Starting phenix.real_space_refine on Wed Feb 4 02:09:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9umr_64291/02_2026/9umr_64291.cif Found real_map, /net/cci-nas-00/data/ceres_data/9umr_64291/02_2026/9umr_64291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9umr_64291/02_2026/9umr_64291.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9umr_64291/02_2026/9umr_64291.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9umr_64291/02_2026/9umr_64291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9umr_64291/02_2026/9umr_64291.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 46 5.16 5 C 5270 2.51 5 N 1416 2.21 5 O 1503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8235 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2246 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain: "B" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1497 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2435 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 6, 'ARG:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 382 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1613 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 50 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'MEA:plan-2': 1, 'ZAL:plan-1': 1, 'ALC:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Time building chain proxies: 1.43, per 1000 atoms: 0.17 Number of scatterers: 8235 At special positions: 0 Unit cell: (124.568, 122.149, 101.59, 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 46 16.00 O 1503 8.00 N 1416 7.00 C 5270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 333.1 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB ZAL L 4 " Input residue name is d-peptide pdb=" CB DAR L 6 " Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 37.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'D' and resid 34 through 65 removed outlier: 3.820A pdb=" N ILE D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 39 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 88 removed outlier: 4.238A pdb=" N ILE D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 4.020A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 139 removed outlier: 3.912A pdb=" N ALA D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Proline residue: D 113 - end of helix removed outlier: 4.303A pdb=" N ILE D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 removed outlier: 3.519A pdb=" N ASN D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 174 removed outlier: 3.751A pdb=" N ALA D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 195 through 230 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.613A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 3.616A pdb=" N MET D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 303 removed outlier: 4.618A pdb=" N SER D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N CYS D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 4.054A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.967A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.790A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.704A pdb=" N TRP B 212 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 215 " --> pdb=" O TRP B 212 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 216 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.654A pdb=" N ASN B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.878A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.521A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.779A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 37 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.757A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.565A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.984A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 175 through 180 removed outlier: 3.530A pdb=" N VAL D 176 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 189 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 180 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS D 185 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.674A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.674A pdb=" N VAL B 186 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.557A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 338 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.939A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 81 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.881A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.812A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.818A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.471A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.553A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.720A pdb=" N SER H 71 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.138A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AB5, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB6, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.644A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1315 1.32 - 1.44: 2351 1.44 - 1.57: 4685 1.57 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 8410 Sorted by residual: bond pdb=" C PRO H 75 " pdb=" O PRO H 75 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" CA ZAL L 4 " pdb=" C ZAL L 4 " ideal model delta sigma weight residual 1.525 1.568 -0.043 2.10e-02 2.27e+03 4.24e+00 bond pdb=" C LEU D 89 " pdb=" N PRO D 90 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.19e-02 7.06e+03 4.19e+00 bond pdb=" C PRO H 148 " pdb=" O PRO H 148 " ideal model delta sigma weight residual 1.233 1.212 0.021 1.10e-02 8.26e+03 3.81e+00 bond pdb=" C VAL H 147 " pdb=" N PRO H 148 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.32e-02 5.74e+03 3.55e+00 ... (remaining 8405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11223 1.72 - 3.45: 192 3.45 - 5.17: 37 5.17 - 6.89: 5 6.89 - 8.62: 2 Bond angle restraints: 11459 Sorted by residual: angle pdb=" C PRO H 75 " pdb=" CA PRO H 75 " pdb=" CB PRO H 75 " ideal model delta sigma weight residual 112.64 105.56 7.08 1.74e+00 3.30e-01 1.65e+01 angle pdb=" N ALA C 56 " pdb=" CA ALA C 56 " pdb=" C ALA C 56 " ideal model delta sigma weight residual 107.20 113.74 -6.54 1.70e+00 3.46e-01 1.48e+01 angle pdb=" N LYS C 57 " pdb=" CA LYS C 57 " pdb=" C LYS C 57 " ideal model delta sigma weight residual 111.02 115.08 -4.06 1.25e+00 6.40e-01 1.05e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 122.74 126.98 -4.24 1.44e+00 4.82e-01 8.68e+00 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" CB VAL C 90 " ideal model delta sigma weight residual 112.35 108.49 3.86 1.38e+00 5.25e-01 7.81e+00 ... (remaining 11454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 4513 22.41 - 44.82: 344 44.82 - 67.23: 29 67.23 - 89.63: 6 89.63 - 112.04: 3 Dihedral angle restraints: 4895 sinusoidal: 1657 harmonic: 3238 Sorted by residual: dihedral pdb=" CA PRO D 183 " pdb=" C PRO D 183 " pdb=" N PRO D 184 " pdb=" CA PRO D 184 " ideal model delta harmonic sigma weight residual -180.00 -154.74 -25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -120.70 34.70 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CG ALC L 5 " pdb=" CD2 ALC L 5 " pdb=" CE2 ALC L 5 " pdb=" CZ ALC L 5 " ideal model delta sinusoidal sigma weight residual 55.58 -56.46 112.04 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 4892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.031: 1346 1.031 - 2.062: 0 2.062 - 3.093: 0 3.093 - 4.123: 0 4.123 - 5.154: 1 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CG ALC L 5 " pdb=" CB ALC L 5 " pdb=" CD1 ALC L 5 " pdb=" CD2 ALC L 5 " both_signs ideal model delta sigma weight residual False -2.52 2.63 -5.15 2.00e-01 2.50e+01 6.64e+02 chirality pdb=" CA ZAL L 4 " pdb=" N ZAL L 4 " pdb=" C ZAL L 4 " pdb=" CB ZAL L 4 " both_signs ideal model delta sigma weight residual False -2.48 -2.33 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE H 189 " pdb=" N ILE H 189 " pdb=" C ILE H 189 " pdb=" CB ILE H 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1344 