Starting phenix.real_space_refine on Sat Sep 12 05:17:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m74_23708/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2026/7m74_23708.map" } 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-2.2.1-6174/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: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 3.27, per 1000 atoms: 0.24 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: 1.13 Conformation dependent library (CDL) restraints added in 684.6 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: 0.44 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: 2.35 Time building geometry restraints manager: 1.52 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: 18599 3.66 - 7.32: 103 7.32 - 10.99: 12 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: 8093 23.56 - 47.12: 130 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=" C3' AMP G 403 " pdb=" C2' AMP G 403 " pdb=" C4' AMP G 403 " pdb=" O3' AMP G 403 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.34e+00 ... (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: 1.710 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 13.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- 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 : 0.004 0.104 13788 Z= 0.209 Angle : 0.752 18.309 18732 Z= 0.421 Chirality : 0.114 4.737 2087 Planarity : 0.007 0.071 2363 Dihedral : 9.617 117.795 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 0.00351 / 0.21 (13781) covalent geometry : angle 0.74148 / 0.42 (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 : 0.583 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: 0.1519 time to fit residues: 57.6575 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 : 0.566 ------------------------------------------------------------------------------- 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 = 0.050319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035381 restraints weight = 105964.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.036536 restraints weight = 61828.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037312 restraints weight = 44015.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.037811 restraints weight = 35235.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.038143 restraints weight = 30544.755| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 13788 Z= 0.201 Angle : 0.705 11.768 18732 Z= 0.345 Chirality : 0.043 0.161 2087 Planarity : 0.005 0.076 2363 Dihedral : 7.997 119.315 1889 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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 : -1.47 (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 0.00432 / 0.20 (13781) covalent geometry : angle 0.70498 / 0.35 (18716) SS BOND : bond 0.00700 / 0.40 ( 5) SS BOND : angle 1.24724 / 0.68 ( 10) hydrogen bonds : bond 0.03835 / 2.61 ( 455) hydrogen bonds : angle 5.87241 / 4.14 ( 1347) link_ALPHA1-4 : bond 0.00670 / 0.35 ( 1) link_ALPHA1-4 : angle 0.80433 / 0.45 ( 3) link_TRANS : bond 0.00306 / 0.16 ( 1) link_TRANS : angle 0.40829 / 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 : 0.574 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: 0.9096 (mt0) cc_final: 0.8634 (mp10) REVERT: A 136 MET cc_start: 0.8853 (mmm) cc_final: 0.8234 (mmp) REVERT: B 257 HIS cc_start: 0.7934 (t70) cc_final: 0.7722 (t70) REVERT: G 41 LEU cc_start: 0.8822 (mm) cc_final: 0.8303 (mm) REVERT: G 239 ASP cc_start: 0.7855 (t0) cc_final: 0.7314 (m-30) REVERT: H 160 ASP cc_start: 0.8948 (m-30) cc_final: 0.8308 (m-30) REVERT: N 40 ARG cc_start: 0.8778 (mtm110) cc_final: 0.7179 (tpt90) outliers start: 26 outliers final: 14 residues processed: 128 average time/residue: 0.1213 time to fit residues: 22.9432 Evaluate side-chains 96 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.049852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.034842 restraints weight = 107210.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.036012 restraints weight = 62334.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.036784 restraints weight = 44187.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.037275 restraints weight = 35544.