Starting phenix.real_space_refine on Thu Sep 18 04:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m74_23708/09_2025/7m74_23708.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m74_23708/09_2025/7m74_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 { model { file = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2025/7m74_23708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2025/7m74_23708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2025/7m74_23708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m74_23708/09_2025/7m74_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-2.0-5805/lib/python3.9/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 dihedrals: 3 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, 'AMP%rna2p': 1, 'ATP': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 3.03, per 1000 atoms: 0.23 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: 0.84 Conformation dependent library (CDL) restraints added in 459.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.64 Time building geometry restraints manager: 1.08 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: 18596 3.66 - 7.32: 106 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: 8149 23.56 - 47.12: 133 47.12 - 70.68: 16 70.68 - 94.24: 4 94.24 - 117.79: 7 Dihedral angle restraints: 8309 sinusoidal: 3347 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 8306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1821 0.073 - 0.145: 245 0.145 - 0.218: 17 0.218 - 0.291: 2 0.291 - 0.364: 2 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 -2.04 -2.40 0.36 2.00e-01 2.50e+01 3.31e+00 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: 1.340 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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= 0.210 Angle : 0.757 18.309 18732 Z= 0.422 Chirality : 0.049 0.364 2087 Planarity : 0.007 0.071 2363 Dihedral : 9.736 117.795 5107 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 aren 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 covalent geometry : bond 0.00353 (13781) covalent geometry : angle 0.74693 (18716) SS BOND : bond 0.00351 ( 5) SS BOND : angle 5.44655 ( 10) hydrogen bonds : bond 0.21995 ( 455) hydrogen bonds : angle 8.63997 ( 1347) link_ALPHA1-4 : bond 0.00564 ( 1) link_ALPHA1-4 : angle 1.41648 ( 3) link_TRANS : bond 0.00105 ( 1) link_TRANS : angle 0.03163 ( 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 : 0.564 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: 0.1404 time to fit residues: 52.9278 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 : 0.512 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3590 r_free = 0.3590 target = 0.050429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.035550 restraints weight = 106145.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.036704 restraints weight = 61956.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.037469 restraints weight = 44018.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.037980 restraints weight = 35253.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.038260 restraints weight = 30585.124| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13788 Z= 0.197 Angle : 0.695 11.716 18732 Z= 0.342 Chirality : 0.043 0.177 2087 Planarity : 0.005 0.075 2363 Dihedral : 8.455 119.105 1952 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.91 % Allowed : 9.62 % 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 aren not related in a simple way. whole: -1.60 (0.19), residues: 1683 helix: -0.52 (0.23), residues: 443 sheet: -0.74 (0.27), residues: 358 loop : -1.46 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 344 TYR 0.022 0.002 TYR L 50 PHE 0.021 0.002 PHE A 465 TRP 0.015 0.002 TRP N 45 HIS 0.008 0.001 HIS M 64 Details of bonding type rmsd covalent geometry : bond 0.00422 (13781) covalent geometry : angle 0.69446 (18716) SS BOND : bond 0.00833 ( 5) SS BOND : angle 1.32104 ( 10) hydrogen bonds : bond 0.03844 ( 455) hydrogen bonds : angle 5.86446 ( 1347) link_ALPHA1-4 : bond 0.00100 ( 1) link_ALPHA1-4 : angle 1.31243 ( 3) link_TRANS : bond 0.00282 ( 1) link_TRANS : angle 0.39491 ( 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 136 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.540 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 52 GLN cc_start: 0.9099 (mt0) cc_final: 0.8641 (mp10) REVERT: A 136 MET cc_start: 0.8856 (mmm) cc_final: 0.8239 (mmp) REVERT: B 257 HIS cc_start: 0.7923 (t70) cc_final: 0.7711 (t70) REVERT: G 41 LEU