Starting phenix.real_space_refine on Fri Jul 3 11:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m74_23708/07_2026/7m74_23708.cif" } resolution = 3.93 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= 0.001 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 51 5.16 5 C 8589 2.51 5 N 2260 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13457 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3083 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 19, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 736 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 11, 'TRANS': 81} Chain: "G" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2421 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "M" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2834 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain: "L" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Chain: "H" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1723 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 214} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'TAK': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 2.64, per 1000 atoms: 0.20 Number of scatterers: 13457 At special positions: 0 Unit cell: (101.016, 135.792, 167.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 6 15.00 O 2551 8.00 N 2260 7.00 C 8589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " TRANS " VAL A 13 " - " PHE M 371 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 589.1 milliseconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3184 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 24 sheets defined 29.4% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.687A pdb=" N ILE A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 114 through 135 removed outlier: 3.564A pdb=" N ARG A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 removed outlier: 3.568A pdb=" N GLY A 169 " --> pdb=" O MET A 165 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.999A pdb=" N THR A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.955A pdb=" N ASP A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 240 through 251 removed outlier: 3.646A pdb=" N ILE A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 407 through 422 Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.689A pdb=" N CYS A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 549 removed outlier: 3.791A pdb=" N ILE A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 3.550A pdb=" N LEU B 213 " --> pdb=" O PRO B 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.771A pdb=" N SER G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 42 removed outlier: 3.719A pdb=" N ASP G 40 " --> pdb=" O ARG G 37 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE G 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 68 removed outlier: 3.610A pdb=" N ALA G 60 " --> pdb=" O GLN G 56 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 98 Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 113 through 122 removed outlier: 3.693A pdb=" N VAL G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.967A pdb=" N ALA G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.841A pdb=" N LEU G 178 " --> pdb=" O LYS G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 223 removed outlier: 3.906A pdb=" N ALA G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 removed outlier: 3.824A pdb=" N ALA G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 261 through 267 Processing helix chain 'G' and resid 268 through 270 No H-bonds generated for 'chain 'G' and resid 268 through 270' Processing helix chain 'G' and resid 284 through 295 removed outlier: 3.541A pdb=" N ALA G 295 " --> pdb=" O ARG G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 324 removed outlier: 3.573A pdb=" N GLN G 320 " --> pdb=" O SER G 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 32 removed outlier: 3.695A pdb=" N LEU M 20 " --> pdb=" O GLY M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 52 Proline residue: M 48 - end of helix Processing helix chain 'M' and resid 66 through 73 removed outlier: 3.819A pdb=" N SER M 73 " --> pdb=" O GLY M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 88 Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 131 through 140 removed outlier: 3.885A pdb=" N GLU M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 163 removed outlier: 4.019A pdb=" N THR M 157 " --> pdb=" O GLU M 153 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.688A pdb=" N ILE M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 219 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 231 through 239 Processing helix chain 'M' and resid 272 through 284 Processing helix chain 'M' and resid 286 through 297 removed outlier: 3.632A pdb=" N LEU M 290 " --> pdb=" O THR M 286 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU M 291 " --> pdb=" O ASP M 287 