Starting phenix.real_space_refine on Wed Mar 4 06:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7khf_22879/03_2026/7khf_22879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7khf_22879/03_2026/7khf_22879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7khf_22879/03_2026/7khf_22879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7khf_22879/03_2026/7khf_22879.map" model { file = "/net/cci-nas-00/data/ceres_data/7khf_22879/03_2026/7khf_22879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7khf_22879/03_2026/7khf_22879.cif" } resolution = 3.54 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= -0.003 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7283 2.51 5 N 1924 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11559 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3250 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3253 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Chain: "B" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.78, per 1000 atoms: 0.24 Number of scatterers: 11559 At special positions: 0 Unit cell: (106.134, 137.541, 132.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2314 8.00 N 1924 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 339 " - pdb=" SG CYS B 213 " distance=2.71 Simple disulfide: pdb=" SG CYS H 352 " - pdb=" SG CYS H 408 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 264 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 207 " " NAG E 1 " - " ASN H 186 " " NAG F 1 " - " ASN H 246 " " NAG G 1 " - " ASN A 186 " " NAG H 501 " - " ASN H 207 " " NAG I 1 " - " ASN A 246 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 468.6 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 31 sheets defined 15.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 63 through 69 removed outlier: 3.814A pdb=" N LYS H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 69 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 removed outlier: 3.749A pdb=" N TYR H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 197 " --> pdb=" O ARG H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 197' Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.632A pdb=" N ALA L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 29' Processing helix chain 'L' and resid 123 through 129 removed outlier: 4.050A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.562A pdb=" N LYS L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.044A pdb=" N GLY A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.035A pdb=" N GLY A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.596A pdb=" N HIS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.819A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 303 Processing helix chain 'C' and resid 187 through 205 removed outlier: 4.052A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.637A pdb=" N GLU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.018A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.256A pdb=" N ILE C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.551A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 303 removed outlier: 3.622A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.708A pdb=" N ARG H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.201A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY H 35 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN H 109 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 132 through 136 removed outlier: 4.049A pdb=" N GLN H 136 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR H 148 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 183 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU H 313 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 223 " --> pdb=" O LEU H 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY H 198 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 161 " --> pdb=" O TYR H 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN H 172 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 175 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN C 276 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.107A pdb=" N VAL H 247 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 240 through 241 removed outlier: 3.752A pdb=" N TYR H 300 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 333 through 336 removed outlier: 3.686A pdb=" N GLY H 351 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP H 356 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 388 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER H 391 " --> pdb=" O PRO H 379 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 393 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR H 377 " --> pdb=" O VAL H 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 363 through 366 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.541A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.674A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.752A pdb=" N SER L 139 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR L 174 " --> pdb=" O ASP L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.554A pdb=" N LYS L 206 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 97 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 115 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS A 99 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 113 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 132 through 136 removed outlier: 3.926A pdb=" N THR A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.620A pdb=" N VAL A 161 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 159 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 172 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 235 removed outlier: 5.711A pdb=" N VAL A 247 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 284 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.711A pdb=" N SER A 325 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 300 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 274 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.388A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 155 through 156 436 hydrogen bonds defined for protein. 1086 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: 1.89 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1887 1.30 - 1.43: 3082 1.43 - 1.56: 6816 1.56 - 1.69: 0 1.69 - 1.82: 44 Bond restraints: 11829 Sorted by residual: bond pdb=" CA CYS H 352 " pdb=" C CYS H 352 " ideal model delta sigma weight residual 1.522 1.395 0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C PRO A 361 " pdb=" O PRO A 361 " ideal model delta sigma weight residual 1.235 1.178 0.057 7.90e-03 1.60e+04 5.16e+01 bond pdb=" C PRO A 359 " pdb=" O PRO A 359 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.10e-02 8.26e+03 3.39e+01 bond pdb=" N CYS H 352 " pdb=" CA CYS H 352 " ideal model delta sigma weight residual 1.454 1.386 0.069 1.27e-02 6.20e+03 2.92e+01 bond pdb=" CA SER H 389 " pdb=" CB SER H 389 " ideal model delta sigma weight residual 1.535 1.433 0.102 1.90e-02 2.77e+03 2.88e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15669 2.85 - 5.71: 402 5.71 - 8.56: 43 8.56 - 11.41: 10 11.41 - 14.26: 2 Bond angle restraints: 16126 Sorted by residual: angle pdb=" C PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 111.23 96.97 14.26 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C PRO A 361 " pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " ideal model delta sigma weight residual 111.87 103.74 8.13 8.40e-01 1.42e+00 9.37e+01 angle pdb=" C THR A 372 " pdb=" CA THR A 372 " pdb=" CB THR A 372 " ideal model delta sigma weight residual 110.81 122.95 -12.14 1.73e+00 3.34e-01 4.93e+01 angle pdb=" CA PRO H 338 " pdb=" C PRO H 338 " pdb=" O PRO H 338 " ideal model delta sigma weight residual 119.34 109.12 10.22 1.47e+00 4.63e-01 4.84e+01 angle pdb=" C PRO H 335 " pdb=" CA PRO H 335 " pdb=" CB PRO H 335 " ideal model delta sigma weight residual 110.98 102.28 8.70 1.31e+00 5.83e-01 4.42e+01 ... (remaining 16121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6859 23.42 - 46.83: 347 46.83 - 70.25: 36 70.25 - 93.67: 10 93.67 - 117.09: 5 Dihedral angle restraints: 7257 sinusoidal: 2891 harmonic: 4366 Sorted by residual: dihedral pdb=" C PRO A 331 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta harmonic sigma weight residual -120.70 -102.15 -18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C PRO A 359 " pdb=" N PRO A 359 " pdb=" CA PRO A 359 " pdb=" CB PRO A 359 " ideal model delta harmonic sigma weight residual -120.70 -105.80 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CB CYS A 251 " pdb=" SG CYS A 251 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 7254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1796 0.154 - 0.308: 58 0.308 - 0.462: 9 0.462 - 0.616: 