Starting phenix.real_space_refine on Fri Jul 19 13:34:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmt_33304/07_2024/7xmt_33304.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmt_33304/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmt_33304/07_2024/7xmt_33304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmt_33304/07_2024/7xmt_33304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmt_33304/07_2024/7xmt_33304.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmt_33304/07_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 Residue "R ARG 110": "NH1" <-> "NH2" Residue "R ARG 153": "NH1" <-> "NH2" Residue "R ARG 252": "NH1" <-> "NH2" Residue "R ASP 316": "OD1" <-> "OD2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 201": "OD1" <-> "OD2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.78, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.6 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: 0.95 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: 2.15 Time building geometry restraints manager: 3.27 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: 100.32 - 107.05: 199 107.05 - 113.79: 4647 113.79 - 120.52: 3214 120.52 - 127.25: 3150 127.25 - 133.99: 84 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 2.440 nonbonded pdb=" O SER A 326 " pdb=" OG1 THR A 329 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.299 2.440 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.306 2.520 nonbonded pdb=" OG SER S 106 " pdb=" OD1 ASP S 109 " model vdw 2.310 2.440 ... (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 ========== 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: 0.010 Normalize map: mean=0, sd=1: 1.620 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.670 Find NCS groups from input model: 0.120 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:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.410 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.844 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: 0.9341 time to fit residues: 183.8854 Evaluate side-chains 116 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 0.0670 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN A 269 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 110 ASN B 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2584 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 : 0.597 11.817 11294 Z= 0.295 Chirality : 0.042 0.164 1308 Planarity : 0.004 0.052 1427 Dihedral : 3.906 21.993 1175 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.11 % Allowed : 12.54 % Favored : 85.35 % 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: -2.28 (0.24), residues: 1050 helix: -0.94 (0.27), residues: 326 sheet: -1.50 (0.32), residues: 233 loop : -1.83 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.005 0.001 HIS A 188 PHE 0.016 0.002 PHE R 184 TYR 0.016 0.002 TYR R 85 ARG 0.005 0.000 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 147 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.7188 (m-80) cc_final: 0.6875 (m-80) REVERT: B 289 TYR cc_start: 0.6436 (m-10) cc_final: 0.6187 (m-10) REVERT: B 335 PHE cc_start: 0.6821 (m-10) cc_final: 0.6493 (m-10) outliers start: 18 outliers final: 7 residues processed: 142 average time/residue: 0.9642 time to fit residues: 147.1612 Evaluate side-chains 107 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain B residue 232 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 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 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN R 282 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN B 156 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8307 Z= 0.218 Angle : 0.596 9.837 11294 Z= 0.296 Chirality : 0.042 0.178 1308 Planarity : 0.004 0.049 1427 Dihedral : 3.997 20.930 1175 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.70 % Allowed : 14.89 % Favored : 82.42 % 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: 0.10 (0.29), residues: 326 sheet: -1.16 (0.32), residues: 263 loop : -1.48 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.001 PHE B 222 TYR 0.017 0.002 TYR R 85 ARG 0.008 0.001 ARG S 67 *********************** 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 130 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 0.943 Fit side-chains REVERT: B 111 TYR cc_start: 0.7411 (m-80) cc_final: 0.7098 (m-80) outliers start: 23 outliers final: 13 residues processed: 123 average time/residue: 1.0717 time to fit residues: 141.3404 Evaluate side-chains 112 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 HIS Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain A residue 221 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 186 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS 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: 2.