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA M 292 " --> pdb=" O GLU M 288 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL M 293 " --> pdb=" O GLY M 289 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 312 removed outlier: 3.899A pdb=" N GLU M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 314 through 326 Processing helix chain 'M' and resid 334 through 352 removed outlier: 4.055A pdb=" N ALA M 338 " --> pdb=" O PRO M 334 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR M 341 " --> pdb=" O SER M 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA M 342 " --> pdb=" O ALA M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 367 Processing helix chain 'L' and resid 185 through 188 removed outlier: 3.982A pdb=" N GLU L 188 " --> pdb=" O ALA L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 185 through 188' Processing helix chain 'H' and resid 203 through 208 removed outlier: 4.515A pdb=" N THR H 207 " --> pdb=" O SER H 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 100 removed outlier: 4.044A pdb=" N THR N 100 " --> pdb=" O PRO N 97 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.757A pdb=" N VAL A 34 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 23 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL A 32 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY A 25 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLY A 30 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASP A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N SER A 86 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 92 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL A 84 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 94 " --> pdb=" O TYR A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404 removed outlier: 3.690A pdb=" N ILE A 402 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 438 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 241 through 243 removed outlier: 3.802A pdb=" N ALA B 255 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL G 49 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TRP G 75 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE G 51 " --> pdb=" O TRP G 75 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY G 84 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP G 76 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE G 82 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 154 through 156 removed outlier: 7.077A pdb=" N VAL G 155 " --> pdb=" O LEU G 164 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 164 " --> pdb=" O VAL G 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 227 through 228 Processing sheet with id=AA7, first strand: chain 'G' and resid 278 through 279 removed outlier: 4.311A pdb=" N GLY G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.460A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA M 264 " --> pdb=" O PRO M 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.460A pdb=" N LEU M 7 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU M 38 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE M 9 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL M 8 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE M 61 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP M 10 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA M 63 " --> pdb=" O TRP M 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB2, first strand: chain 'M' and resid 145 through 147 removed outlier: 8.142A pdb=" N SER M 145 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR M 225 " --> pdb=" O SER M 145 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LEU M 147 " --> pdb=" O THR M 225 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ASN M 227 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA M 223 " --> pdb=" O ASN M 118 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN M 227 " --> pdb=" O SER M 114 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER M 114 " --> pdb=" O ASN M 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 170 through 171 removed outlier: 3.914A pdb=" N LYS M 170 " --> pdb=" O ASP M 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.591A pdb=" N SER L 68 " --> pdb=" O ASP L 71 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER L 66 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.963A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 45 through 49 removed outlier: 6.963A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.696A pdb=" N PHE L 119 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA L 131 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 146 through 149 removed outlier: 3.689A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR L 193 " --> pdb=" O PHE L 210 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE L 210 " --> pdb=" O TYR L 193 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS L 195 " --> pdb=" O LYS L 208 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.699A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER H 10 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.560A pdb=" N THR H 123 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR H 98 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 136 through 139 removed outlier: 6.450A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 136 through 139 removed outlier: 6.450A pdb=" N TYR H 192 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 167 through 170 Processing sheet with id=AC5, first strand: chain 'N' and resid 14 through 16 removed outlier: 3.696A pdb=" N GLN N 14 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA N 32 " --> pdb=" O GLN N 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS N 31 " --> pdb=" O VAL N 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 67 through 69 removed outlier: 3.636A pdb=" N PHE N 68 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP N 45 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL N 59 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET N 43 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER N 44 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL N 102 " --> pdb=" O GLN N 48 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 101 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL N 126 " --> pdb=" O ALA N 101 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS N 105 " --> pdb=" O GLN N 122 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN N 122 " --> pdb=" O CYS N 105 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE N 107 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP N 120 " --> pdb=" O ILE N 107 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4254 1.34 - 1.46: 3217 1.46 - 1.58: 6220 1.58 - 1.70: 9 1.70 - 1.82: 81 Bond restraints: 13781 Sorted by residual: bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C5 ATP G 401 " pdb=" C6 ATP G 401 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.24e+01 bond pdb=" C PHE G 183 " pdb=" N PRO G 184 " ideal model delta sigma weight residual 1.334 1.437 -0.104 2.34e-02 1.83e+03 1.96e+01 bond pdb=" C5 ATP G 401 " pdb=" N7 ATP G 401 " ideal model delta sigma weight residual 1.387 1.346 0.041 1.00e-02 1.00e+04 1.66e+01 ... (remaining 13776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 18604 3.66 - 7.32: 100 7.32 - 10.99: 10 10.99 - 14.65: 1 14.65 - 18.31: 1 Bond angle restraints: 18716 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP G 401 " pdb=" O3A ATP G 401 " pdb=" PB ATP G 401 " ideal model delta sigma weight residual 136.83 122.34 14.49 1.00e+00 1.00e+00 2.10e+02 angle pdb=" C5 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N3 ATP G 401 " pdb=" C4 ATP G 401 " pdb=" N9 ATP G 401 " ideal model delta sigma weight residual 127.04 134.92 -7.88 1.15e+00 7.59e-01 4.71e+01 angle pdb=" N1 ATP G 401 " pdb=" C2 ATP G 401 " pdb=" N3 ATP G 401 " ideal model delta sigma weight residual 128.69 123.61 5.08 1.00e+00 1.00e+00 2.58e+01 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.56: 8094 23.56 - 47.12: 129 47.12 - 70.68: 12 70.68 - 94.24: 4 94.24 - 117.79: 7 Dihedral angle restraints: 8246 sinusoidal: 3284 harmonic: 4962 Sorted by residual: dihedral pdb=" CB CYS L 135 " pdb=" SG CYS L 135 " pdb=" SG CYS L 195 " pdb=" CB CYS L 195 " ideal model delta sinusoidal sigma weight residual 93.00 23.06 69.94 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" C5' AMP G 403 " pdb=" O5' AMP G 403 " pdb=" P AMP G 403 " pdb=" O3P AMP G 403 " ideal model delta sinusoidal sigma weight residual -60.00 57.80 -117.79 1 2.00e+01 2.50e-03 3.52e+01 dihedral pdb=" C2 TAK A 601 " pdb=" C1 TAK A 601 " pdb=" N1 TAK A 601 " pdb=" C5 TAK A 601 " ideal model delta sinusoidal sigma weight residual -59.56 51.63 -111.19 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 8243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.947: 2086 0.947 - 1.895: 0 1.895 - 2.842: 0 2.842 - 3.789: 0 3.789 - 4.737: 1 Chirality restraints: 2087 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False 2.33 -2.40 4.74 2.00e-01 2.50e+01 5.61e+02 chirality pdb=" CB ILE G 106 " pdb=" CA ILE G 106 " pdb=" CG1 ILE G 106 " pdb=" CG2 ILE G 106 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB THR N 100 " pdb=" CA THR N 100 " pdb=" OG1 THR N 100 " pdb=" CG2 THR N 100 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 2084 not shown) Planarity restraints: 2364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY L 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO L 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO A 144 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO L 9 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.028 5.00e-02 4.00e+02 ... (remaining 2361 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4165 2.85 - 3.36: 11214 3.36 - 3.87: 21217 