cc_start: 0.8846 (mm) cc_final: 0.8332 (mm) REVERT: G 239 ASP cc_start: 0.7892 (t0) cc_final: 0.7336 (m-30) REVERT: L 48 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9155 (mp) REVERT: H 160 ASP cc_start: 0.8961 (m-30) cc_final: 0.8318 (m-30) REVERT: N 40 ARG cc_start: 0.8788 (mtm110) cc_final: 0.7193 (tpt90) outliers start: 28 outliers final: 14 residues processed: 130 average time/residue: 0.1108 time to fit residues: 20.8933 Evaluate side-chains 95 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain L residue 48 LEU 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: 2.9990 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3546 r_free = 0.3546 target = 0.048971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.033867 restraints weight = 107367.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.034997 restraints weight = 62844.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.035750 restraints weight = 45001.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.036223 restraints weight = 36398.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.036549 restraints weight = 31820.666| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13788 Z= 0.170 Angle : 0.631 11.188 18732 Z= 0.310 Chirality : 0.042 0.171 2087 Planarity : 0.004 0.054 2363 Dihedral : 8.004 120.247 1952 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.05 % Allowed : 8.94 % Favored : 89.01 % 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 aren not related in a simple way. whole: -1.03 (0.20), residues: 1683 helix: 0.22 (0.24), residues: 453 sheet: -0.40 (0.27), residues: 350 loop : -1.28 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.017 0.001 TYR A 207 PHE 0.015 0.002 PHE A 279 TRP 0.016 0.002 TRP N 45 HIS 0.005 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00366 (13781) covalent geometry : angle 0.63031 (18716) SS BOND : bond 0.00419 ( 5) SS BOND : angle 1.28401 ( 10) hydrogen bonds : bond 0.03438 ( 455) hydrogen bonds : angle 5.21081 ( 1347) link_ALPHA1-4 : bond 0.00126 ( 1) link_ALPHA1-4 : angle 1.32340 ( 3) link_TRANS : bond 0.00192 ( 1) link_TRANS : angle 0.45623 ( 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 113 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.491 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: 0.8973 (mmm) cc_final: 0.8458 (mmp) REVERT: A 256 MET cc_start: 0.8729 (mmp) cc_final: 0.8505 (mmp) REVERT: B 208 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7348 (pp) REVERT: B 237 MET cc_start: 0.7889 (pmm) cc_final: 0.7429 (pmm) REVERT: B 240 HIS cc_start: 0.8505 (m90) cc_final: 0.8300 (m90) REVERT: B 257 HIS cc_start: 0.8145 (t70) cc_final: 0.7814 (t70) REVERT: M 330 MET cc_start: 0.8455 (mtm) cc_final: 0.8222 (mtt) REVERT: M 336 MET cc_start: 0.8707 (tpt) cc_final: 0.8496 (tpp) REVERT: L 48 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9054 (mp) REVERT: N 40 ARG cc_start: 0.8748 (mtm110) cc_final: 0.7268 (tpt170) REVERT: N 53 GLU cc_start: 0.8646 (tp30) cc_final: 0.8402 (tp30) outliers start: 30 outliers final: 15 residues processed: 105 average time/residue: 0.1004 time to fit residues: 16.2362 Evaluate side-chains 92 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 208 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 117 ASP 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: 9.9990 chunk 108 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 156 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS G 105 GLN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.046016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.030959 restraints weight = 109655.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.032004 restraints weight = 64724.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.032685 restraints weight = 46889.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.033119 restraints weight = 38426.