Starting phenix.real_space_refine on Sat Jul 4 02:51:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzu_48769/07_2026/9mzu_48769_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzu_48769/07_2026/9mzu_48769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzu_48769/07_2026/9mzu_48769_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzu_48769/07_2026/9mzu_48769_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzu_48769/07_2026/9mzu_48769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzu_48769/07_2026/9mzu_48769.map" } resolution = 2.4 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= 0.001 sd= 0.044 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 60 5.16 5 C 11085 2.51 5 N 2916 2.21 5 O 3447 1.98 5 H 6 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17517 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3594 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 27, 'TRANS': 417} Chain: "B" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2111 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 239} Chain: "C" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3594 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 27, 'TRANS': 417} Chain: "D" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2111 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 239} Chain: "E" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3594 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 27, 'TRANS': 417} Chain: "F" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2111 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 239} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Unusual residues: {'FUC': 1, 'GCU': 1, 'GLC': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Unusual residues: {'FUC': 1, 'GCU': 1, 'GLC': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Unusual residues: {'FUC': 1, 'GCU': 1, 'GLC': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Unusual residues: {'FUC': 1, 'GCU': 1, 'GLC': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Unusual residues: {'FUC': 1, 'GCU': 1, 'GLC': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Unusual residues: {'FUC': 1, 'GCU': 1, 'GLC': 1, 'MAN': 1, 'RAM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Classifications: {'water': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.21 Number of scatterers: 17517 At special positions: 0 Unit cell: (184.258, 115.29, 92.6437, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 60 16.00 O 3447 8.00 N 2916 7.00 C 11085 6.00 H 6 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 1 " - " GCU G 2 " " MAN H 1 " - " GCU H 2 " " MAN I 1 " - " GCU I 2 " " MAN J 1 " - " GCU J 2 " " MAN K 1 " - " GCU K 2 " " MAN L 1 " - " GCU L 2 " ALPHA1-4 " GCU G 2 " - " GLC G 3 " " GCU H 2 " - " GLC H 3 " " GCU I 2 " - " GLC I 3 " " GCU J 2 " - " GLC J 3 " " GCU K 2 " - " GLC K 3 " " GCU L 2 " - " GLC L 3 " BETA1-4 " MAN G 1 " - " RAM G 5 " ~> Even though RAM is an alpha isomer, a beta linkage is required... " GLC G 3 " - " FUC G 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN H 1 " - " RAM H 5 " " GLC H 3 " - " FUC H 4 " " MAN I 1 " - " RAM I 5 " " GLC I 3 " - " FUC I 4 " " MAN J 1 " - " RAM J 5 " " GLC J 3 " - " FUC J 4 " " MAN K 1 " - " RAM K 5 " " GLC K 3 " - " FUC K 4 " " MAN L 1 " - " RAM L 5 " " GLC L 3 " - " FUC L 4 " MAN-SER " MAN B 401 " - " SER B 272 " " MAN D 401 " - " SER D 272 " " MAN F 401 " - " SER F 272 " " MAN G 1 " - " SER A 106 " " MAN I 1 " - " SER C 106 " " MAN K 1 " - " SER E 106 " MAN-THR " MAN H 1 " - " THR A 222 " " MAN J 1 " - " THR C 222 " " MAN L 1 " - " THR E 222 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 766.7 milliseconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 31 sheets defined 28.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.658A pdb=" N PHE A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.145A pdb=" N ASN A 203 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 Processing helix chain 'A' and resid 259 through 265 removed outlier: 3.843A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 292 through 310 removed outlier: 3.529A pdb=" N GLY A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.296A pdb=" N ASP A 371 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'B' and resid 49 through 59 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.574A pdb=" N LEU B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 137' Processing helix chain 'B' and resid 214 through 222 Proline residue: B 219 - end of helix Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 269 through 291 Processing helix chain 'C' and resid 92 through 113 removed outlier: 3.685A pdb=" N PHE C 99 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 259 through 265 removed outlier: 3.862A pdb=" N PHE C 265 " --> pdb=" O TRP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 292 through 310 removed outlier: 3.559A pdb=" N GLY C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 368 through 372 removed outlier: 4.128A pdb=" N ASP C 371 " --> pdb=" O TYR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 428 through 431 Processing helix chain 'D' and resid 49 through 59 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.570A pdb=" N LEU D 86 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 132 through 137 removed outlier: 3.534A pdb=" N LEU D 136 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP D 137 " --> pdb=" O GLN D 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 132 through 137' Processing helix chain 'D' and resid 214 through 222 Proline residue: D 219 - end of helix Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 262 through 266 Processing helix chain 'D' and resid 269 through 292 removed outlier: 4.217A pdb=" N PHE D 292 " --> pdb=" O ARG