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 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 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 GLN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN B 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.4118 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= 0.208 Angle : 0.594 9.838 11294 Z= 0.294 Chirality : 0.042 0.275 1308 Planarity : 0.004 0.050 1427 Dihedral : 4.071 20.041 1175 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.05 % Allowed : 16.65 % 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: -1.02 (0.26), residues: 1050 helix: 0.56 (0.30), residues: 326 sheet: -1.03 (0.32), residues: 264 loop : -1.29 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.002 PHE R 184 TYR 0.017 0.001 TYR R 85 ARG 0.009 0.001 ARG S 67 *********************** 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 156 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 0.945 Fit side-chains REVERT: A 38 LEU cc_start: 0.7662 (pp) cc_final: 0.7413 (mp) REVERT: B 111 TYR cc_start: 0.7404 (m-80) cc_final: 0.7117 (m-80) REVERT: B 290 ASP cc_start: 0.6579 (p0) cc_final: 0.6327 (p0) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 1.0449 time to fit residues: 160.3028 Evaluate side-chains 125 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 150 HIS Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain R residue 303 ASN Chi-restraints excluded: chain A residue 200 ASP 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 186 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 322 ASP 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: 5.9990 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8307 Z= 0.282 Angle : 0.661 10.865 11294 Z= 0.330 Chirality : 0.044 0.237 1308 Planarity : 0.004 0.050 1427 Dihedral : 4.541 17.883 1175 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.93 % Allowed : 20.52 % Favored : 76.55 % 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: 0.64 (0.30), residues: 326 sheet: -0.89 (0.32), residues: 264 loop : -1.23 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 339 HIS 0.005 0.002 HIS S 35 PHE 0.013 0.002 PHE B 253 TYR 0.017 0.002 TYR R 85 ARG 0.011 0.001 ARG S 67 *********************** 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 163 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.877 Fit side-chains REVERT: R 88 ASN cc_start: 0.7161 (t0) cc_final: 0.6435 (t0) REVERT: R 97 MET cc_start: 0.3954 (mtt) cc_final: 0.3449 (mmp) REVERT: A 305 CYS cc_start: 0.7488 (m) cc_final: 0.7067 (m) REVERT: B 111 TYR cc_start: 0.7609 (m-80) cc_final: 0.7406 (m-80) REVERT: B 221 THR cc_start: 0.7776 (t) cc_final: 0.7499 (m) REVERT: B 290 ASP cc_start: 0.6857 (p0) cc_final: 0.6546 (p0) outliers start: 25 outliers final: 14 residues processed: 154 average time/residue: 0.9792 time to fit residues: 161.9043 Evaluate side-chains 127 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 122 VAL 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 31 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP 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: 0.6980 chunk 91 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 53 optimal weight: 0.0770 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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** ** 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: 0.6894 moved from start: 0.5054 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= 0.173 Angle : 0.586 9.923 11294 Z= 0.291 Chirality : 0.041 0.229 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.202 18.144 1175 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.11 % Allowed : 23.33 % Favored : 74.56 % 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: 0.72 (0.30), residues: 331 sheet: -0.81 (0.32), residues: 257 loop : -1.16 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 PHE 0.014 0.001 PHE R 184 TYR 0.013 0.001 TYR R 85 ARG 0.012 0.000 ARG S 67 *********************** 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 140 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.890 Fit side-chains REVERT: R 86 LEU cc_start: 0.7315 (mm) cc_final: 0.6786 (pp) REVERT: R 88 ASN cc_start: 0.7153 (t0) cc_final: 0.6367 (t0) REVERT: B 111 TYR cc_start: 0.7480 (m-80) cc_final: 0.7213 (m-80) REVERT: B 221 THR cc_start: 0.7828 (t) cc_final: 0.7560 (m) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 0.9722 time to fit residues: 138.0492 Evaluate side-chains 123 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 63 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain B residue 146 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** 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: 0.7042 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8307 Z= 0.326 Angle : 0.691 10.556 11294 Z= 0.345 Chirality : 0.044 0.168 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.746 18.344 1175 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.28 % Allowed : 21.69 % Favored : 75.03 % 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: 0.68 (0.30), residues: 328 sheet: -0.75 (0.33), residues: 253 loop : -1.16 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.006 0.001 HIS S 167 PHE 0.013 0.002 PHE A 323 TYR 0.017 0.002 TYR R 85 ARG 0.008 0.001 ARG S 67 *********************** 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 152 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.918 Fit side-chains REVERT: R 97 MET cc_start: 0.4098 (mtt) cc_final: 0.3372 (mmp) REVERT: R 110 ARG cc_start: 0.7137 (ttt90) cc_final: 0.6530 (tpp80) REVERT: S 76 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7902 (mtpp) REVERT: B 172 GLU cc_start: 0.7124 (pm20) cc_final: 0.6853 (pm20) outliers start: 28 outliers final: 15 residues processed: 142 average time/residue: 1.0050 time to fit residues: 153.0471 Evaluate side-chains 132 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU 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 234 PHE 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: 0.6980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8307 Z= 0.238 Angle : 0.646 11.728 11294 Z= 0.320 Chirality : 0.044 0.352 1308 Planarity : 0.004 0.049 1427 Dihedral : 4.618 17.262 1175 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.63 % Allowed : 22.27 % Favored : 74.09 % 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: -0.70 (0.26), residues: 1050 helix: 0.64 (0.30), residues: 334 sheet: -0.72 (0.32), residues: 263 loop : -1.04 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 99 HIS 0.003 0.001 HIS S 167 PHE 0.013 0.001 PHE R 184 TYR 0.012 0.002 TYR R 85 ARG 0.008 0.001 ARG S 67 *********************** 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 152 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 0.876 Fit side-chains REVERT: R 97 MET cc_start: 0.4018 (mtt) cc_final: 0.3314 (mmp) REVERT: R 110 ARG cc_start: 0.6971 (ttt90) cc_final: 0.6556 (tpp80) REVERT: R 259 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6290 (ttp-110) REVERT: A 198 MET cc_start: 0.6531 (mtp) cc_final: 0.6205 (mtm) REVERT: A 256 ASN cc_start: 0.7364 (p0) cc_final: 0.7085 (p0) REVERT: A 349 LYS cc_start: 0.6970 (ttmm) cc_final: 0.6683 (mtmm) REVERT: B 172 GLU cc_start: 0.7027 (pm20) cc_final: 0.6807 (pm20) outliers start: 31 outliers final: 17 residues processed: 141 average time/residue: 1.0399 time to fit residues: 157.0052 Evaluate side-chains 128 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 146 LEU 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 88 optimal weight: 3.9990 chunk 94 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 0.0980 chunk 74 optimal weight: 0.0030 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.3968 ------------------------------------------------------------------------------- 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 A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.5646 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= 0.178 Angle : 0.617 12.235 11294 Z= 0.300 Chirality : 0.042 0.362 1308 Planarity : 0.004 0.048 1427 Dihedral : 4.373 18.958 1175 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 24.27 % 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: -0.56 (0.26), residues: 1050 helix: 0.77 (0.31), residues: 333 sheet: -0.66 (0.32), residues: 257 loop : -0.95 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 272 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE A 189 TYR 0.010 0.001 TYR S 103 ARG 0.007 0.000 ARG S 67 *********************** 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 131 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.876 Fit side-chains REVERT: R 97 MET cc_start: 0.3898 (mtt) cc_final: 0.3226 (mmp) REVERT: R 110 ARG cc_start: 0.6916 (ttt90) cc_final: 0.6491 (tpp80) REVERT: R 131 PHE cc_start: 0.6783 (m-10) cc_final: 0.6471 (m-80) REVERT: R 259 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.6242 (ttp-110) REVERT: A 306 GLN cc_start: 0.6270 (mm-40) cc_final: 0.6065 (tm-30) REVERT: A 349 LYS cc_start: 0.6994 (ttmm) cc_final: 0.6736 (mtmm) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 1.0650 time to fit residues: 144.9575 Evaluate side-chains 118 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 146 LEU 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 99 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.0970 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.5693 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= 0.191 Angle : 0.637 12.469 11294 Z= 0.307 Chirality : 0.043 0.358 1308 Planarity : 0.003 0.047 1427 Dihedral : 4.340 17.927 1175 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.99 % Allowed : 24.50 % 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: -0.51 (0.26), residues: 1050 helix: 0.82 (0.31), residues: 333 sheet: -0.64 (0.32), residues: 262 loop : -0.92 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 272 HIS 0.003 0.001 HIS A 322 PHE 0.022 0.001 PHE B 335 TYR 0.012 0.001 TYR S 95 ARG 0.007 0.000 ARG S 67 ********************** 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 130 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: R 97 MET cc_start: 0.3833 (mtt) cc_final: 0.3186 (mmp) REVERT: R 110 ARG cc_start: 0.6916 (ttt90) cc_final: 0.6494 (tpp80) REVERT: R 259 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6242 (ttp-110) REVERT: A 305 CYS cc_start: 0.7438 (m) cc_final: 0.7094 (m) REVERT: A 349 LYS cc_start: 0.6958 (ttmm) cc_final: 0.6735 (mtmm) REVERT: S 76 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7872 (mtpp) REVERT: B 111 TYR cc_start: 0.7333 (m-80) cc_final: 0.7132 (m-80) outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 1.0390 time to fit residues: 141.4015 Evaluate side-chains 124 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 ASN Chi-restraints excluded: chain R residue 259 ARG Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain B residue 146 LEU 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 88 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 34 optimal weight: 0.0070 chunk 85 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.3198 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.190727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.152262 restraints weight = 8195.399| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.74 r_work: 0.3786 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 8307 Z= 0.228 Angle : 0.956 59.200 11294 Z= 0.555 Chirality : 0.046 0.631 1308 Planarity : 0.004 0.059 1427 Dihedral : 4.436 33.085 1175 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 2.11 % Allowed : 24.62 % Favored : 73.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.53 (0.26), residues: 1050 helix: 0.77 (0.31), residues: 333 sheet: -0.64 (0.32), residues: 262 loop : -0.92 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 272 HIS 0.002 0.001 HIS S 35 PHE 0.019 0.001 PHE B 335 TYR 0.011 0.001 TYR A 230 ARG 0.007 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.67 seconds wall clock time: 70 minutes 44.84 seconds (4244.84 seconds total)