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 112 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO D 113 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET H 192 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C MET H 192 " 0.031 2.00e-02 2.50e+03 pdb=" O MET H 192 " -0.012 2.00e-02 2.50e+03 pdb=" N SER H 193 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 209 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C LEU D 209 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU D 209 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY D 210 " -0.010 2.00e-02 2.50e+03 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1424 2.77 - 3.30: 7277 3.30 - 3.83: 12503 3.83 - 4.37: 13590 4.37 - 4.90: 25398 Nonbonded interactions: 60192 Sorted by model distance: nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.236 3.040 nonbonded pdb=" O THR B 324 " pdb=" OG1 THR B 327 " model vdw 2.245 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.316 3.040 nonbonded pdb=" ND2 ASN C 230 " pdb=" OD1 ASP C 246 " model vdw 2.320 3.120 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.335 3.120 ... (remaining 60187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 8414 Z= 0.190 Angle : 0.609 8.617 11465 Z= 0.349 Chirality : 0.146 5.154 1347 Planarity : 0.004 0.058 1452 Dihedral : 15.167 112.042 2796 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.38 % Allowed : 15.83 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1100 helix: 1.86 (0.28), residues: 381 sheet: -0.08 (0.31), residues: 284 loop : -1.39 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 228 TYR 0.013 0.001 TYR D 258 PHE 0.014 0.001 PHE D 93 TRP 0.015 0.001 TRP C 211 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8410) covalent geometry : angle 0.60926 (11459) SS BOND : bond 0.00610 ( 3) SS BOND : angle 0.63816 ( 6) hydrogen bonds : bond 0.17488 ( 388) hydrogen bonds : angle 5.98420 ( 1116) Misc. bond : bond 0.10115 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.228 Fit side-chains REVERT: D 93 PHE cc_start: 0.8638 (t80) cc_final: 0.8398 (t80) REVERT: D 102 TRP cc_start: 0.7320 (t-100) cc_final: 0.7026 (t-100) REVERT: D 259 GLN cc_start: 0.7658 (mt0) cc_final: 0.7419 (mm-40) REVERT: D 280 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8331 (mmtp) REVERT: D 281 LEU cc_start: 0.7482 (mt) cc_final: 0.6840 (mm) REVERT: D 285 CYS cc_start: 0.7931 (m) cc_final: 0.7544 (m) REVERT: D 287 SER cc_start: 0.8520 (t) cc_final: 0.8135 (p) REVERT: C 40 VAL cc_start: 0.8585 (m) cc_final: 0.8322 (p) REVERT: C 247 ASP cc_start: 0.7640 (t0) cc_final: 0.7204 (t0) REVERT: C 270 ILE cc_start: 0.8515 (pt) cc_final: 0.8134 (mp) REVERT: C 289 TYR cc_start: 0.8202 (m-80) cc_final: 0.7654 (m-80) REVERT: H 82 GLN cc_start: 0.7350 (tp40) cc_final: 0.7012 (tp40) outliers start: 3 outliers final: 2 residues processed: 171 average time/residue: 0.0825 time to fit residues: 19.1172 Evaluate side-chains 154 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 PRO Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100428 restraints weight = 13319.408| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.16 r_work: 0.3163 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8414 Z= 0.176 Angle : 0.597 8.123 11465 Z= 0.323 Chirality : 0.044 0.178 1347 Planarity : 0.004 0.053 1452 Dihedral : 5.675 89.924 1212 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.64 % Allowed : 18.97 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.26), residues: 1100 helix: 1.91 (0.28), residues: 379 sheet: -0.07 (0.30), residues: 290 loop : -1.42 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 134 TYR 0.018 0.002 TYR D 258 PHE 0.015 0.002 PHE D 251 TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8410) covalent geometry : angle 0.59704 (11459) SS BOND : bond 0.01196 ( 3) SS BOND : angle 1.00770 ( 6) hydrogen bonds : bond 0.06331 ( 388) hydrogen bonds : angle 4.68081 ( 1116) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.187 Fit side-chains REVERT: D 102 TRP cc_start: 0.7660 (t-100) cc_final: 0.7399 (t-100) REVERT: D 148 ARG cc_start: 0.8350 (ttt-90) cc_final: 0.8102 (ttt-90) REVERT: D 176 VAL cc_start: 0.7855 (p) cc_final: 0.7645 (t) REVERT: D 287 SER cc_start: 0.8820 (t) cc_final: 0.8546 (p) REVERT: B 284 LEU cc_start: 0.8363 (tp) cc_final: 0.8139 (tt) REVERT: B 291 TYR cc_start: 0.8395 (t80) cc_final: 0.8031 (t80) REVERT: C 40 VAL cc_start: 0.8954 (m) cc_final: 0.8730 (p) REVERT: C 247 ASP cc_start: 0.8172 (t0) cc_final: 0.7759 (t0) REVERT: C 289 TYR cc_start: 0.8583 (m-80) cc_final: 0.7962 (m-80) REVERT: C 298 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7474 (t0) REVERT: H 18 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7590 (tpp80) REVERT: H 82 GLN cc_start: 0.7870 (tp40) cc_final: 0.7553 (tp40) outliers start: 29 outliers final: 20 residues processed: 177 average time/residue: 0.1014 time to fit residues: 23.3104 Evaluate side-chains 184 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 28 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 39 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.099846 restraints weight = 13123.068| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.16 r_work: 0.3163 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8414 Z= 0.159 Angle : 0.562 8.181 11465 Z= 0.305 Chirality : 0.043 0.133 1347 Planarity : 0.004 0.048 1452 Dihedral : 5.524 80.944 1209 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.52 % Allowed : 20.23 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1100 helix: 1.96 (0.28), residues: 381 sheet: -0.14 (0.30), residues: 294 loop : -1.45 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 228 TYR 0.016 0.002 TYR D 300 PHE 0.013 0.002 PHE D 251 TRP 0.012 0.001 TRP C 82 HIS 0.007 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8410) covalent geometry : angle 0.56211 (11459) SS BOND : bond 0.01055 ( 3) SS BOND : angle 0.75843 ( 6) hydrogen bonds : bond 0.06049 ( 388) hydrogen bonds : angle 4.47451 ( 1116) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.256 Fit side-chains REVERT: D 102 TRP cc_start: 0.7614 (t-100) cc_final: 0.7366 (t-100) REVERT: D 176 VAL cc_start: 0.7883 (p) cc_final: 0.7679 (t) REVERT: D 287 SER cc_start: 0.8821 (t) cc_final: 0.8558 (p) REVERT: B 191 THR cc_start: 0.8268 (p) cc_final: 0.8051 (m) REVERT: B 248 LEU cc_start: 0.8517 (mt) cc_final: 0.8275 (mp) REVERT: C 137 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8206 (mtp85) REVERT: C 233 CYS cc_start: 0.8744 (p) cc_final: 0.8349 (t) REVERT: C 247 ASP cc_start: 0.8126 (t0) cc_final: 0.7619 (t0) REVERT: C 289 TYR cc_start: 0.8477 (m-80) cc_final: 0.7955 (m-80) REVERT: C 298 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7491 (t70) REVERT: H 6 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7903 (mt-10) REVERT: H 82 GLN cc_start: 0.7722 (tp40) cc_final: 0.7410 (tt0) outliers start: 28 outliers final: 21 residues processed: 186 average time/residue: 0.1046 time to fit residues: 25.1242 Evaluate side-chains 186 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097359 restraints weight = 13262.836| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.21 r_work: 0.3135 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8414 Z= 0.190 Angle : 0.596 8.467 11465 Z= 0.325 Chirality : 0.044 0.146 1347 Planarity : 0.004 0.049 1452 Dihedral : 5.657 82.619 1209 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.90 % Allowed : 21.36 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1100 helix: 1.86 (0.28), residues: 380 sheet: -0.09 (0.30), residues: 294 loop : -1.59 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 200 TYR 0.016 0.002 TYR D 258 PHE 0.016 0.002 PHE D 251 TRP 0.015 0.002 TRP C 82 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8410) covalent geometry : angle 0.59607 (11459) SS BOND : bond 0.01193 ( 3) SS BOND : angle 0.88233 ( 6) hydrogen bonds : bond 0.06630 ( 388) hydrogen bonds : angle 4.50870 ( 1116) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.351 Fit side-chains REVERT: D 176 VAL cc_start: 0.7898 (p) cc_final: 