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.033355 restraints weight = 33947.763| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 13788 Z= 0.270 Angle : 0.735 12.676 18732 Z= 0.361 Chirality : 0.044 0.201 2087 Planarity : 0.005 0.054 2363 Dihedral : 7.199 107.400 1952 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.73 % Allowed : 9.22 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1683 helix: 0.56 (0.25), residues: 448 sheet: -0.67 (0.26), residues: 369 loop : -1.02 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 197 TYR 0.028 0.002 TYR H 97 PHE 0.022 0.002 PHE A 279 TRP 0.022 0.002 TRP G 117 HIS 0.007 0.002 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00570 (13781) covalent geometry : angle 0.73409 (18716) SS BOND : bond 0.01194 ( 5) SS BOND : angle 1.75264 ( 10) hydrogen bonds : bond 0.03653 ( 455) hydrogen bonds : angle 5.25495 ( 1347) link_ALPHA1-4 : bond 0.00113 ( 1) link_ALPHA1-4 : angle 1.13350 ( 3) link_TRANS : bond 0.00416 ( 1) link_TRANS : angle 0.62484 ( 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 115 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.533 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: 0.9067 (mmm) cc_final: 0.8648 (mmp) REVERT: B 208 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (pp) REVERT: M 330 MET cc_start: 0.8436 (mtm) cc_final: 0.8160 (mtt) REVERT: L 48 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9031 (mp) outliers start: 40 outliers final: 25 residues processed: 108 average time/residue: 0.0950 time to fit residues: 16.0228 Evaluate side-chains 92 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 207 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 271 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 40 optimal weight: 0.0670 chunk 82 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 HIS B 257 HIS G 67 ASN ** L 90 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 = 0.3500 r_free = 0.3500 target = 0.047469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032364 restraints weight = 106934.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.033475 restraints weight = 62321.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.034215 restraints weight = 44567.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.034616 restraints weight = 36173.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034957 restraints weight = 31975.463| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13788 Z= 0.105 Angle : 0.583 7.736 18732 Z= 0.284 Chirality : 0.042 0.224 2087 Planarity : 0.004 0.051 2363 Dihedral : 6.366 90.409 1952 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.91 % Allowed : 9.97 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.20), residues: 1683 helix: 0.75 (0.25), residues: 451 sheet: -0.53 (0.26), residues: 373 loop : -0.84 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 299 TYR 0.013 0.001 TYR L 50 PHE 0.011 0.001 PHE A 122 TRP 0.011 0.001 TRP A 269 HIS 0.007 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00234 (13781) covalent geometry : angle 0.58291 (18716) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.97469 ( 10) hydrogen bonds : bond 0.02824 ( 455) hydrogen bonds : angle 4.80165 ( 1347) link_ALPHA1-4 : bond 0.00235 ( 1) link_ALPHA1-4 : angle 1.04213 ( 3) link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.26734 ( 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 104 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.563 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: 0.9050 (mmm) cc_final: 0.8635 (mmp) REVERT: M 336 MET cc_start: 0.8972 (tpt) cc_final: 0.8374 (tpp) REVERT: L 48 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8983 (mp) REVERT: H 114 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7975 (mm-30) outliers start: 28 outliers final: 16 residues processed: 98 average time/residue: 0.1091 time to fit residues: 15.9736 Evaluate side-chains 81 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain 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 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: 9.9990 chunk 7 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 55 optimal weight: 0.0170 chunk 154 optimal weight: 20.0000 chunk 118 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS B 214 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** 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 = 0.3515 r_free = 0.3515 target = 0.048013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.032940 restraints weight = 107736.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034074 restraints weight = 62582.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.034813 restraints weight = 44657.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.035293 restraints weight = 36163.