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037535 restraints weight = 30943.543| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13788 Z= 0.133 Angle : 0.608 10.373 18732 Z= 0.294 Chirality : 0.042 0.168 2087 Planarity : 0.004 0.055 2363 Dihedral : 7.571 119.254 1889 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.37 % Allowed : 9.69 % Favored : 88.94 % 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: -1.09 (0.20), residues: 1683 helix: 0.19 (0.24), residues: 451 sheet: -0.37 (0.27), residues: 342 loop : -1.34 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.014 0.001 TYR A 454 PHE 0.011 0.001 PHE A 279 TRP 0.021 0.002 TRP N 45 HIS 0.004 0.001 HIS L 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13781) covalent geometry : angle 0.60729 / 0.29 (18716) SS BOND : bond 0.00496 / 0.27 ( 5) SS BOND : angle 1.26886 / 0.70 ( 10) hydrogen bonds : bond 0.03360 / 2.26 ( 455) hydrogen bonds : angle 5.27511 / 3.75 ( 1347) link_ALPHA1-4 : bond 0.00053 / 0.03 ( 1) link_ALPHA1-4 : angle 1.76446 / 0.89 ( 3) link_TRANS : bond 0.00100 / 0.05 ( 1) link_TRANS : angle 0.35430 / 0.16 ( 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 106 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.556 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: 0.8917 (mmm) cc_final: 0.8359 (mmp) REVERT: A 153 MET cc_start: 0.8828 (mmp) cc_final: 0.8570 (tpp) REVERT: A 256 MET cc_start: 0.8700 (mmp) cc_final: 0.8349 (mmp) REVERT: B 237 MET cc_start: 0.7820 (pmm) cc_final: 0.7214 (pmm) REVERT: B 257 HIS cc_start: 0.8049 (t70) cc_final: 0.7702 (t70) REVERT: M 336 MET cc_start: 0.8602 (tpt) cc_final: 0.8350 (tpp) REVERT: H 160 ASP cc_start: 0.8910 (m-30) cc_final: 0.8413 (m-30) REVERT: N 40 ARG cc_start: 0.8706 (mtm110) cc_final: 0.7000 (tpt90) REVERT: N 53 GLU cc_start: 0.8620 (tp30) cc_final: 0.8345 (tp30) outliers start: 20 outliers final: 11 residues processed: 99 average time/residue: 0.1194 time to fit residues: 17.8787 Evaluate side-chains 87 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 540 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 197 VAL 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: 4.9990 chunk 108 optimal weight: 8.9990 chunk 31 optimal weight: 0.0060 chunk 66 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 131 optimal weight: 0.0020 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 67 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.049059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034018 restraints weight = 106184.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.035148 restraints weight = 62482.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.035908 restraints weight = 44806.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.036366 restraints weight = 36235.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.036688 restraints weight = 31723.234| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13788 Z= 0.132 Angle : 0.586 10.030 18732 Z= 0.284 Chirality : 0.041 0.193 2087 Planarity : 0.004 0.054 2363 Dihedral : 6.050 107.281 1889 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.91 % Allowed : 9.01 % Favored : 89.08 % 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: -0.77 (0.20), residues: 1683 helix: 0.59 (0.25), residues: 453 sheet: -0.39 (0.27), residues: 345 loop : -1.13 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.014 0.001 TYR L 50 PHE 0.020 0.001 PHE N 77 TRP 0.013 0.001 TRP G 117 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13781) covalent geometry : angle 0.58545 / 0.28 (18716) SS BOND : bond 0.00655 / 0.33 ( 5) SS BOND : angle 0.89676 / 0.52 ( 10) hydrogen bonds : bond 0.02927 / 2.00 ( 455) hydrogen bonds : angle 4.90685 / 3.51 ( 1347) link_ALPHA1-4 : bond 0.00660 / 0.35 ( 1) link_ALPHA1-4 : angle 1.34752 / 0.70 ( 3) link_TRANS : bond 0.00144 / 0.08 ( 1) link_TRANS : angle 0.38929 / 0.18 ( 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 110 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.503 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: 0.8913 (mmm) cc_final: 0.8410 (mmp) REVERT: B 237 MET cc_start: 0.8042 (pmm) cc_final: 0.7142 (pmm) REVERT: B 257 HIS cc_start: 0.8020 (t70) cc_final: 0.7766 (t-90) REVERT: G 239 ASP cc_start: 0.8032 (t0) cc_final: 0.7485 (m-30) REVERT: M 330 MET cc_start: 0.8367 (mtp) cc_final: 0.6924 (ttp) REVERT: N 40 ARG cc_start: 0.8759 (mtm110) cc_final: 0.7060 (tpt90) REVERT: N 53 GLU cc_start: 0.8646 (tp30) cc_final: 0.8445 (tp30) REVERT: N 92 MET cc_start: 0.9083 (mpp) cc_final: 0.8858 (mpp) outliers start: 28 outliers final: 18 residues processed: 103 average time/residue: 0.1117 time to fit residues: 17.8091 Evaluate side-chains 93 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 544 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 HIS 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 135 CYS Chi-restraints excluded: chain L residue 195 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 188 SER 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: 8.9990 chunk 153 optimal weight: 0.0070 chunk 40 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 ASN B 235 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.046018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.030886 restraints weight = 110548.