0 0.616 - 0.770: 2 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CA CYS H 352 " pdb=" N CYS H 352 " pdb=" C CYS H 352 " pdb=" CB CYS H 352 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR A 372 " pdb=" N THR A 372 " pdb=" C THR A 372 " pdb=" CB THR A 372 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1862 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 338 " 0.028 2.00e-02 2.50e+03 6.20e-02 3.84e+01 pdb=" C PRO H 338 " -0.107 2.00e-02 2.50e+03 pdb=" O PRO H 338 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS H 339 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " 0.001 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN A 246 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 335 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C PRO H 335 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO H 335 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 336 " -0.018 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 673 2.72 - 3.27: 11207 3.27 - 3.81: 16916 3.81 - 4.36: 19939 4.36 - 4.90: 36296 Nonbonded interactions: 85031 Sorted by model distance: nonbonded pdb=" OE2 GLU A 6 " pdb=" N GLY A 118 " model vdw 2.179 3.120 nonbonded pdb=" NZ LYS B 168 " pdb=" OD1 ASN B 172 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG H 68 " pdb=" OD2 ASP H 91 " model vdw 2.219 3.120 nonbonded pdb=" NZ LYS H 130 " pdb=" OG1 THR A 70 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU H 265 " pdb=" NH2 ARG H 301 " model vdw 2.318 3.120 ... (remaining 85026 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 501)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.010 0.674 11854 Z= 0.556 Angle : 1.000 19.369 16186 Z= 0.630 Chirality : 0.069 0.770 1865 Planarity : 0.005 0.062 2064 Dihedral : 13.715 117.086 4424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 0.94 % Allowed : 1.57 % Favored : 97.49 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.23), residues: 1504 helix: 0.24 (0.40), residues: 178 sheet: 0.32 (0.23), residues: 553 loop : -1.03 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 341 TYR 0.040 0.002 TYR A 357 PHE 0.035 0.002 PHE A 358 TRP 0.013 0.001 TRP H 256 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00772 (11829) covalent geometry : angle 0.97674 (16126) SS BOND : bond 0.17422 ( 15) SS BOND : angle 3.76488 ( 30) hydrogen bonds : bond 0.26211 ( 414) hydrogen bonds : angle 9.30235 ( 1086) link_BETA1-4 : bond 0.01065 ( 4) link_BETA1-4 : angle 2.62473 ( 12) link_NAG-ASN : bond 0.00443 ( 6) link_NAG-ASN : angle 4.03690 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7848 (t0) cc_final: 0.7599 (t0) REVERT: H 256 TRP cc_start: 0.7843 (t60) cc_final: 0.7637 (t-100) REVERT: H 257 MET cc_start: 0.7819 (mpp) cc_final: 0.7349 (mpp) REVERT: L 200 GLU cc_start: 0.7704 (pp20) cc_final: 0.7417 (pp20) REVERT: A 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 341 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5018 (tpp-160) REVERT: A 357 TYR cc_start: 0.8367 (p90) cc_final: 0.7530 (p90) REVERT: B 130 ASN cc_start: 0.8460 (m-40) cc_final: 0.7908 (t0) REVERT: D 288 GLN cc_start: 0.8516 (tp40) cc_final: 0.8274 (tp40) REVERT: D 294 ILE cc_start: 0.8587 (mm) cc_final: 0.8334 (tt) REVERT: C 230 THR cc_start: 0.9337 (m) cc_final: 0.9021 (p) REVERT: C 290 ASP cc_start: 0.7646 (m-30) cc_final: 0.7142 (m-30) outliers start: 12 outliers final: 4 residues processed: 186 average time/residue: 0.1007 time to fit residues: 27.2507 Evaluate side-chains 145 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082140 restraints weight = 22295.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085355 restraints weight = 10971.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.087388 restraints weight = 7203.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088693 restraints weight = 5542.