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.035553 restraints weight = 31554.515| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13788 Z= 0.094 Angle : 0.571 9.956 18732 Z= 0.273 Chirality : 0.041 0.205 2087 Planarity : 0.005 0.123 2363 Dihedral : 5.643 56.005 1952 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.57 % Allowed : 9.97 % 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 aren not related in a simple way. whole: -0.39 (0.20), residues: 1683 helix: 0.91 (0.25), residues: 452 sheet: -0.22 (0.27), residues: 354 loop : -0.87 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 529 TYR 0.013 0.001 TYR L 193 PHE 0.022 0.001 PHE L 210 TRP 0.009 0.001 TRP A 269 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00212 (13781) covalent geometry : angle 0.57123 (18716) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.61581 ( 10) hydrogen bonds : bond 0.02693 ( 455) hydrogen bonds : angle 4.55068 ( 1347) link_ALPHA1-4 : bond 0.00017 ( 1) link_ALPHA1-4 : angle 1.05699 ( 3) link_TRANS : bond 0.00029 ( 1) link_TRANS : angle 0.24903 ( 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 93 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.452 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 107 ILE cc_start: 0.9403 (mm) cc_final: 0.9134 (tp) REVERT: A 136 MET cc_start: 0.8981 (mmm) cc_final: 0.8562 (mmp) REVERT: A 141 ASP cc_start: 0.8267 (m-30) cc_final: 0.7731 (p0) REVERT: G 267 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9165 (tm-30) REVERT: L 48 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8991 (mp) REVERT: H 114 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7767 (mm-30) REVERT: N 113 TYR cc_start: 0.6785 (t80) cc_final: 0.6419 (t80) outliers start: 23 outliers final: 17 residues processed: 90 average time/residue: 0.0907 time to fit residues: 12.9522 Evaluate side-chains 83 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 236 VAL 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 48 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** 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 = 0.3492 r_free = 0.3492 target = 0.047150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.032067 restraints weight = 107748.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.033181 restraints weight = 63001.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033898 restraints weight = 45157.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034364 restraints weight = 36677.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.034612 restraints weight = 32151.807| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13788 Z= 0.123 Angle : 0.572 8.729 18732 Z= 0.274 Chirality : 0.041 0.215 2087 Planarity : 0.004 0.071 2363 Dihedral : 5.251 41.042 1952 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.57 % Allowed : 10.44 % 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 aren not related in a simple way. whole: -0.19 (0.21), residues: 1683 helix: 1.08 (0.25), residues: 453 sheet: -0.16 (0.27), residues: 368 loop : -0.72 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 354 TYR 0.012 0.001 TYR L 50 PHE 0.011 0.001 PHE L 210 TRP 0.012 0.001 TRP G 117 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00274 (13781) covalent geometry : angle 0.57196 (18716) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.70039 ( 10) hydrogen bonds : bond 0.02648 ( 455) hydrogen bonds : angle 4.54132 ( 1347) link_ALPHA1-4 : bond 0.00231 ( 1) link_ALPHA1-4 : angle 1.03070 ( 3) link_TRANS : bond 0.00161 ( 1) link_TRANS : angle 0.34739 ( 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 91 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.533 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 107 ILE cc_start: 0.9448 (mm) cc_final: 0.9203 (tp) REVERT: A 136 MET cc_start: 0.8984 (mmm) cc_final: 0.8547 (mmp) REVERT: B 226 ASP cc_start: 0.6115 (m-30) cc_final: 0.5376 (t70) REVERT: G 33 MET cc_start: 0.9293 (ptt) cc_final: 0.8807 (ppp) REVERT: M 330 MET cc_start: 0.8420 (mtm) cc_final: 0.8129 (mtt) REVERT: M 336 MET cc_start: 0.9286 (tpp) cc_final: 0.8847 (tpt) REVERT: L 48 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8960 (mp) REVERT: H 114 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7763 (mm-30) REVERT: N 43 MET cc_start: 0.8129 (tpp) cc_final: 0.7822 (tpt) REVERT: N 113 TYR cc_start: 0.6776 (t80) cc_final: 0.6486 (t80) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 0.0926 time to fit residues: 12.8885 Evaluate side-chains 87 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 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 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3491 r_free = 0.3491 target = 0.047083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.031926 restraints weight = 105969.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.033047 restraints weight = 61569.