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.031938 restraints weight = 64532.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032637 restraints weight = 46493.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033080 restraints weight = 37942.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.033366 restraints weight = 33403.030| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 13788 Z= 0.262 Angle : 0.714 12.534 18732 Z= 0.352 Chirality : 0.043 0.252 2087 Planarity : 0.005 0.053 2363 Dihedral : 6.531 99.294 1889 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.39 % Allowed : 9.35 % Favored : 88.26 % 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: -0.68 (0.20), residues: 1683 helix: 0.58 (0.25), residues: 452 sheet: -0.43 (0.27), residues: 359 loop : -0.98 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 70 TYR 0.026 0.002 TYR H 97 PHE 0.022 0.002 PHE L 210 TRP 0.020 0.002 TRP G 117 HIS 0.007 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.26 (13781) covalent geometry : angle 0.71359 / 0.35 (18716) SS BOND : bond 0.00231 / 0.13 ( 5) SS BOND : angle 1.15561 / 0.62 ( 10) hydrogen bonds : bond 0.03508 / 2.42 ( 455) hydrogen bonds : angle 5.09046 / 3.64 ( 1347) link_ALPHA1-4 : bond 0.00003 / 0.00 ( 1) link_ALPHA1-4 : angle 1.36165 / 0.72 ( 3) link_TRANS : bond 0.00375 / 0.20 ( 1) link_TRANS : angle 0.62872 / 0.29 ( 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 111 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.570 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: 0.9056 (mmm) cc_final: 0.8626 (mmp) REVERT: B 226 ASP cc_start: 0.6092 (m-30) cc_final: 0.5547 (p0) REVERT: B 237 MET cc_start: 0.8183 (pmm) cc_final: 0.7509 (pmm) REVERT: B 247 LYS cc_start: 0.7843 (mttt) cc_final: 0.7620 (mtpt) REVERT: B 251 MET cc_start: 0.8682 (mtm) cc_final: 0.8462 (mtm) REVERT: G 33 MET cc_start: 0.9382 (mtp) cc_final: 0.9164 (ptp) REVERT: G 85 MET cc_start: 0.8907 (mmm) cc_final: 0.8595 (tpp) REVERT: M 336 MET cc_start: 0.9094 (tpt) cc_final: 0.8684 (tpp) REVERT: L 5 MET cc_start: 0.8445 (pmm) cc_final: 0.8099 (pmm) REVERT: H 114 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7965 (mm-30) outliers start: 35 outliers final: 24 residues processed: 107 average time/residue: 0.1219 time to fit residues: 19.6197 Evaluate side-chains 92 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 G residue 94 ILE 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 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 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: 4.9990 chunk 7 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.045960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.030949 restraints weight = 110975.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032016 restraints weight = 64301.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032726 restraints weight = 46072.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.033193 restraints weight = 37506.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.033428 restraints weight = 32852.244| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13788 Z= 0.198 Angle : 0.635 11.375 18732 Z= 0.310 Chirality : 0.042 0.218 2087 Planarity : 0.005 0.139 2363 Dihedral : 6.213 86.564 1889 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.25 % Allowed : 9.90 % Favored : 87.85 % 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: -0.54 (0.20), residues: 1683 helix: 0.73 (0.24), residues: 452 sheet: -0.40 (0.26), residues: 366 loop : -0.88 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 62 TYR 0.019 0.002 TYR L 50 PHE 0.012 0.002 PHE A 279 TRP 0.013 0.001 TRP G 117 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (13781) covalent geometry : angle 0.63474 / 0.31 (18716) SS BOND : bond 0.00235 / 0.14 ( 5) SS BOND : angle 0.76567 / 0.42 ( 10) hydrogen bonds : bond 0.03064 / 2.11 ( 455) hydrogen bonds : angle 4.92748 / 3.52 ( 1347) link_ALPHA1-4 : bond 0.00029 / 0.02 ( 1) link_ALPHA1-4 : angle 1.37687 / 0.75 ( 3) link_TRANS : bond 0.00282 / 0.15 ( 1) link_TRANS : angle 0.48566 / 0.23 ( 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 104 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 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: A 136 MET cc_start: 0.9064 (mmm) cc_final: 0.8639 (mmp) REVERT: A 412 MET cc_start: 0.9237 (tmm) cc_final: 0.8870 (ptp) REVERT: B 226 ASP cc_start: 