3.87 - 4.39: 23011 4.39 - 4.90: 41111 Nonbonded interactions: 100718 Sorted by model distance: nonbonded pdb=" OG1 THR M 53 " pdb=" OD1 ASP M 55 " model vdw 2.337 3.040 nonbonded pdb=" OG SER M 233 " pdb=" O ASP M 296 " model vdw 2.352 3.040 nonbonded pdb=" OD2 ASP M 30 " pdb=" OH TYR M 283 " model vdw 2.357 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.365 3.040 nonbonded pdb=" OD2 ASP G 52 " pdb=" OG SER G 54 " model vdw 2.366 3.040 ... (remaining 100713 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 group one per residue 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.520 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 0.104 13788 Z= 0.208 Angle : 0.743 18.309 18732 Z= 0.419 Chirality : 0.114 4.737 2087 Planarity : 0.007 0.071 2363 Dihedral : 9.609 117.795 5044 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -3.25 (0.16), residues: 1683 helix: -2.70 (0.16), residues: 431 sheet: -1.44 (0.26), residues: 357 loop : -2.16 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 66 TYR 0.015 0.001 TYR M 341 PHE 0.024 0.002 PHE A 538 TRP 0.014 0.001 TRP H 119 HIS 0.006 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.21 (13781) covalent geometry : angle 0.73210 / 0.41 (18716) SS BOND : bond 0.00351 / 0.19 ( 5) SS BOND : angle 5.44655 / 3.03 ( 10) hydrogen bonds : bond 0.21995 / 14.26 ( 455) hydrogen bonds : angle 8.63997 / 5.97 ( 1347) link_ALPHA1-4 : bond 0.00564 / 0.30 ( 1) link_ALPHA1-4 : angle 1.41648 / 0.83 ( 3) link_TRANS : bond 0.00105 / 0.06 ( 1) link_TRANS : angle 0.03163 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9005 (mt0) cc_final: 0.8581 (mp10) REVERT: A 446 TYR cc_start: 0.6632 (p90) cc_final: 0.6115 (p90) REVERT: B 257 HIS cc_start: 0.8211 (t70) cc_final: 0.7748 (t-90) REVERT: G 41 LEU cc_start: 0.8261 (mm) cc_final: 0.8029 (mm) REVERT: G 98 TYR cc_start: 0.8081 (m-80) cc_final: 0.7539 (m-10) REVERT: M 148 MET cc_start: 0.8562 (mtp) cc_final: 0.8062 (mmm) REVERT: M 354 ARG cc_start: 0.8510 (ttm110) cc_final: 0.7960 (mtm-85) REVERT: L 146 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8309 (tptp) REVERT: N 37 THR cc_start: 0.8138 (m) cc_final: 0.7351 (p) REVERT: N 104 TYR cc_start: 0.8133 (m-80) cc_final: 0.7808 (m-80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1512 time to fit residues: 57.4449 Evaluate side-chains 112 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 135 HIS A 220 HIS A 249 HIS A 390 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 240 HIS G 26 ASN G 36 HIS G 80 GLN G 148 ASN G 169 HIS G 197 GLN ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 HIS M 335 GLN ** M 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN L 156 GLN L 199 HIS H 85 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.050329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035409 restraints weight = 106024.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.036547 restraints weight = 61900.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.037331 restraints weight = 43995.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.037838 restraints weight = 35171.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.038149 restraints weight = 30497.504| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 13788 Z= 0.197 Angle : 0.697 11.665 18732 Z= 0.342 Chirality : 0.043 0.172 2087 Planarity : 0.005 0.074 2363 Dihedral : 8.139 119.279 1889 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.77 % Allowed : 9.76 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.59 (0.19), residues: 1683 helix: -0.48 (0.23), residues: 443 sheet: -0.73 (0.27), residues: 357 loop : -1.48 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 344 TYR 0.022 0.002 TYR L 50 PHE 0.021 0.002 PHE A 465 TRP 0.016 0.002 TRP N 45 HIS 0.008 0.001 HIS M 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (13781) covalent geometry : angle 0.69675 / 0.34 (18716) SS BOND : bond 0.00610 / 0.31 ( 5) SS BOND : angle 1.29483 / 0.71 ( 10) hydrogen bonds : bond 0.03868 / 2.63 ( 455) hydrogen bonds : angle 5.88158 / 4.15 ( 1347) link_ALPHA1-4 : bond 0.00368 / 0.19 ( 1) link_ALPHA1-4 : angle 0.52305 / 0.28 ( 3) link_TRANS : bond 0.00294 / 0.15 ( 1) link_TRANS : angle 0.40939 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9098 (mt0) cc_final: 0.8636 (mp10) REVERT: A 136 MET cc_start: 0.8852 (mmm) cc_final: 0.8234 (mmp) REVERT: B 257 HIS cc_start: 0.7952 (t70) cc_final: 0.7741 (t70) REVERT: G 41 LEU cc_start: 0.8821 (mm) cc_final: 0.8304 (mm) REVERT: G 239 ASP cc_start: 0.7835 (t0) cc_final: 0.7305 (m-30) REVERT: H 160 ASP cc_start: 0.8946 (m-30) cc_final: 0.8304 (m-30) REVERT: N 40 ARG cc_start: 0.8777 (mtm110) cc_final: 0.7177 (tpt90) outliers start: 26 outliers final: 15 residues processed: 128 average time/residue: 0.1206 time to fit residues: 22.6667 Evaluate side-chains 96 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 216 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 139 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN M 124 ASN M 365 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN H 6 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.049157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.034096 restraints weight = 107330.