0.7685 (t) REVERT: D 178 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7728 (mtm180) REVERT: D 200 ARG cc_start: 0.7594 (tpp80) cc_final: 0.7223 (tpp80) REVERT: D 287 SER cc_start: 0.8873 (t) cc_final: 0.8619 (p) REVERT: B 191 THR cc_start: 0.8308 (p) cc_final: 0.8058 (m) REVERT: B 248 LEU cc_start: 0.8563 (mt) cc_final: 0.8361 (mp) REVERT: C 55 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7559 (mp) REVERT: C 211 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.6916 (m-90) REVERT: C 233 CYS cc_start: 0.8744 (p) cc_final: 0.8406 (t) REVERT: C 247 ASP cc_start: 0.8178 (t0) cc_final: 0.7705 (t0) REVERT: C 289 TYR cc_start: 0.8492 (m-80) cc_final: 0.7962 (m-80) REVERT: H 6 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7921 (mt-10) REVERT: H 38 ARG cc_start: 0.8704 (ptt-90) cc_final: 0.8466 (ptt180) REVERT: H 82 GLN cc_start: 0.7770 (tp40) cc_final: 0.7491 (tt0) outliers start: 39 outliers final: 31 residues processed: 192 average time/residue: 0.1009 time to fit residues: 25.3378 Evaluate side-chains 204 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.098879 restraints weight = 13073.675| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.21 r_work: 0.3133 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8414 Z= 0.171 Angle : 0.574 8.470 11465 Z= 0.312 Chirality : 0.043 0.136 1347 Planarity : 0.004 0.048 1452 Dihedral : 5.623 81.823 1209 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.28 % Allowed : 21.61 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1100 helix: 1.95 (0.28), residues: 381 sheet: -0.08 (0.30), residues: 293 loop : -1.64 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 228 TYR 0.014 0.002 TYR D 258 PHE 0.014 0.002 PHE D 251 TRP 0.014 0.001 TRP D 213 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8410) covalent geometry : angle 0.57433 (11459) SS BOND : bond 0.01108 ( 3) SS BOND : angle 0.82694 ( 6) hydrogen bonds : bond 0.06328 ( 388) hydrogen bonds : angle 4.47049 ( 1116) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.304 Fit side-chains REVERT: D 176 VAL cc_start: 0.7901 (p) cc_final: 0.7670 (t) REVERT: D 178 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7757 (mtm180) REVERT: D 200 ARG cc_start: 0.7658 (tpp80) cc_final: 0.7233 (tpp80) REVERT: D 287 SER cc_start: 0.8876 (t) cc_final: 0.8618 (p) REVERT: B 191 THR cc_start: 0.8299 (p) cc_final: 0.8063 (m) REVERT: C 55 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7561 (mp) REVERT: C 211 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.6849 (m-90) REVERT: C 233 CYS cc_start: 0.8712 (p) cc_final: 0.8436 (t) REVERT: C 234 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: C 247 ASP cc_start: 0.8184 (t0) cc_final: 0.7719 (t0) REVERT: C 289 TYR cc_start: 0.8471 (m-80) cc_final: 0.7938 (m-80) REVERT: C 298 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7294 (t70) REVERT: H 6 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7931 (mt-10) REVERT: H 38 ARG cc_start: 0.8684 (ptt-90) cc_final: 0.8474 (ptt180) REVERT: H 82 GLN cc_start: 0.7738 (tp40) cc_final: 0.7469 (tt0) outliers start: 42 outliers final: 35 residues processed: 195 average time/residue: 0.1034 time to fit residues: 26.3932 Evaluate side-chains 208 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100006 restraints weight = 12936.445| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.19 r_work: 0.3159 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8414 Z= 0.143 Angle : 0.536 8.733 11465 Z= 0.291 Chirality : 0.042 0.130 1347 Planarity : 0.004 0.044 1452 Dihedral : 5.493 81.006 1209 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.90 % Allowed : 23.12 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1100 helix: 2.04 (0.28), residues: 381 sheet: -0.04 (0.30), residues: 293 loop : -1.63 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 228 TYR 0.012 0.001 TYR D 300 PHE 0.014 0.001 PHE C 199 TRP 0.014 0.001 TRP D 213 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8410) covalent geometry : angle 0.53574 (11459) SS BOND : bond 