0.6072 (m-30) cc_final: 0.5331 (t70) REVERT: B 237 MET cc_start: 0.8094 (pmm) cc_final: 0.7578 (pmm) REVERT: G 33 MET cc_start: 0.9362 (mtp) cc_final: 0.9121 (ptp) REVERT: M 336 MET cc_start: 0.9083 (tpt) cc_final: 0.8864 (tpt) REVERT: H 113 MET cc_start: 0.7950 (ttt) cc_final: 0.7443 (ttp) REVERT: H 114 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7888 (mm-30) REVERT: N 113 TYR cc_start: 0.7153 (t80) cc_final: 0.6826 (t80) outliers start: 33 outliers final: 23 residues processed: 99 average time/residue: 0.1050 time to fit residues: 16.3641 Evaluate side-chains 87 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 544 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 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 96 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 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=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: 8.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 30.0000 chunk 142 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 HIS G 67 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.045023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030035 restraints weight = 109092.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.031062 restraints weight = 63606.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.031742 restraints weight = 45949.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.032175 restraints weight = 37492.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.032406 restraints weight = 33013.526| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.6496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 13788 Z= 0.257 Angle : 0.704 11.546 18732 Z= 0.343 Chirality : 0.043 0.298 2087 Planarity : 0.005 0.080 2363 Dihedral : 6.111 69.888 1889 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.77 % Allowed : 10.03 % Favored : 88.19 % 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: -0.60 (0.20), residues: 1683 helix: 0.72 (0.24), residues: 452 sheet: -0.55 (0.26), residues: 372 loop : -0.89 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 62 TYR 0.023 0.002 TYR L 50 PHE 0.015 0.002 PHE A 279 TRP 0.016 0.002 TRP G 117 HIS 0.007 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.26 (13781) covalent geometry : angle 0.70374 / 0.34 (18716) SS BOND : bond 0.00229 / 0.13 ( 5) SS BOND : angle 0.83881 / 0.45 ( 10) hydrogen bonds : bond 0.03336 / 2.29 ( 455) hydrogen bonds : angle 5.14113 / 3.66 ( 1347) link_ALPHA1-4 : bond 0.00757 / 0.40 ( 1) link_ALPHA1-4 : angle 1.17850 / 0.65 ( 3) link_TRANS : bond 0.00349 / 0.18 ( 1) link_TRANS : angle 0.57830 / 0.27 ( 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 92 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.543 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: 0.9041 (mmm) cc_final: 0.8644 (mmp) REVERT: B 226 ASP cc_start: 0.5880 (m-30) cc_final: 0.5156 (t70) REVERT: B 237 MET cc_start: 0.8092 (pmm) cc_final: 0.7762 (pmm) REVERT: G 33 MET cc_start: 0.9315 (mtp) cc_final: 0.9081 (ptp) REVERT: M 336 MET cc_start: 0.9185 (tpt) cc_final: 0.8981 (tpt) REVERT: H 113 MET cc_start: 0.8115 (ttt) cc_final: 0.7600 (ttp) REVERT: H 114 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7933 (mm-30) REVERT: N 113 TYR cc_start: 0.7190 (t80) cc_final: 0.6772 (t80) outliers start: 26 outliers final: 25 residues processed: 89 average time/residue: 0.1092 time to fit residues: 15.2464 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 : 0.562 ------------------------------------------------------------------------------- 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 544 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 176 LEU 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 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 L residue 206 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 207 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 156 optimal weight: 0.0040 chunk 28 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.0050 chunk 87 optimal weight: 5.9990 overall best weight: 1.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 HIS B 214 GLN G 67 ASN ** 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 = 0.3466 r_free = 0.3466 target = 0.046220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031206 restraints weight = 106085.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.032269 restraints weight = 61633.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.032976 restraints weight = 44288.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033417 restraints weight = 35959.