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.035237 restraints weight = 63047.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.035986 restraints weight = 44930.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.036470 restraints weight = 36239.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.036787 restraints weight = 31659.073| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13788 Z= 0.166 Angle : 0.629 11.267 18732 Z= 0.308 Chirality : 0.042 0.189 2087 Planarity : 0.004 0.055 2363 Dihedral : 7.709 120.605 1889 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.84 % Allowed : 9.42 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.02 (0.20), residues: 1683 helix: 0.24 (0.24), residues: 450 sheet: -0.38 (0.27), residues: 342 loop : -1.27 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.017 0.001 TYR A 207 PHE 0.015 0.002 PHE A 279 TRP 0.015 0.001 TRP A 269 HIS 0.004 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (13781) covalent geometry : angle 0.62827 / 0.31 (18716) SS BOND : bond 0.00498 / 0.26 ( 5) SS BOND : angle 1.25728 / 0.69 ( 10) hydrogen bonds : bond 0.03447 / 2.32 ( 455) hydrogen bonds : angle 5.25087 / 3.74 ( 1347) link_ALPHA1-4 : bond 0.00082 / 0.04 ( 1) link_ALPHA1-4 : angle 1.80705 / 0.91 ( 3) link_TRANS : bond 0.00180 / 0.09 ( 1) link_TRANS : angle 0.44038 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.8964 (mmm) cc_final: 0.8443 (mmp) REVERT: A 256 MET cc_start: 0.8754 (mmp) cc_final: 0.8514 (mmp) REVERT: A 411 ILE cc_start: 0.9151 (mm) cc_final: 0.8924 (mt) REVERT: B 237 MET cc_start: 0.7874 (pmm) cc_final: 0.7310 (pmm) REVERT: B 257 HIS cc_start: 0.8141 (t70) cc_final: 0.7807 (t70) REVERT: M 330 MET cc_start: 0.8445 (mtm) cc_final: 0.8204 (mtt) REVERT: M 336 MET cc_start: 0.8708 (tpt) cc_final: 0.8489 (tpp) REVERT: N 40 ARG cc_start: 0.8744 (mtm110) cc_final: 0.7273 (tpt170) REVERT: N 53 GLU cc_start: 0.8625 (tp30) cc_final: 0.8386 (tp30) outliers start: 27 outliers final: 15 residues processed: 106 average time/residue: 0.1075 time to fit residues: 17.3295 Evaluate side-chains 89 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN B 235 HIS G 105 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.045669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.030658 restraints weight = 109967.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031678 restraints weight = 64920.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.032361 restraints weight = 47308.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.032817 restraints weight = 38770.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.033026 restraints weight = 34103.920| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 13788 Z= 0.298 Angle : 0.767 13.142 18732 Z= 0.382 Chirality : 0.044 0.210 2087 Planarity : 0.005 0.054 2363 Dihedral : 7.104 103.781 1889 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.46 % Allowed : 9.22 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.90 (0.20), residues: 1683 helix: 0.42 (0.25), residues: 445 sheet: -0.63 (0.26), residues: 357 loop : -1.08 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 197 TYR 0.030 0.002 TYR H 97 PHE 0.024 0.002 PHE A 279 TRP 0.023 0.002 TRP G 117 HIS 0.008 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.30 (13781) covalent geometry : angle 0.76665 / 0.38 (18716) SS BOND : bond 0.01132 / 0.56 ( 5) SS BOND : angle 1.32401 / 0.77 ( 10) hydrogen bonds : bond 0.03811 / 2.62 ( 455) hydrogen bonds : angle 5.41602 / 3.87 ( 1347) link_ALPHA1-4 : bond 0.00350 / 0.18 ( 1) link_ALPHA1-4 : angle 1.21127 / 0.65 ( 3) link_TRANS : bond 0.00468 / 0.25 ( 1) link_TRANS : angle 0.68995 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9089 (mmm) cc_final: 0.8676 (mmp) REVERT: B 237 MET cc_start: 0.7742 (pmm) cc_final: 0.7324 (pmm) REVERT: M 330 MET cc_start: 0.8422 (mtm) cc_final: 0.8165 (mtt) REVERT: L 48 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9050 (mp) REVERT: H 160 ASP cc_start: 0.9065 (m-30) cc_final: 0.8197 (p0) outliers start: 36 outliers final: 25 residues processed: 104 average time/residue: 0.0983 time to fit residues: 15.9341 Evaluate side-chains 91 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 40 optimal weight: 0.0370 chunk 82 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.047031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.031970 restraints weight = 106075.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033053 restraints weight = 61606.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.033764 restraints weight = 44154.