0.00981 ( 3) SS BOND : angle 0.71335 ( 6) hydrogen bonds : bond 0.05652 ( 388) hydrogen bonds : angle 4.34424 ( 1116) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.222 Fit side-chains REVERT: D 176 VAL cc_start: 0.7920 (p) cc_final: 0.7708 (t) REVERT: D 178 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7783 (mtm180) REVERT: D 200 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7181 (tpp80) REVERT: D 287 SER cc_start: 0.8822 (t) cc_final: 0.8538 (p) REVERT: B 191 THR cc_start: 0.8287 (p) cc_final: 0.8046 (m) REVERT: B 222 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8003 (mm) REVERT: C 211 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.6830 (m-90) REVERT: C 233 CYS cc_start: 0.8671 (p) cc_final: 0.8423 (t) REVERT: C 234 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: C 247 ASP cc_start: 0.8127 (t0) cc_final: 0.7623 (t0) REVERT: C 254 ASP cc_start: 0.7985 (t0) cc_final: 0.7692 (t0) REVERT: C 289 TYR cc_start: 0.8436 (m-80) cc_final: 0.7967 (m-80) REVERT: C 298 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7288 (t70) REVERT: C 327 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8276 (t) REVERT: H 82 GLN cc_start: 0.7663 (tp40) cc_final: 0.7426 (tt0) outliers start: 39 outliers final: 26 residues processed: 194 average time/residue: 0.1008 time to fit residues: 25.8657 Evaluate side-chains 197 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 0.0970 chunk 85 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.117712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.098835 restraints weight = 13098.745| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.21 r_work: 0.3139 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8414 Z= 0.168 Angle : 0.571 8.967 11465 Z= 0.309 Chirality : 0.043 0.132 1347 Planarity : 0.004 0.046 1452 Dihedral : 5.563 81.899 1209 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.90 % Allowed : 23.12 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1100 helix: 1.95 (0.28), residues: 383 sheet: 0.02 (0.31), residues: 291 loop : -1.66 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 228 TYR 0.014 0.002 TYR D 258 PHE 0.015 0.002 PHE D 251 TRP 0.014 0.001 TRP D 213 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8410) covalent geometry : angle 0.57055 (11459) SS BOND : bond 0.01119 ( 3) SS BOND : angle 1.27091 ( 6) hydrogen bonds : bond 0.06207 ( 388) hydrogen bonds : angle 4.41882 ( 1116) Misc. bond : bond 0.00050 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.275 Fit side-chains REVERT: D 176 VAL cc_start: 0.7922 (p) cc_final: 0.7699 (t) REVERT: D 178 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7806 (mtm180) REVERT: D 199 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6254 (tp30) REVERT: D 200 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7205 (tpp80) REVERT: D 287 SER cc_start: 0.8927 (t) cc_final: 0.8649 (p) REVERT: B 191 THR cc_start: 0.8311 (p) cc_final: 0.8053 (m) REVERT: B 222 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8000 (mm) REVERT: C 211 TRP cc_start: 0.8024 (OUTLIER) cc_final: 0.6765 (m-90) REVERT: C 233 CYS cc_start: 0.8706 (p) cc_final: 0.8440 (t) REVERT: C 234 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: C 247 ASP cc_start: 0.8133 (t0) cc_final: 0.7657 (t0) REVERT: C 254 ASP cc_start: 0.8089 (t0) cc_final: 0.7797 (t0) REVERT: C 289 TYR cc_start: 0.8473 (m-80) cc_final: 0.8009 (m-80) REVERT: C 327 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8258 (t) REVERT: H 82 GLN cc_start: 0.7694 (tp40) cc_final: 0.7465 (tt0) outliers start: 39 outliers final: 30 residues processed: 196 average time/residue: 0.1006 time to fit residues: 26.1347 Evaluate side-chains 201 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 101 optimal weight: 0.0270 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100854 restraints weight = 13142.173| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.21 r_work: 0.3163 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8414 Z= 0.126 Angle : 0.526 8.802 11465 Z= 