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.089493 restraints weight = 4669.532| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11854 Z= 0.182 Angle : 0.675 8.621 16186 Z= 0.340 Chirality : 0.045 0.212 1865 Planarity : 0.004 0.040 2064 Dihedral : 9.297 103.516 1851 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.10 % Allowed : 8.30 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 1504 helix: 0.10 (0.39), residues: 187 sheet: 0.39 (0.24), residues: 552 loop : -0.99 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.014 0.001 TYR A 228 PHE 0.032 0.001 PHE A 358 TRP 0.010 0.001 TRP H 272 HIS 0.004 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00428 (11829) covalent geometry : angle 0.66646 (16126) SS BOND : bond 0.00285 ( 15) SS BOND : angle 0.65824 ( 30) hydrogen bonds : bond 0.04287 ( 414) hydrogen bonds : angle 6.49678 ( 1086) link_BETA1-4 : bond 0.00686 ( 4) link_BETA1-4 : angle 2.84079 ( 12) link_NAG-ASN : bond 0.00237 ( 6) link_NAG-ASN : angle 2.47516 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.443 Fit side-chains REVERT: H 154 ASP cc_start: 0.8205 (t0) cc_final: 0.8002 (t0) REVERT: H 256 TRP cc_start: 0.8117 (t60) cc_final: 0.7815 (t-100) REVERT: H 257 MET cc_start: 0.8002 (mpp) cc_final: 0.7747 (mpp) REVERT: H 353 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8026 (tp) REVERT: L 130 ASN cc_start: 0.8935 (t0) cc_final: 0.8663 (t0) REVERT: A 336 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8493 (pp) REVERT: A 409 ASN cc_start: 0.8598 (m-40) cc_final: 0.8351 (m-40) REVERT: B 130 ASN cc_start: 0.8512 (m-40) cc_final: 0.7904 (t0) REVERT: B 140 ASP cc_start: 0.8290 (m-30) cc_final: 0.8076 (m-30) REVERT: B 168 LYS cc_start: 0.8444 (tptt) cc_final: 0.8045 (tptt) REVERT: D 279 ASP cc_start: 0.8242 (p0) cc_final: 0.8005 (p0) REVERT: D 288 GLN cc_start: 0.8284 (tp40) cc_final: 0.7964 (tp40) REVERT: C 219 ASP cc_start: 0.6943 (t70) cc_final: 0.6540 (t70) REVERT: C 223 TYR cc_start: 0.6161 (p90) cc_final: 0.5938 (p90) REVERT: C 290 ASP cc_start: 0.8084 (m-30) cc_final: 0.7327 (m-30) outliers start: 14 outliers final: 9 residues processed: 169 average time/residue: 0.0958 time to fit residues: 23.8281 Evaluate side-chains 154 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 146 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.086323 restraints weight = 22829.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089564 restraints weight = 11354.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091658 restraints weight = 7532.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092993 restraints weight = 5816.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093881 restraints weight = 4914.434| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11854 Z= 0.140 Angle : 0.619 8.999 16186 Z= 0.307 Chirality : 0.043 0.206 1865 Planarity : 0.004 0.037 2064 Dihedral : 8.815 100.611 1847 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.96 % Allowed : 10.18 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1504 helix: 0.14 (0.39), residues: 187 sheet: 0.47 (0.23), residues: 562 loop : -0.92 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 275 TYR 0.038 0.001 TYR A 357 PHE 0.030 0.001 PHE H 334 TRP 0.010 0.001 TRP L 187 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00330 (11829) covalent geometry : angle 0.60871 (16126) SS BOND : bond 0.00292 ( 15) SS BOND : angle 0.61095 ( 30) hydrogen bonds : bond 0.03643 ( 414) hydrogen bonds : angle 5.92255 ( 1086) link_BETA1-4 : bond 0.00579 ( 4) link_BETA1-4 : angle 2.76741 ( 12) link_NAG-ASN : bond 0.00232 ( 6) link_NAG-ASN : angle 2.60883 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.8228 (t0) cc_final: 0.8002 (t0) REVERT: H 256 TRP cc_start: 0.8108 (t60) cc_final: 0.7790 (t-100) REVERT: H 420 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: L 35 TYR cc_start: 0.9009 (m-80) cc_final: 0.8680 (m-80) REVERT: L 130 ASN cc_start: 0.8984 (t0) cc_final: 0.8668 (t0) REVERT: A 336 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8518 (pp) REVERT: A 409 ASN cc_start: 0.8652 (m-40) cc_final: 0.8340 (m-40) REVERT: B 78 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8371 (mp10) REVERT: B 130 ASN cc_start: 0.8496 (m-40) cc_final: 0.7895 (t0) REVERT: B 140 ASP cc_start: 0.8377 (m-30) cc_final: 0.8119 (m-30) REVERT: D 288 GLN cc_start: 0.8263 (tp40) cc_final: 0.7942 (tp40) REVERT: C 219 ASP cc_start: 0.6896 (t70) cc_final: 0.6608 (t70) REVERT: C 290 ASP cc_start: 0.8066 (m-30) cc_final: 0.7321 (m-30) outliers start: 25 outliers final: 18 residues processed: 167 average time/residue: 0.1003 time to fit residues: 24.7775 Evaluate side-chains 166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 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 = 0.3431 r_free = 0.3431 target = 0.105982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081133 restraints weight = 22602.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084351 restraints weight = 11103.