 ILE 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 215 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 325 MET 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 84 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 199 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8307 Z= 0.204 Angle : 0.620 10.158 11294 Z= 0.303 Chirality : 0.043 0.271 1308 Planarity : 0.004 0.048 1427 Dihedral : 4.251 16.170 1175 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.11 % Allowed : 20.63 % Favored : 77.26 % 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: -0.89 (0.26), residues: 1050 helix: 0.71 (0.30), residues: 323 sheet: -1.10 (0.32), residues: 258 loop : -1.14 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.003 0.001 HIS S 167 PHE 0.010 0.001 PHE B 151 TYR 0.018 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 144 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.904 Fit side-chains REVERT: R 88 ASN cc_start: 0.7215 (t0) cc_final: 0.7010 (t0) REVERT: R 97 MET cc_start: 0.3746 (mtt) cc_final: 0.3266 (mmp) REVERT: R 243 LEU cc_start: 0.7636 (tt) cc_final: 0.7408 (tp) REVERT: B 111 TYR cc_start: 0.7466 (m-80) cc_final: 0.7239 (m-80) REVERT: B 318 LEU cc_start: 0.7663 (tt) cc_final: 0.7215 (tp) outliers start: 18 outliers final: 11 residues processed: 133 average time/residue: 1.0177 time to fit residues: 145.5764 Evaluate side-chains 123 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 215 THR 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 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8307 Z= 0.210 Angle : 0.611 8.963 11294 Z= 0.304 Chirality : 0.043 0.277 1308 Planarity : 0.004 0.047 1427 Dihedral : 4.341 16.395 1175 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.23 % Allowed : 21.69 % Favored : 76.08 % 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: -0.76 (0.26), residues: 1050 helix: 0.88 (0.30), residues: 323 sheet: -1.04 (0.31), residues: 262 loop : -1.09 (0.29), residues: 465 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 0.014 0.001 PHE R 184 TYR 0.018 0.001 TYR B 264 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 147 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.878 Fit side-chains REVERT: R 243 LEU cc_start: 0.7666 (tt) cc_final: 0.7461 (tp) REVERT: B 111 TYR cc_start: 0.7496 (m-80) cc_final: 0.7261 (m-80) REVERT: B 318 LEU cc_start: 0.7694 (tt) cc_final: 0.7339 (tp) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.9750 time to fit residues: 146.9343 Evaluate side-chains 131 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 25 SER 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 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 97 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8307 Z= 0.224 Angle : 0.650 11.958 11294 Z= 0.319 Chirality : 0.043 0.278 1308 Planarity : 0.004 0.046 1427 Dihedral : 4.436 19.113 1175 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.46 % Allowed : 23.56 % Favored : 73.97 % 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: -0.77 (0.26), residues: 1050 helix: 0.78 (0.30), residues: 332 sheet: -1.03 (0.31), residues: 261 loop : -1.07 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS S 167 PHE 0.011 0.001 PHE B 222 TYR 0.030 0.002 TYR B 264 ARG 0.004 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 148 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.908 Fit side-chains REVERT: R 97 MET cc_start: 0.4015 (mtt) cc_final: 0.3243 (mmp) REVERT: B 172 GLU cc_start: 0.6744 (pm20) cc_final: 0.6484 (pm20) REVERT: B 318 LEU cc_start: 0.7782 (tt) cc_final: 0.7433 (tp) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 1.0613 time to fit residues: 155.9165 Evaluate side-chains 129 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 210 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 40 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.0050 chunk 68 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 0.0030 chunk 96 optimal weight: 0.5980 overall best weight: 0.2604 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8307 Z= 0.160 Angle : 0.609 9.913 11294 Z= 0.298 Chirality : 0.042 0.263 1308 Planarity : 0.003 0.045 1427 Dihedral : 4.261 20.570 1175 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.76 % Allowed : 24.50 % Favored : 73.74 % 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: 0.94 (0.30), residues: 332 sheet: -0.84 (0.32), residues: 244 loop : -1.12 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 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 141 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.927 Fit side-chains REVERT: R 97 MET cc_start: 0.3995 (mtt) cc_final: 0.3253 (mmp) REVERT: B 111 TYR cc_start: 0.7296 (m-80) cc_final: 0.7072 (m-80) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 1.0353 time to fit residues: 152.1248 Evaluate side-chains 126 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 215 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8307 Z= 0.210 Angle : 0.656 13.476 11294 Z= 0.320 Chirality : 0.043 0.262 1308 Planarity : 0.004 0.045 1427 Dihedral : 4.419 20.148 1175 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 24.50 % Favored : 73.74 % 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: -0.58 (0.26), residues: 1050 helix: 0.95 (0.30), residues: 332 sheet: -0.89 (0.32), residues: 256 loop : -0.99 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 171 HIS 0.004 0.001 HIS S 167 PHE 0.012 0.001 PHE A 191 TYR 0.012 0.001 TYR R 85 ARG 0.008 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: 15 poor density : 129 time to evaluate : 0.980 Fit side-chains REVERT: R 88 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.5987 (t0) REVERT: R 97 MET cc_start: 0.3965 (mtt) cc_final: 0.3233 (mmp) REVERT: R 159 ARG cc_start: 0.6685 (mtt-85) cc_final: 0.6425 (mtt-85) REVERT: B 135 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8265 (p) outliers start: 15 outliers final: 11 residues processed: 137 average time/residue: 1.0419 time to fit residues: 152.8954 Evaluate side-chains 133 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 88 ASN 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 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU 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 99 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8307 Z= 0.204 Angle : 0.641 9.568 11294 Z= 0.316 Chirality : 0.043 0.251 1308 Planarity : 0.004 0.045 1427 Dihedral : 4.525 19.811 1175 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 25.56 % Favored : 72.68 % 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: -0.58 (0.26), residues: 1050 helix: 0.91 (0.31), residues: 333 sheet: -0.79 (0.32), residues: 242 loop : -1.03 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 272 HIS 0.004 0.001 HIS S 167 PHE 0.029 0.001 PHE B 335 TYR 0.010 0.001 TYR B 264 ARG 0.008 0.000 ARG B 197 ********************** 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 132 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.027 Fit side-chains REVERT: R 86 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6780 (mp) REVERT: R 97 MET cc_start: 0.3804 (mtt) cc_final: 0.3162 (mmp) REVERT: R 159 ARG cc_start: 0.6679 (mtt-85) cc_final: 0.6422 (mtt-85) REVERT: A 305 CYS cc_start: 0.7492 (m) cc_final: 0.7139 (m) REVERT: S 220 GLU cc_start: 0.7519 (mp0) cc_final: 0.6703 (mp0) REVERT: B 135 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8255 (p) outliers start: 15 outliers final: 9 residues processed: 125 average time/residue: 1.0737 time to fit residues: 143.8583 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 : 0.874 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- 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 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.189546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.150489 restraints weight = 8148.039| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.71 r_work: 0.3767 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8307 Z= 0.241 Angle : 0.688 13.282 11294 Z= 0.337 Chirality : 0.044 0.248 1308 Planarity : 0.004 0.046 1427 Dihedral : 4.650 19.183 1175 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.76 % Allowed : 25.44 % Favored : 72.80 % 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: -0.58 (0.26), residues: 1050 helix: 0.92 (0.31), residues: 332 sheet: -0.84 (0.32), residues: 246 loop : -1.00 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.005 0.001 HIS S 167 PHE 0.031 0.002 PHE B 335 TYR 0.010 0.001 TYR B 264 ARG 0.008 0.000 ARG R 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3989.08 seconds wall clock time: 72 minutes 2.52 seconds (4322.52 seconds total)