0.282 Chirality : 0.041 0.128 1347 Planarity : 0.004 0.042 1452 Dihedral : 5.408 80.448 1209 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.52 % Allowed : 24.50 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 1100 helix: 2.07 (0.28), residues: 383 sheet: 0.11 (0.31), residues: 286 loop : -1.64 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 228 TYR 0.011 0.001 TYR H 190 PHE 0.014 0.001 PHE C 199 TRP 0.013 0.001 TRP D 213 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8410) covalent geometry : angle 0.52587 (11459) SS BOND : bond 0.00913 ( 3) SS BOND : angle 0.85340 ( 6) hydrogen bonds : bond 0.05187 ( 388) hydrogen bonds : angle 4.25910 ( 1116) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.303 Fit side-chains REVERT: D 176 VAL cc_start: 0.7827 (p) cc_final: 0.7613 (t) REVERT: D 178 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7784 (mtm180) REVERT: D 199 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6207 (tp30) REVERT: D 200 ARG cc_start: 0.7508 (tpp80) cc_final: 0.7164 (tpp80) REVERT: D 255 TRP cc_start: 0.8346 (m100) cc_final: 0.7900 (m100) REVERT: D 287 SER cc_start: 0.8836 (t) cc_final: 0.8552 (p) REVERT: B 191 THR cc_start: 0.8277 (p) cc_final: 0.8034 (m) REVERT: B 222 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8050 (mm) REVERT: C 211 TRP cc_start: 0.7932 (OUTLIER) cc_final: 0.6719 (m-90) REVERT: C 233 CYS cc_start: 0.8690 (p) cc_final: 0.8447 (t) REVERT: C 234 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: C 247 ASP cc_start: 0.8069 (t0) cc_final: 0.7553 (t0) REVERT: C 254 ASP cc_start: 0.8002 (t0) cc_final: 0.7784 (t0) REVERT: C 289 TYR cc_start: 0.8401 (m-80) cc_final: 0.7928 (m-80) REVERT: C 327 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8281 (t) REVERT: H 82 GLN cc_start: 0.7601 (tp40) cc_final: 0.7374 (tt0) outliers start: 36 outliers final: 27 residues processed: 200 average time/residue: 0.0999 time to fit residues: 26.1265 Evaluate side-chains 202 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 51 optimal weight: 0.0170 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100230 restraints weight = 13104.185| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.25 r_work: 0.3164 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8414 Z= 0.131 Angle : 0.530 9.175 11465 Z= 0.285 Chirality : 0.041 0.130 1347 Planarity : 0.004 0.042 1452 Dihedral : 5.356 79.757 1209 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.77 % Allowed : 24.37 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1100 helix: 2.10 (0.28), residues: 383 sheet: 0.08 (0.29), residues: 308 loop : -1.61 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 228 TYR 0.011 0.001 TYR H 190 PHE 0.013 0.001 PHE C 199 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8410) covalent geometry : angle 0.53002 (11459) SS BOND : bond 0.00975 ( 3) SS BOND : angle 0.83430 ( 6) hydrogen bonds : bond 0.05361 ( 388) hydrogen bonds : angle 4.25575 ( 1116) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.307 Fit side-chains REVERT: D 120 MET cc_start: 0.7304 (mtp) cc_final: 0.7083 (mtm) REVERT: D 176 VAL cc_start: 0.7855 (p) cc_final: 0.7639 (t) REVERT: D 178 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7809 (mtm180) REVERT: D 199 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6224 (tp30) REVERT: D 200 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7256 (tpp80) REVERT: D 255 TRP cc_start: 0.8399 (m100) cc_final: 0.7949 (m100) REVERT: D 287 SER cc_start: 0.8873 (t) cc_final: 0.8560 (p) REVERT: B 191 THR cc_start: 0.8281 (p) cc_final: 0.8026 (m) REVERT: B 222 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8043 (mm) REVERT: C 211 TRP cc_start: 0.7927 (OUTLIER) cc_final: 0.6751 (m-90) REVERT: C 233 CYS cc_start: 0.8720 (p) cc_final: 0.8477 (t) REVERT: C 234 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: C 247 ASP cc_start: 0.8050 (t0) cc_final: 0.7515 (t0) REVERT: C 254 ASP cc_start: 0.8052 (t0) cc_final: 0.7802 (t0) REVERT: C 289 TYR cc_start: 0.8415 (m-80) cc_final: 0.7920 (m-80) REVERT: C 327 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8254 (t) REVERT: H 82 GLN cc_start: 0.7596 (tp40) cc_final: 0.7378 (tt0) outliers start: 38 outliers final: 27 residues processed: 194 average time/residue: 0.0960 time to fit residues: 24.8337 Evaluate side-chains 198 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.119122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.100268 restraints weight = 12973.117| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.22 r_work: 0.3163 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8414 Z= 0.136 Angle : 0.535 9.075 11465 Z= 0.288 Chirality : 0.042 0.134 1347 Planarity : 0.004 0.042 1452 Dihedral : 5.367 80.126 1209 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.40 % Allowed : 24.62 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1100 helix: 2.04 (0.28), residues: 382 sheet: 0.04 (0.29), residues: 309 loop : -1.59 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 228 TYR 0.011 0.001 TYR H 190 PHE 0.014 0.001 PHE C 199 TRP 0.011 0.001 TRP D 213 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8410) covalent geometry : angle 0.53502 (11459) SS BOND : bond 0.00964 ( 3) SS BOND : angle 0.79248 ( 6) hydrogen bonds : bond 0.05399 ( 388) hydrogen bonds : angle 4.26904 ( 1116) Misc. bond : bond 0.00028 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.360 Fit side-chains REVERT: D 120 MET cc_start: 0.7320 (mtp) cc_final: 0.7118 (mtm) REVERT: D 176 VAL cc_start: 0.7850 (p) cc_final: 0.7626 (t) REVERT: D 178 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7797 (mtm180) REVERT: D 199 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6203 (tp30) REVERT: D 255 TRP cc_start: 0.8406 (m100) cc_final: 0.7958 (m100) REVERT: D 287 SER cc_start: 0.8884 (t) cc_final: 0.8569 (p) REVERT: B 191 THR cc_start: 0.8298 (p) cc_final: 0.8046 (m) REVERT: B 222 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8043 (mm) REVERT: C 211 TRP cc_start: 0.7935 (OUTLIER) cc_final: 0.6714 (m-90) REVERT: C 233 CYS cc_start: 0.8709 (p) cc_final: 0.8459 (t) REVERT: C 234 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: C 247 ASP cc_start: 0.8057 (t0) cc_final: 0.7525 (t0) REVERT: C 254 ASP cc_start: 0.8065 (t0) cc_final: 0.7849 (t0) REVERT: C 289 TYR cc_start: 0.8399 (m-80) cc_final: 0.7904 (m-80) REVERT: C 327 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8258 (t) REVERT: H 6 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7853 (mp0) REVERT: H 82 GLN cc_start: 0.7592 (tp40) cc_final: 0.7377 (tt0) outliers start: 35 outliers final: 29 residues processed: 193 average time/residue: 0.1031 time to fit residues: 26.4204 Evaluate side-chains 198 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 354 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 195 LEU Chi-restraints excluded: chain H residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 87 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.0070 chunk 88 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100158 restraints weight = 12999.309| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.23 r_work: 0.3161 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8414 Z= 0.138 Angle : 0.538 9.294 11465 Z= 0.290 Chirality : 0.042 0.134 1347 Planarity : 0.004 0.042 1452 Dihedral : 5.369 80.082 1209 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.65 % Allowed : 23.99 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.26), residues: 1100 helix: 2.03 (0.28), residues: 382 sheet: 0.05 (0.29), residues: 309 loop : -1.58 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 200 TYR 0.011 0.001 TYR H 190 PHE 0.013 0.001 PHE C 199 TRP 0.011 0.001 TRP D 213 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8410) covalent geometry : angle 0.53773 (11459) SS BOND : bond 0.00986 ( 3) SS BOND : angle 0.77630 ( 6) hydrogen bonds : bond 0.05479 ( 388) hydrogen bonds : angle 4.27507 ( 1116) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.35 seconds wall clock time: 36 minutes 56.20 seconds (2216.20 seconds total)