D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 113 removed outlier: 3.679A pdb=" N PHE E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 192 through 196 Processing helix chain 'E' and resid 198 through 203 removed outlier: 4.052A pdb=" N ASN E 203 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 245 Processing helix chain 'E' and resid 259 through 265 removed outlier: 3.804A pdb=" N PHE E 265 " --> pdb=" O TRP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 292 through 310 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 368 through 372 removed outlier: 4.284A pdb=" N ASP E 371 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 431 Processing helix chain 'F' and resid 49 through 59 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.650A pdb=" N LEU F 86 " --> pdb=" O ASN F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 109 Processing helix chain 'F' and resid 132 through 137 removed outlier: 3.581A pdb=" N LEU F 136 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP F 137 " --> pdb=" O GLN F 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 132 through 137' Processing helix chain 'F' and resid 214 through 222 Proline residue: F 219 - end of helix Processing helix chain 'F' and resid 239 through 245 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 269 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 127 removed outlier: 5.815A pdb=" N GLU A 127 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N THR A 135 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 164 Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 185 Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 225 Processing sheet with id=AA7, first strand: chain 'A' and resid 453 through 457 removed outlier: 7.363A pdb=" N GLN A 433 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR A 402 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL A 435 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA A 397 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.536A pdb=" N PHE B 210 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.536A pdb=" N PHE B 210 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 172 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE B 191 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR B 170 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 168 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET B 195 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 166 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL B 71 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR B 255 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR B 73 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AB2, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 62 Processing sheet with id=AB4, first strand: chain 'C' and resid 124 through 127 removed outlier: 6.374A pdb=" N GLU C 127 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR C 135 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 164 Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 185 Processing sheet with id=AB7, first strand: chain 'C' and resid 217 through 225 Processing sheet with id=AB8, first strand: chain 'C' and resid 453 through 457 removed outlier: 7.371A pdb=" N GLN C 433 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR C 402 " --> pdb=" O GLN C 433 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL C 435 " --> pdb=" O THR C 400 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 397 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.651A pdb=" N PHE D 210 " --> pdb=" O PRO D 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 115 through 116 removed outlier: 4.651A pdb=" N PHE D 210 " --> pdb=" O PRO D 193 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS D 172 " --> pdb=" O GLN D 189 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 191 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR D 170 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA D 168 " --> pdb=" O PRO D 193 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET D 195 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL D 166 " --> pdb=" O MET D 195 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL D 71 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR D 255 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR D 73 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AC3, first strand: chain 'D' and resid 225 through 226 Processing sheet with id=AC4, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 57 through 62 Processing sheet with id=AC6, first strand: chain 'E' and resid 124 through 127 removed outlier: 5.987A pdb=" N GLU E 127 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N THR E 135 " --> pdb=" O GLU E 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 162 through 164 Processing sheet with id=AC8, first strand: chain 'E' and resid 179 through 185 Processing sheet with id=AC9, first strand: chain 'E' and resid 217 through 225 Processing sheet with id=AD1, first strand: chain 'E' and resid 453 through 457 removed outlier: 7.341A pdb=" N GLN E 433 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR E 402 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL E 435 " --> pdb=" O THR E 400 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ALA E 397 " --> pdb=" O GLY E 466 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 115 through 116 removed outlier: 4.684A pdb=" N PHE F 210 " --> pdb=" O PRO F 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 115 through 116 removed outlier: 4.684A pdb=" N PHE F 210 " --> pdb=" O PRO F 193 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS F 172 " --> pdb=" O GLN F 189 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE F 191 " --> pdb=" O TYR F 170 