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.033762 restraints weight = 43999.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.034181 restraints weight = 35638.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.034508 restraints weight = 31341.852| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13788 Z= 0.116 Angle : 0.572 7.988 18732 Z= 0.275 Chirality : 0.041 0.194 2087 Planarity : 0.004 0.052 2363 Dihedral : 5.234 41.829 1952 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.50 % Allowed : 10.24 % 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 aren not related in a simple way. whole: -0.10 (0.21), residues: 1683 helix: 1.16 (0.25), residues: 453 sheet: -0.03 (0.27), residues: 365 loop : -0.70 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.017 0.001 TYR N 104 PHE 0.012 0.001 PHE N 77 TRP 0.010 0.001 TRP G 117 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00259 (13781) covalent geometry : angle 0.57114 (18716) SS BOND : bond 0.00219 ( 5) SS BOND : angle 1.46339 ( 10) hydrogen bonds : bond 0.02576 ( 455) hydrogen bonds : angle 4.49292 ( 1347) link_ALPHA1-4 : bond 0.00025 ( 1) link_ALPHA1-4 : angle 0.97315 ( 3) link_TRANS : bond 0.00126 ( 1) link_TRANS : angle 0.31319 ( 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 89 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.487 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 107 ILE cc_start: 0.9458 (mm) cc_final: 0.9221 (tp) REVERT: A 136 MET cc_start: 0.8973 (mmm) cc_final: 0.8558 (mmp) REVERT: A 141 ASP cc_start: 0.8383 (m-30) cc_final: 0.7857 (p0) REVERT: B 226 ASP cc_start: 0.6120 (m-30) cc_final: 0.5382 (t70) REVERT: M 330 MET cc_start: 0.8438 (mtm) cc_final: 0.8102 (mtt) REVERT: M 336 MET cc_start: 0.9306 (tpp) cc_final: 0.8867 (tpt) REVERT: L 48 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8956 (mp) REVERT: H 114 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7745 (mm-30) REVERT: N 113 TYR cc_start: 0.6793 (t80) cc_final: 0.6428 (t80) outliers start: 22 outliers final: 20 residues processed: 86 average time/residue: 0.0942 time to fit residues: 12.7892 Evaluate side-chains 87 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 145 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** L 90 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.046418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.031270 restraints weight = 109671.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.032360 restraints weight = 62977.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033073 restraints weight = 45080.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.033526 restraints weight = 36631.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033776 restraints weight = 32160.492| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13788 Z= 0.153 Angle : 0.598 8.918 18732 Z= 0.289 Chirality : 0.041 0.181 2087 Planarity : 0.004 0.053 2363 Dihedral : 5.321 44.240 1952 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.50 % Allowed : 10.17 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1683 helix: 1.22 (0.25), residues: 453 sheet: -0.04 (0.26), residues: 371 loop : -0.67 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 62 TYR 0.015 0.001 TYR N 104 PHE 0.010 0.001 PHE A 279 TRP 0.013 0.001 TRP G 117 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00335 (13781) covalent geometry : angle 0.59657 (18716) SS BOND : bond 0.00315 ( 5) SS BOND : angle 1.88133 ( 10) hydrogen bonds : bond 0.02717 ( 455) hydrogen bonds : angle 4.58940 ( 1347) link_ALPHA1-4 : bond 0.00063 ( 1) link_ALPHA1-4 : angle 1.03545 ( 3) link_TRANS : bond 0.00206 ( 1) link_TRANS : angle 0.34822 ( 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: 22 poor density : 68 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: A 107 ILE cc_start: 0.9463 (mm) cc_final: 0.9247 (tp) REVERT: A 136 MET cc_start: 0.8987 (mmm) cc_final: 0.8573 (mmp) REVERT: B 226 ASP cc_start: 0.5957 (m-30) cc_final: 0.5218 (t70) REVERT: M 330 MET cc_start: 0.8431 (mtm) cc_final: 0.8148 (mtt) REVERT: M 336 MET cc_start: 0.9330 (tpp) cc_final: 0.8886 (tpt) REVERT: L 48 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8938 (mp) REVERT: H 114 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7913 (mm-30) REVERT: N 77 PHE cc_start: 0.8801 (m-10) cc_final: 0.8416 (m-10) REVERT: N 113 TYR cc_start: 0.6871 (t80) cc_final: 0.6565 (t80) outliers start: 22 outliers final: 19 residues processed: 87 average time/residue: 0.0902 time to fit residues: 12.5124 Evaluate side-chains 87 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 0.2980 chunk 115 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** 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 = 0.3474 r_free = 0.3474 target = 0.046412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.031331 restraints weight = 108432.