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.034168 restraints weight = 35797.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.034497 restraints weight = 31547.863| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13788 Z= 0.114 Angle : 0.582 8.653 18732 Z= 0.283 Chirality : 0.041 0.228 2087 Planarity : 0.004 0.053 2363 Dihedral : 6.274 91.527 1889 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.37 % Allowed : 10.58 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.63 (0.20), residues: 1683 helix: 0.64 (0.25), residues: 451 sheet: -0.40 (0.27), residues: 356 loop : -0.95 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 299 TYR 0.019 0.001 TYR N 113 PHE 0.009 0.001 PHE A 122 TRP 0.011 0.001 TRP G 117 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (13781) covalent geometry : angle 0.58165 / 0.28 (18716) SS BOND : bond 0.00226 / 0.13 ( 5) SS BOND : angle 0.94380 / 0.49 ( 10) hydrogen bonds : bond 0.02896 / 1.98 ( 455) hydrogen bonds : angle 4.89974 / 3.52 ( 1347) link_ALPHA1-4 : bond 0.00199 / 0.10 ( 1) link_ALPHA1-4 : angle 1.41497 / 0.75 ( 3) link_TRANS : bond 0.00086 / 0.05 ( 1) link_TRANS : angle 0.32852 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9086 (mmm) cc_final: 0.8661 (mmp) REVERT: B 237 MET cc_start: 0.7847 (pmm) cc_final: 0.7390 (pmm) REVERT: M 330 MET cc_start: 0.8469 (mtm) cc_final: 0.8140 (mtt) REVERT: H 114 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7830 (mm-30) outliers start: 20 outliers final: 16 residues processed: 92 average time/residue: 0.1165 time to fit residues: 16.2795 Evaluate side-chains 80 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.0570 chunk 154 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 17 optimal weight: 0.0370 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 1.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** 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 = 0.3488 r_free = 0.3488 target = 0.047059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.031981 restraints weight = 108712.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033094 restraints weight = 62800.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033817 restraints weight = 44894.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.034273 restraints weight = 36467.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.034523 restraints weight = 32008.861| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13788 Z= 0.121 Angle : 0.572 8.660 18732 Z= 0.275 Chirality : 0.041 0.205 2087 Planarity : 0.005 0.142 2363 Dihedral : 5.796 74.425 1889 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.71 % Allowed : 10.17 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.45 (0.21), residues: 1683 helix: 0.86 (0.25), residues: 452 sheet: -0.40 (0.27), residues: 361 loop : -0.84 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 62 TYR 0.016 0.001 TYR L 193 PHE 0.020 0.001 PHE L 210 TRP 0.011 0.001 TRP G 117 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13781) covalent geometry : angle 0.57177 / 0.28 (18716) SS BOND : bond 0.00210 / 0.13 ( 5) SS BOND : angle 0.70067 / 0.37 ( 10) hydrogen bonds : bond 0.02759 / 1.89 ( 455) hydrogen bonds : angle 4.71321 / 3.38 ( 1347) link_ALPHA1-4 : bond 0.00156 / 0.08 ( 1) link_ALPHA1-4 : angle 1.33469 / 0.72 ( 3) link_TRANS : bond 0.00142 / 0.07 ( 1) link_TRANS : angle 0.35993 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ILE cc_start: 0.9421 (mm) cc_final: 0.9175 (tp) REVERT: A 136 MET cc_start: 0.9031 (mmm) cc_final: 0.8596 (mmp) REVERT: B 226 ASP cc_start: 0.6122 (m-30) cc_final: 0.5379 (t70) REVERT: B 237 MET cc_start: 0.7933 (pmm) cc_final: 0.7420 (pmm) REVERT: M 330 MET cc_start: 0.8506 (mtm) cc_final: 0.8176 (mtt) REVERT: L 48 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8983 (mp) REVERT: H 114 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7923 (mm-30) REVERT: N 113 TYR cc_start: 0.6928 (t80) cc_final: 0.6637 (t80) outliers start: 25 outliers final: 17 residues processed: 89 average time/residue: 0.1065 time to fit residues: 15.0177 Evaluate side-chains 84 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 166 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 30.0000 chunk 142 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** 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 = 0.3438 r_free = 0.3438 target = 0.045244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.030275 restraints weight = 108482.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.031317 restraints weight = 63417.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.031994 restraints weight = 45640.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.032428 restraints weight = 37194.