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086382 restraints weight = 7349.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.087688 restraints weight = 5698.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088472 restraints weight = 4814.586| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11854 Z= 0.208 Angle : 0.645 9.430 16186 Z= 0.320 Chirality : 0.044 0.211 1865 Planarity : 0.004 0.036 2064 Dihedral : 8.616 96.563 1847 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.58 % Allowed : 11.51 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1504 helix: 0.17 (0.39), residues: 187 sheet: 0.40 (0.23), residues: 566 loop : -0.96 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.026 0.001 TYR A 357 PHE 0.019 0.002 PHE H 334 TRP 0.008 0.001 TRP A 49 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00501 (11829) covalent geometry : angle 0.63455 (16126) SS BOND : bond 0.00277 ( 15) SS BOND : angle 0.62274 ( 30) hydrogen bonds : bond 0.03669 ( 414) hydrogen bonds : angle 5.70329 ( 1086) link_BETA1-4 : bond 0.00672 ( 4) link_BETA1-4 : angle 2.64989 ( 12) link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 2.83771 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7835 (mpp) cc_final: 0.7160 (mpp) REVERT: H 336 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8804 (pp) REVERT: H 353 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8002 (tp) REVERT: H 420 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: L 35 TYR cc_start: 0.9065 (m-80) cc_final: 0.8756 (m-80) REVERT: L 110 GLN cc_start: 0.8517 (mp10) cc_final: 0.8273 (pm20) REVERT: L 130 ASN cc_start: 0.9027 (t0) cc_final: 0.8699 (t0) REVERT: A 409 ASN cc_start: 0.8718 (m-40) cc_final: 0.8410 (m-40) REVERT: B 78 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8387 (mp10) REVERT: B 130 ASN cc_start: 0.8582 (m-40) cc_final: 0.7940 (t0) REVERT: D 288 GLN cc_start: 0.8311 (tp40) cc_final: 0.7979 (tp40) REVERT: C 219 ASP cc_start: 0.6949 (t0) cc_final: 0.6705 (t70) REVERT: C 290 ASP cc_start: 0.7912 (m-30) cc_final: 0.7194 (m-30) outliers start: 33 outliers final: 24 residues processed: 163 average time/residue: 0.1002 time to fit residues: 24.2631 Evaluate side-chains 166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 99 optimal weight: 0.0970 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** B 37 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 = 0.3418 r_free = 0.3418 target = 0.106670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083502 restraints weight = 21270.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.086538 restraints weight = 10815.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088455 restraints weight = 7182.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089710 restraints weight = 5568.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.090505 restraints weight = 4708.135| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11854 Z= 0.122 Angle : 0.598 9.931 16186 Z= 0.293 Chirality : 0.043 0.211 1865 Planarity : 0.004 0.035 2064 Dihedral : 8.229 92.719 1847 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.43 % Allowed : 12.92 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.23), residues: 1504 helix: 0.19 (0.40), residues: 181 sheet: 0.53 (0.23), residues: 566 loop : -0.86 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.022 0.001 TYR A 357 PHE 0.015 0.001 PHE H 334 TRP 0.006 0.001 TRP A 49 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00287 (11829) covalent geometry : angle 0.58739 (16126) SS BOND : bond 0.00225 ( 15) SS BOND : angle 0.49836 ( 30) hydrogen bonds : bond 0.03072 ( 414) hydrogen bonds : angle 5.46613 ( 1086) link_BETA1-4 : bond 0.00772 ( 4) link_BETA1-4 : angle 2.66702 ( 12) link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 2.71744 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 256 TRP cc_start: 0.7923 (t60) cc_final: 0.7639 (t-100) REVERT: H 257 MET cc_start: 0.7744 (mpp) cc_final: 0.7389 (mpp) REVERT: H 353 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8290 (tp) REVERT: H 420 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: L 35 TYR cc_start: 0.8979 (m-80) cc_final: 0.8758 (m-80) REVERT: L 130 ASN cc_start: 0.8832 (t0) cc_final: 0.8535 (t0) REVERT: A 409 ASN cc_start: 0.8669 (m-40) cc_final: 0.8359 (m-40) REVERT: B 78 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8462 (mp10) REVERT: B 130 ASN cc_start: 0.8536 (m-40) cc_final: 0.7961 (t0) REVERT: D 288 GLN cc_start: 0.8467 (tp40) cc_final: 0.8147 (tp40) REVERT: C 290 ASP cc_start: 0.7867 (m-30) cc_final: 0.7242 (m-30) outliers start: 31 outliers final: 18 residues processed: 170 average time/residue: 0.0967 time to fit residues: 24.5778 Evaluate side-chains 158 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 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 = 0.3398 r_free = 0.3398 target = 0.105207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.081959 restraints weight = 21377.