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.033736 restraints weight = 31505.929| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13788 Z= 0.112 Angle : 0.589 8.673 18732 Z= 0.284 Chirality : 0.042 0.176 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.098 54.377 1889 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.43 % Allowed : 10.58 % Favored : 87.99 % 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: 0.98 (0.24), residues: 458 sheet: -0.43 (0.26), residues: 369 loop : -0.81 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 299 TYR 0.014 0.001 TYR L 50 PHE 0.009 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 0.00251 / 0.11 (13781) covalent geometry : angle 0.58842 / 0.28 (18716) SS BOND : bond 0.00185 / 0.10 ( 5) SS BOND : angle 0.69012 / 0.35 ( 10) hydrogen bonds : bond 0.02781 / 1.89 ( 455) hydrogen bonds : angle 4.77168 / 3.38 ( 1347) link_ALPHA1-4 : bond 0.00413 / 0.22 ( 1) link_ALPHA1-4 : angle 1.45264 / 0.80 ( 3) link_TRANS : bond 0.00068 / 0.04 ( 1) link_TRANS : angle 0.36354 / 0.17 ( 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 93 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.527 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: 0.9016 (mmm) cc_final: 0.8602 (mmp) REVERT: A 141 ASP cc_start: 0.8234 (m-30) cc_final: 0.7786 (p0) REVERT: B 226 ASP cc_start: 0.5590 (m-30) cc_final: 0.4924 (t70) REVERT: B 237 MET cc_start: 0.8022 (pmm) cc_final: 0.7724 (pmm) REVERT: G 33 MET cc_start: 0.9340 (mtp) cc_final: 0.9109 (ptp) REVERT: M 336 MET cc_start: 0.9102 (tpt) cc_final: 0.8900 (tpt) REVERT: H 114 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7925 (mm-30) REVERT: N 113 TYR cc_start: 0.6988 (t80) cc_final: 0.6552 (t80) outliers start: 21 outliers final: 19 residues processed: 89 average time/residue: 0.1015 time to fit residues: 14.0414 Evaluate side-chains 83 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 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 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 105 CYS 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: 2.9990 chunk 97 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 152 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 390 HIS ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 159 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 = 0.3441 r_free = 0.3441 target = 0.045407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.030340 restraints weight = 108176.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.031380 restraints weight = 62958.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032077 restraints weight = 45307.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.032517 restraints weight = 36930.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.032773 restraints weight = 32416.201| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6638 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= 0.187 Angle : 0.639 12.759 18732 Z= 0.308 Chirality : 0.041 0.166 2087 Planarity : 0.004 0.055 2363 Dihedral : 5.196 57.013 1889 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.57 % Allowed : 10.72 % Favored : 87.71 % 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: 0.97 (0.25), residues: 458 sheet: -0.45 (0.26), residues: 372 loop : -0.79 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 119 TYR 0.019 0.001 TYR L 50 PHE 0.011 0.001 PHE A 279 TRP 0.014 0.001 TRP G 117 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (13781) covalent geometry : angle 0.63922 / 0.31 (18716) SS BOND : bond 0.00173 / 0.09 ( 5) SS BOND : angle 0.69328 / 0.36 ( 10) hydrogen bonds : bond 0.02977 / 2.04 ( 455) hydrogen bonds : angle 4.87383 / 3.45 ( 1347) link_ALPHA1-4 : bond 0.00144 / 0.08 ( 1) link_ALPHA1-4 : angle 1.23038 / 0.69 ( 3) link_TRANS : bond 0.00256 / 0.13 ( 1) link_TRANS : angle 0.46885 / 0.22 ( 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 90 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.541 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: 0.9025 (mmm) cc_final: 0.8617 (mmp) REVERT: B 226 ASP cc_start: 0.5603 (m-30) cc_final: 0.4934 (t70) REVERT: B 237 MET cc_start: 0.8101 (pmm) cc_final: 0.7769 (pmm) REVERT: M 336 MET cc_start: 0.9194 (tpt) cc_final: 0.8981 (tpt) REVERT: H 114 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7920 (mm-30) REVERT: N 29 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8768 (mm) REVERT: N 113 TYR cc_start: 0.7236 (t80) cc_final: 0.6770 (t80) outliers start: 23 outliers final: 19 residues processed: 86 average time/residue: 0.1023 time to fit residues: 13.8926 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 : 0.488 ------------------------------------------------------------------------------- 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 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 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 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 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 = 0.3439 r_free = 0.3439 target = 0.045410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.030223 restraints weight = 109212.