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.032413 restraints weight = 62727.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.033136 restraints weight = 44971.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033583 restraints weight = 36525.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033834 restraints weight = 32054.379| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13788 Z= 0.139 Angle : 0.606 9.525 18732 Z= 0.290 Chirality : 0.041 0.181 2087 Planarity : 0.004 0.052 2363 Dihedral : 5.357 45.886 1952 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.50 % Allowed : 10.17 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.21), residues: 1683 helix: 1.28 (0.25), residues: 453 sheet: -0.18 (0.27), residues: 356 loop : -0.59 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.015 0.001 TYR N 104 PHE 0.010 0.001 PHE H 71 TRP 0.011 0.001 TRP A 426 HIS 0.005 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00303 (13781) covalent geometry : angle 0.60562 (18716) SS BOND : bond 0.00183 ( 5) SS BOND : angle 1.48528 ( 10) hydrogen bonds : bond 0.02685 ( 455) hydrogen bonds : angle 4.56527 ( 1347) link_ALPHA1-4 : bond 0.00277 ( 1) link_ALPHA1-4 : angle 0.93446 ( 3) link_TRANS : bond 0.00143 ( 1) link_TRANS : angle 0.35934 ( 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 92 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.617 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 107 ILE cc_start: 0.9489 (mm) cc_final: 0.9280 (tp) REVERT: A 136 MET cc_start: 0.8983 (mmm) cc_final: 0.8575 (mmp) REVERT: B 226 ASP cc_start: 0.5859 (m-30) cc_final: 0.5139 (t70) REVERT: M 330 MET cc_start: 0.8452 (mtm) cc_final: 0.8169 (mtt) REVERT: M 336 MET cc_start: 0.9343 (tpp) cc_final: 0.8858 (tpt) REVERT: L 48 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8931 (mp) REVERT: H 114 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7787 (mm-30) REVERT: N 77 PHE cc_start: 0.8873 (m-10) cc_final: 0.8545 (m-10) REVERT: N 113 TYR cc_start: 0.6876 (t80) cc_final: 0.6518 (t80) outliers start: 22 outliers final: 18 residues processed: 89 average time/residue: 0.0987 time to fit residues: 14.0238 Evaluate side-chains 87 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 238 TYR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain G residue 301 VAL Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 216 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 122 optimal weight: 0.3980 chunk 148 optimal weight: 0.0770 chunk 107 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.7256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3504 r_free = 0.3504 target = 0.047447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032312 restraints weight = 108255.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.033429 restraints weight = 62573.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.034152 restraints weight = 44787.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.034639 restraints weight = 36345.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034893 restraints weight = 31773.587| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13788 Z= 0.091 Angle : 0.582 9.637 18732 Z= 0.276 Chirality : 0.041 0.171 2087 Planarity : 0.003 0.052 2363 Dihedral : 5.050 42.610 1952 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.09 % Allowed : 10.72 % 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 aren not related in a simple way. whole: 0.05 (0.21), residues: 1683 helix: 1.35 (0.25), residues: 453 sheet: -0.15 (0.26), residues: 361 loop : -0.54 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.014 0.001 TYR N 104 PHE 0.010 0.001 PHE A 122 TRP 0.010 0.001 TRP A 398 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00207 (13781) covalent geometry : angle 0.58167 (18716) SS BOND : bond 0.00168 ( 5) SS BOND : angle 1.35511 ( 10) hydrogen bonds : bond 0.02509 ( 455) hydrogen bonds : angle 4.37370 ( 1347) link_ALPHA1-4 : bond 0.00148 ( 1) link_ALPHA1-4 : angle 0.99042 ( 3) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.25413 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.86 seconds wall clock time: 42 minutes 24.61 seconds (2544.61 seconds total)