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.084917 restraints weight = 10869.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086844 restraints weight = 7256.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.088055 restraints weight = 5621.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088787 restraints weight = 4777.601| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11854 Z= 0.183 Angle : 0.632 10.302 16186 Z= 0.310 Chirality : 0.043 0.225 1865 Planarity : 0.004 0.035 2064 Dihedral : 8.020 88.034 1845 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.43 % Allowed : 13.86 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1504 helix: 0.17 (0.39), residues: 187 sheet: 0.53 (0.23), residues: 573 loop : -0.94 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.019 0.001 TYR A 357 PHE 0.013 0.001 PHE H 334 TRP 0.006 0.001 TRP H 366 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00441 (11829) covalent geometry : angle 0.62198 (16126) SS BOND : bond 0.00237 ( 15) SS BOND : angle 0.53778 ( 30) hydrogen bonds : bond 0.03358 ( 414) hydrogen bonds : angle 5.42882 ( 1086) link_BETA1-4 : bond 0.00691 ( 4) link_BETA1-4 : angle 2.64659 ( 12) link_NAG-ASN : bond 0.00286 ( 6) link_NAG-ASN : angle 2.80455 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7782 (mpp) cc_final: 0.7362 (mpp) REVERT: H 353 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8373 (tp) REVERT: H 420 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: L 35 TYR cc_start: 0.9022 (m-80) cc_final: 0.8821 (m-80) REVERT: L 130 ASN cc_start: 0.8903 (t0) cc_final: 0.8627 (t0) REVERT: A 409 ASN cc_start: 0.8685 (m-40) cc_final: 0.8393 (m-40) REVERT: B 78 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8417 (mp10) REVERT: B 130 ASN cc_start: 0.8581 (m-40) cc_final: 0.7990 (t0) REVERT: D 288 GLN cc_start: 0.8498 (tp40) cc_final: 0.8167 (tp40) REVERT: C 290 ASP cc_start: 0.7866 (m-30) cc_final: 0.7233 (m-30) outliers start: 31 outliers final: 24 residues processed: 157 average time/residue: 0.0994 time to fit residues: 23.3123 Evaluate side-chains 159 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.079130 restraints weight = 22493.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082239 restraints weight = 10941.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.084229 restraints weight = 7207.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085501 restraints weight = 5560.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.086254 restraints weight = 4704.826| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11854 Z= 0.228 Angle : 0.664 10.568 16186 Z= 0.327 Chirality : 0.044 0.229 1865 Planarity : 0.004 0.036 2064 Dihedral : 7.950 83.113 1845 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.43 % Allowed : 14.25 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1504 helix: 0.10 (0.39), residues: 187 sheet: 0.50 (0.23), residues: 581 loop : -1.00 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.017 0.001 TYR A 357 PHE 0.016 0.002 PHE H 334 TRP 0.007 0.001 TRP A 49 HIS 0.006 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00547 (11829) covalent geometry : angle 0.65260 (16126) SS BOND : bond 0.00287 ( 15) SS BOND : angle 0.60140 ( 30) hydrogen bonds : bond 0.03555 ( 414) hydrogen bonds : angle 5.47827 ( 1086) link_BETA1-4 : bond 0.00698 ( 4) link_BETA1-4 : angle 2.72017 ( 12) link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 2.97589 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: H 257 MET cc_start: 0.7954 (mpp) cc_final: 0.7253 (mpp) REVERT: H 353 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8097 (tp) REVERT: H 420 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: L 110 GLN cc_start: 0.8582 (mp10) cc_final: 0.8346 (pm20) REVERT: L 130 ASN cc_start: 0.9083 (t0) cc_final: 0.8798 (t0) REVERT: L 200 GLU cc_start: 0.8177 (pp20) cc_final: 0.7932 (pp20) REVERT: A 257 MET cc_start: 0.8618 (mmm) cc_final: 0.8409 (mmm) REVERT: A 409 ASN cc_start: 0.8725 (m-40) cc_final: 0.8336 (m-40) REVERT: B 78 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8260 (mp10) REVERT: B 130 ASN cc_start: 0.8628 (m-40) cc_final: 0.7967 (t0) REVERT: D 279 ASP cc_start: 0.8241 (p0) cc_final: 0.7851 (p0) REVERT: D 288 GLN cc_start: 0.8395 (tp40) cc_final: 0.8048 (tp40) REVERT: C 238 GLN cc_start: 0.8893 (mt0) cc_final: 0.8634 (mt0) REVERT: C 290 ASP cc_start: 0.7946 (m-30) cc_final: 0.7152 (m-30) outliers start: 31 outliers final: 24 residues processed: 159 average time/residue: 0.0994 time to fit residues: 23.4303 Evaluate side-chains 162 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 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 = 0.3476 r_free = 0.3476 target = 0.111382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.085589 restraints weight = 22966.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.088804 restraints weight = 11468.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090836 restraints weight = 7624.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092163 restraints weight = 5928.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.092953 restraints weight = 5022.309| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11854 Z= 0.143 Angle : 0.620 11.001 16186 Z= 0.303 Chirality : 0.043 0.231 1865 Planarity : 0.004 0.036 2064 Dihedral : 7.626 77.321 1844 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.43 % Allowed : 14.49 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1504 helix: 0.18 (0.39), residues: 187 sheet: 0.54 (0.23), residues: 572 loop : -0.93 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 29 TYR 0.016 0.001 TYR C 223 PHE 0.015 0.001 PHE H 287 TRP 0.006 0.001 TRP H 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00341 (11829) covalent geometry : angle 0.60860 (16126) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.49234 ( 30) hydrogen bonds : bond 0.03142 ( 414) hydrogen bonds : angle 5.36003 ( 1086) link_BETA1-4 : bond 0.00721 ( 4) link_BETA1-4 : angle 2.72086 ( 12) link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 2.94712 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7926 (mpp) cc_final: 0.7260 (mpp) REVERT: H 420 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: L 130 ASN cc_start: 0.9068 (t0) cc_final: 0.8790 (t0) REVERT: L 200 GLU cc_start: 0.8144 (pp20) cc_final: 0.7822 (pp20) REVERT: A 409 ASN cc_start: 0.8716 (m-40) cc_final: 0.8337 (m-40) REVERT: B 78 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8274 (mp10) REVERT: B 130 ASN cc_start: 0.8623 (m-40) cc_final: 0.7962 (t0) REVERT: D 288 GLN cc_start: 0.8354 (tp40) cc_final: 0.8012 (tp40) REVERT: C 290 ASP cc_start: 0.7971 (m-30) cc_final: 0.7165 (m-30) outliers start: 31 outliers final: 23 residues processed: 163 average time/residue: 0.0990 time to fit residues: 24.1914 Evaluate side-chains 157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.082730 restraints weight = 22226.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085960 restraints weight = 10980.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088029 restraints weight = 7285.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089357 restraints weight = 5647.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.090231 restraints weight = 4782.356| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11854 Z= 0.132 Angle : 0.618 11.464 16186 Z= 0.300 Chirality : 0.043 0.236 1865 Planarity : 0.004 0.035 2064 Dihedral : 7.154 68.366 1844 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.11 % Allowed : 15.35 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1504 helix: 0.13 (0.39), residues: 183 sheet: 0.60 (0.23), residues: 573 loop : -0.94 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 29 TYR 0.016 0.001 TYR A 357 PHE 0.013 0.001 PHE H 334 TRP 0.005 0.001 TRP H 49 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00313 (11829) covalent geometry : angle 0.60537 (16126) SS BOND : bond 0.00231 ( 15) SS BOND : angle 0.48001 ( 30) hydrogen bonds : bond 0.03014 ( 414) hydrogen bonds : angle 5.23968 ( 1086) link_BETA1-4 : bond 0.00765 ( 4) link_BETA1-4 : angle 2.72652 ( 12) link_NAG-ASN : bond 0.00375 ( 6) link_NAG-ASN : angle 3.04709 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7825 (mpp) cc_final: 0.7178 (mpp) REVERT: H 420 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: L 130 ASN cc_start: 0.9048 (t0) cc_final: 0.8779 (t0) REVERT: L 200 GLU cc_start: 0.8178 (pp20) cc_final: 0.7690 (pp20) REVERT: A 409 ASN cc_start: 0.8733 (m-40) cc_final: 0.8348 (m-40) REVERT: B 78 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8316 (mp10) REVERT: D 288 GLN cc_start: 0.8368 (tp40) cc_final: 0.8021 (tp40) REVERT: C 290 ASP cc_start: 0.7918 (m-30) cc_final: 0.7103 (m-30) outliers start: 27 outliers final: 22 residues processed: 156 average time/residue: 0.0969 time to fit residues: 22.5749 Evaluate side-chains 158 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 32 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086521 restraints weight = 22858.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089745 restraints weight = 11462.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.091785 restraints weight = 7628.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093155 restraints weight = 5929.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093966 restraints weight = 5009.426| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11854 Z= 0.124 Angle : 0.612 10.449 16186 Z= 0.297 Chirality : 0.042 0.237 1865 Planarity : 0.004 0.035 2064 Dihedral : 6.641 63.290 1843 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.04 % Allowed : 15.66 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.22), residues: 1504 helix: 0.20 (0.39), residues: 183 sheet: 0.63 (0.23), residues: 573 loop : -0.89 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 29 TYR 0.015 0.001 TYR A 357 PHE 0.019 0.001 PHE H 287 TRP 0.005 0.001 TRP H 49 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00296 (11829) covalent geometry : angle 0.59846 (16126) SS BOND : bond 0.00214 ( 15) SS BOND : angle 0.46365 ( 30) hydrogen bonds : bond 0.02882 ( 414) hydrogen bonds : angle 5.15930 ( 1086) link_BETA1-4 : bond 0.00746 ( 4) link_BETA1-4 : angle 2.73563 ( 12) link_NAG-ASN : bond 0.00450 ( 6) link_NAG-ASN : angle 3.26767 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7804 (mpp) cc_final: 0.7183 (mpp) REVERT: H 420 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: L 130 ASN cc_start: 0.9053 (t0) cc_final: 0.8780 (t0) REVERT: L 200 GLU cc_start: 0.8076 (pp20) cc_final: 0.7446 (pp20) REVERT: A 409 ASN cc_start: 0.8707 (m-40) cc_final: 0.8308 (m-40) REVERT: B 78 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8310 (mp10) REVERT: D 288 GLN cc_start: 0.8277 (tp40) cc_final: 0.7922 (tp40) REVERT: C 290 ASP cc_start: 0.7917 (m-30) cc_final: 0.7108 (m-30) outliers start: 26 outliers final: 22 residues processed: 157 average time/residue: 0.0936 time to fit residues: 22.1220 Evaluate side-chains 158 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.0970 chunk 82 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 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 = 0.3500 r_free = 0.3500 target = 0.112445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087198 restraints weight = 22638.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.090387 restraints weight = 11214.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092465 restraints weight = 7413.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.093684 restraints weight = 5711.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094608 restraints weight = 4851.648| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11854 Z= 0.113 Angle : 0.596 7.860 16186 Z= 0.290 Chirality : 0.042 0.239 1865 Planarity : 0.004 0.034 2064 Dihedral : 6.413 59.419 1843 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.72 % Allowed : 16.05 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.22), residues: 1504 helix: 0.24 (0.39), residues: 183 sheet: 0.68 (0.23), residues: 566 loop : -0.86 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.015 0.001 TYR A 357 PHE 0.015 0.001 PHE C 204 TRP 0.005 0.001 TRP H 49 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd covalent geometry : bond 0.00270 (11829) covalent geometry : angle 0.58323 (16126) SS BOND : bond 0.00202 ( 15) SS BOND : angle 0.43520 ( 30) hydrogen bonds : bond 0.02776 ( 414) hydrogen bonds : angle 5.07935 ( 1086) link_BETA1-4 : bond 0.00759 ( 4) link_BETA1-4 : angle 2.73191 ( 12) link_NAG-ASN : bond 0.00430 ( 6) link_NAG-ASN : angle 3.00297 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.07 seconds wall clock time: 35 minutes 12.61 seconds (2112.61 seconds total)