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.032705 restraints weight = 32717.837| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 13788 Z= 0.238 Angle : 0.670 11.838 18732 Z= 0.329 Chirality : 0.042 0.173 2087 Planarity : 0.005 0.080 2363 Dihedral : 5.642 55.087 1889 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.91 % Allowed : 10.03 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.46 (0.21), residues: 1683 helix: 0.82 (0.25), residues: 452 sheet: -0.53 (0.26), residues: 366 loop : -0.76 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 62 TYR 0.021 0.002 TYR L 50 PHE 0.016 0.002 PHE A 279 TRP 0.015 0.002 TRP G 117 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (13781) covalent geometry : angle 0.66958 / 0.33 (18716) SS BOND : bond 0.00967 / 0.72 ( 5) SS BOND : angle 0.91273 / 0.46 ( 10) hydrogen bonds : bond 0.03259 / 2.23 ( 455) hydrogen bonds : angle 4.98658 / 3.58 ( 1347) link_ALPHA1-4 : bond 0.00454 / 0.24 ( 1) link_ALPHA1-4 : angle 1.66518 / 0.92 ( 3) link_TRANS : bond 0.00308 / 0.16 ( 1) link_TRANS : angle 0.47025 / 0.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9053 (mmm) cc_final: 0.8639 (mmp) REVERT: B 226 ASP cc_start: 0.5922 (m-30) cc_final: 0.5185 (t70) REVERT: B 237 MET cc_start: 0.8120 (pmm) cc_final: 0.7639 (pmm) REVERT: M 330 MET cc_start: 0.8483 (mtm) cc_final: 0.8163 (mtt) REVERT: L 48 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8997 (mp) REVERT: H 114 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7962 (mm-30) REVERT: N 113 TYR cc_start: 0.7015 (t80) cc_final: 0.6616 (t80) outliers start: 28 outliers final: 24 residues processed: 92 average time/residue: 0.0994 time to fit residues: 14.6245 Evaluate side-chains 90 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 HIS B 214 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.045779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.030716 restraints weight = 109007.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.031790 restraints weight = 62886.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.032486 restraints weight = 45158.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032933 restraints weight = 36790.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.033181 restraints weight = 32370.316| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13788 Z= 0.162 Angle : 0.601 9.308 18732 Z= 0.293 Chirality : 0.041 0.173 2087 Planarity : 0.004 0.052 2363 Dihedral : 5.439 54.958 1889 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.43 % Allowed : 10.51 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.38 (0.21), residues: 1683 helix: 0.95 (0.25), residues: 453 sheet: -0.52 (0.26), residues: 361 loop : -0.72 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 119 TYR 0.016 0.001 TYR L 50 PHE 0.009 0.001 PHE H 71 TRP 0.010 0.001 TRP A 426 HIS 0.007 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (13781) covalent geometry : angle 0.59987 / 0.29 (18716) SS BOND : bond 0.00281 / 0.19 ( 5) SS BOND : angle 1.71576 / 0.96 ( 10) hydrogen bonds : bond 0.02914 / 1.98 ( 455) hydrogen bonds : angle 4.82121 / 3.44 ( 1347) link_ALPHA1-4 : bond 0.00192 / 0.10 ( 1) link_ALPHA1-4 : angle 1.30845 / 0.72 ( 3) link_TRANS : bond 0.00165 / 0.09 ( 1) link_TRANS : angle 0.44730 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9038 (mmm) cc_final: 0.8628 (mmp) REVERT: B 226 ASP cc_start: 0.5638 (m-30) cc_final: 0.4966 (t70) REVERT: B 237 MET cc_start: 0.8079 (pmm) cc_final: 0.7723 (pmm) REVERT: M 330 MET cc_start: 0.8527 (mtm) cc_final: 0.8203 (mtt) REVERT: L 48 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8965 (mp) REVERT: H 114 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7961 (mm-30) REVERT: N 113 TYR cc_start: 0.7046 (t80) cc_final: 0.6585 (t80) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.1012 time to fit residues: 14.0045 Evaluate side-chains 85 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 HIS A 390 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.046343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.031293 restraints weight = 108664.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.032376 restraints weight = 62391.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.033097 restraints weight = 44687.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.033544 restraints weight = 36285.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033848 restraints weight = 31892.605| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13788 Z= 0.112 Angle : 0.575 8.659 18732 Z= 0.276 Chirality : 0.041 0.164 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.208 59.360 1889 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.57 % Allowed : 10.65 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.19 (0.21), residues: 1683 helix: 1.15 (0.25), residues: 453 sheet: -0.40 (0.26), residues: 360 loop : -0.64 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.013 0.001 TYR L 50 PHE 0.010 0.001 PHE A 122 TRP 0.011 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13781) covalent geometry : angle 0.57338 / 0.28 (18716) SS BOND : bond 0.00208 / 0.13 ( 5) SS BOND : angle 1.67688 / 0.99 ( 10) hydrogen bonds : bond 0.02669 / 1.81 ( 455) hydrogen bonds : angle 4.62267 / 3.29 ( 1347) link_ALPHA1-4 : bond 0.00001 / 0.00 ( 1) link_ALPHA1-4 : angle 1.27283 / 0.70 ( 3) link_TRANS : bond 0.00089 / 0.05 ( 1) link_TRANS : angle 0.34212 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9002 (mmm) cc_final: 0.8609 (mmp) REVERT: A 141 ASP cc_start: 0.8254 (m-30) cc_final: 0.7760 (p0) REVERT: B 226 ASP cc_start: 0.5553 (m-30) cc_final: 0.4904 (t70) REVERT: B 237 MET cc_start: 0.8062 (pmm) cc_final: 0.7709 (pmm) REVERT: M 330 MET cc_start: 0.8536 (mtm) cc_final: 0.8224 (mtt) REVERT: L 48 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8954 (mp) REVERT: H 114 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7991 (mm-30) REVERT: N 113 TYR cc_start: 0.6975 (t80) cc_final: 0.6512 (t80) outliers start: 23 outliers final: 20 residues processed: 93 average time/residue: 0.1002 time to fit residues: 14.7577 Evaluate side-chains 86 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 0.0970 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.045145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.030096 restraints weight = 110322.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.031139 restraints weight = 64127.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.031825 restraints weight = 46309.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.032203 restraints weight = 37883.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.032519 restraints weight = 33696.134| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13788 Z= 0.224 Angle : 0.670 10.139 18732 Z= 0.325 Chirality : 0.042 0.164 2087 Planarity : 0.004 0.063 2363 Dihedral : 5.581 69.769 1889 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.37 % Allowed : 11.06 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.27 (0.21), residues: 1683 helix: 1.03 (0.25), residues: 452 sheet: -0.48 (0.26), residues: 365 loop : -0.64 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 119 TYR 0.019 0.002 TYR L 50 PHE 0.013 0.002 PHE N 77 TRP 0.013 0.001 TRP G 117 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (13781) covalent geometry : angle 0.66931 / 0.32 (18716) SS BOND : bond 0.00300 / 0.21 ( 5) SS BOND : angle 1.71057 / 1.00 ( 10) hydrogen bonds : bond 0.03067 / 2.10 ( 455) hydrogen bonds : angle 4.88054 / 3.48 ( 1347) link_ALPHA1-4 : bond 0.00021 / 0.01 ( 1) link_ALPHA1-4 : angle 1.32544 / 0.75 ( 3) link_TRANS : bond 0.00078 / 0.04 ( 1) link_TRANS : angle 0.27000 / 0.14 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.9037 (mmm) cc_final: 0.8624 (mmp) REVERT: B 226 ASP cc_start: 0.5567 (m-30) cc_final: 0.4913 (t70) REVERT: B 237 MET cc_start: 0.8152 (pmm) cc_final: 0.7794 (pmm) REVERT: L 48 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9014 (mp) REVERT: H 114 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7948 (mm-30) REVERT: N 113 TYR cc_start: 0.7203 (t80) cc_final: 0.6713 (t80) outliers start: 20 outliers final: 19 residues processed: 84 average time/residue: 0.1033 time to fit residues: 13.7839 Evaluate side-chains 83 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 148 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** 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 = 0.3454 r_free = 0.3454 target = 0.045758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.030764 restraints weight = 107007.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.031833 restraints weight = 61844.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.032531 restraints weight = 44326.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.032985 restraints weight = 35956.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.033240 restraints weight = 31395.183| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13788 Z= 0.126 Angle : 0.620 10.280 18732 Z= 0.297 Chirality : 0.042 0.181 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.426 73.065 1889 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.57 % Allowed : 11.13 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -0.20 (0.21), residues: 1683 helix: 1.08 (0.25), residues: 451 sheet: -0.38 (0.26), residues: 379 loop : -0.62 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 299 TYR 0.014 0.001 TYR L 50 PHE 0.010 0.001 PHE H 71 TRP 0.015 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13781) covalent geometry : angle 0.61949 / 0.30 (18716) SS BOND : bond 0.00198 / 0.11 ( 5) SS BOND : angle 1.44791 / 0.83 ( 10) hydrogen bonds : bond 0.02730 / 1.84 ( 455) hydrogen bonds : angle 4.77341 / 3.38 ( 1347) link_ALPHA1-4 : bond 0.00044 / 0.02 ( 1) link_ALPHA1-4 : angle 1.25001 / 0.70 ( 3) link_TRANS : bond 0.00229 / 0.12 ( 1) link_TRANS : angle 0.41071 / 0.24 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.27 seconds wall clock time: 45 minutes 25.38 seconds (2725.38 seconds total)