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.031308 restraints weight = 63135.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.032003 restraints weight = 45417.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.032448 restraints weight = 37088.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032727 restraints weight = 32656.977| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13788 Z= 0.185 Angle : 0.644 12.180 18732 Z= 0.311 Chirality : 0.043 0.288 2087 Planarity : 0.004 0.051 2363 Dihedral : 5.323 60.914 1889 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.43 % Allowed : 10.99 % 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: -0.40 (0.21), residues: 1683 helix: 0.94 (0.25), residues: 459 sheet: -0.53 (0.26), residues: 372 loop : -0.75 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.017 0.001 TYR L 50 PHE 0.012 0.001 PHE H 71 TRP 0.013 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (13781) covalent geometry : angle 0.64374 / 0.31 (18716) SS BOND : bond 0.00209 / 0.12 ( 5) SS BOND : angle 0.69150 / 0.35 ( 10) hydrogen bonds : bond 0.02934 / 2.00 ( 455) hydrogen bonds : angle 4.94377 / 3.49 ( 1347) link_ALPHA1-4 : bond 0.00128 / 0.07 ( 1) link_ALPHA1-4 : angle 1.24809 / 0.70 ( 3) link_TRANS : bond 0.00203 / 0.11 ( 1) link_TRANS : angle 0.52165 / 0.25 ( 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 88 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.557 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: A 136 MET cc_start: 0.9022 (mmm) cc_final: 0.8623 (mmp) REVERT: A 141 ASP cc_start: 0.8316 (m-30) cc_final: 0.7822 (p0) REVERT: B 226 ASP cc_start: 0.5577 (m-30) cc_final: 0.4896 (t70) REVERT: B 237 MET cc_start: 0.8141 (pmm) cc_final: 0.7814 (pmm) REVERT: M 336 MET cc_start: 0.9204 (tpt) cc_final: 0.8988 (tpt) REVERT: H 114 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7941 (mm-30) REVERT: N 29 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8751 (mm) REVERT: N 77 PHE cc_start: 0.8840 (m-10) cc_final: 0.8610 (m-10) REVERT: N 113 TYR cc_start: 0.7307 (t80) cc_final: 0.6826 (t80) outliers start: 21 outliers final: 20 residues processed: 86 average time/residue: 0.1024 time to fit residues: 13.9652 Evaluate side-chains 83 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 105 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 107 optimal weight: 0.0570 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 overall best weight: 3.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 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 = 0.3441 r_free = 0.3441 target = 0.045447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.030377 restraints weight = 108329.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.031425 restraints weight = 62701.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.032123 restraints weight = 45081.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032574 restraints weight = 36609.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.032846 restraints weight = 32099.273| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13788 Z= 0.157 Angle : 0.634 13.491 18732 Z= 0.306 Chirality : 0.042 0.300 2087 Planarity : 0.004 0.050 2363 Dihedral : 5.251 61.554 1889 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.71 % Allowed : 10.65 % Favored : 87.65 % 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: -0.37 (0.21), residues: 1683 helix: 0.97 (0.24), residues: 459 sheet: -0.54 (0.26), residues: 373 loop : -0.73 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.017 0.001 TYR L 50 PHE 0.012 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 0.00345 / 0.16 (13781) covalent geometry : angle 0.63362 / 0.31 (18716) SS BOND : bond 0.00187 / 0.10 ( 5) SS BOND : angle 0.69564 / 0.36 ( 10) hydrogen bonds : bond 0.02886 / 1.95 ( 455) hydrogen bonds : angle 4.93559 / 3.46 ( 1347) link_ALPHA1-4 : bond 0.00175 / 0.09 ( 1) link_ALPHA1-4 : angle 1.25358 / 0.71 ( 3) link_TRANS : bond 0.00147 / 0.08 ( 1) link_TRANS : angle 0.41980 / 0.24 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.36 seconds wall clock time: 46 minutes 21.43 seconds (2781.43 seconds total)