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR F 170 " --> pdb=" O ILE F 191 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA F 168 " --> pdb=" O PRO F 193 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET F 195 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL F 166 " --> pdb=" O MET F 195 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL F 71 " --> pdb=" O THR F 255 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR F 255 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR F 73 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP F 251 " --> pdb=" O ARG F 75 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 225 through 226 509 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.85 - 1.04: 6 1.04 - 1.23: 412 1.23 - 1.42: 7559 1.42 - 1.62: 9888 1.62 - 1.81: 102 Bond restraints: 17967 Sorted by residual: bond pdb=" C1 RAM H 5 " pdb=" O5 RAM H 5 " ideal model delta sigma weight residual 1.401 1.463 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C1 RAM J 5 " pdb=" O5 RAM J 5 " ideal model delta sigma weight residual 1.401 1.462 -0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" C1 RAM L 5 " pdb=" O5 RAM L 5 " ideal model delta sigma weight residual 1.401 1.461 -0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" C1 RAM L 5 " pdb=" C2 RAM L 5 " ideal model delta sigma weight residual 1.530 1.586 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C1 RAM H 5 " pdb=" C2 RAM H 5 " ideal model delta sigma weight residual 1.530 1.585 -0.055 2.00e-02 2.50e+03 7.49e+00 ... (remaining 17962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 23979 1.56 - 3.13: 350 3.13 - 4.69: 50 4.69 - 6.25: 14 6.25 - 7.82: 3 Bond angle restraints: 24396 Sorted by residual: angle pdb=" OG1 THR B 47 " pdb=" CB THR B 47 " pdb=" CG2 THR B 47 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.94e+00 angle pdb=" OG1 THR D 47 " pdb=" CB THR D 47 " pdb=" CG2 THR D 47 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.93e+00 angle pdb=" OG1 THR F 47 " pdb=" CB THR F 47 " pdb=" CG2 THR F 47 " ideal model delta sigma weight residual 109.30 103.34 5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" N GLY C 366 " pdb=" CA GLY C 366 " pdb=" C GLY C 366 " ideal model delta sigma weight residual 115.30 111.36 3.94 1.44e+00 4.82e-01 7.50e+00 angle pdb=" C1 GLC K 3 " pdb=" O5 GLC K 3 " pdb=" C5 GLC K 3 " ideal model delta sigma weight residual 116.10 123.92 -7.82 3.00e+00 1.11e-01 6.79e+00 ... (remaining 24391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.18: 9860 20.18 - 40.36: 992 40.36 - 60.54: 270 60.54 - 80.71: 27 80.71 - 100.89: 20 Dihedral angle restraints: 11169 sinusoidal: 4998 harmonic: 6171 Sorted by residual: dihedral pdb=" C2 GLC G 3 " pdb=" C1 GLC G 3 " pdb=" O5 GLC G 3 " pdb=" C5 GLC G 3 " ideal model delta sinusoidal sigma weight residual -59.66 41.23 -100.89 1 3.00e+01 1.11e-03 1.27e+01 dihedral pdb=" C2 GLC K 3 " pdb=" C1 GLC K 3 " pdb=" O5 GLC K 3 " pdb=" C5 GLC K 3 " ideal model delta sinusoidal sigma weight residual -59.66 41.05 -100.71 1 3.00e+01 1.11e-03 1.26e+01 dihedral pdb=" CA ASN A 385 " pdb=" C ASN A 385 " pdb=" N ASP A 386 " pdb=" CA ASP A 386 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 11166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1988 0.041 - 0.083: 465 0.083 - 0.124: 169 0.124 - 0.166: 13 0.166 - 0.207: 5 Chirality restraints: 2640 Sorted by residual: chirality pdb=" C1 RAM L 5 " pdb=" O4 MAN L 1 " pdb=" C2 RAM L 5 " pdb=" O5 RAM L 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.32e+00 chirality pdb=" C1 RAM H 5 " pdb=" O4 MAN H 1 " pdb=" C2 RAM H 5 " pdb=" O5 RAM H 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.26e+00 chirality pdb=" C1 RAM J 5 " pdb=" O4 MAN J 1 " pdb=" C2 RAM J 5 " pdb=" O5 RAM J 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.64e+00 ... (remaining 2637 not shown) Planarity restraints: 3147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 343 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 344 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 343 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO C 344 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 343 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 344 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 344 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 344 " -0.019 5.00e-02 4.00e+02 ... (remaining 3144 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.56: 49 2.56 - 3.07: 11772 3.07 - 3.58: 19433 3.58 - 4.09: 33112 4.09 - 4.60: 47057 Nonbonded interactions: 111423 Sorted by model distance: nonbonded pdb="CA CA E 501 " pdb=" O HOH E 601 " model vdw 2.048 3.130 nonbonded pdb="CA CA C 501 " pdb=" O HOH C 601 " model vdw 2.086 3.130 nonbonded pdb="CA CA A 501 " pdb=" O HOH A 601 " model vdw 2.093 3.130 nonbonded pdb=" OE2 GLU C 90 " pdb="CA CA C 501 " model vdw 2.169 3.130 nonbonded pdb=" O ASP C 391 " pdb="CA CA C 501 " model vdw 2.176 3.130 ... (remaining 111418 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.730 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17994 Z= 0.126 Angle : 0.530 8.407 24483 Z= 0.257 Chirality : 0.041 0.207 2640 Planarity : 0.003 0.043 3147 Dihedral : 17.084 100.893 7209 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 2.00 % Allowed : 22.40 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2082 helix: 1.09 (0.25), residues: 462 sheet: -0.43 (0.30), residues: 285 loop : 0.10 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 261 TYR 0.010 0.001 TYR C 102 PHE 0.014 0.001 PHE C 306 TRP 0.016 0.001 TRP E 399 HIS 0.002 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17961) covalent geometry : angle 0.49518 / 0.25 (24393) hydrogen bonds : bond 0.14053 / 9.80 ( 497) hydrogen bonds : angle 5.93969 / 4.15 ( 1353) link_ALPHA1-2 : bond 0.00725 / 0.43 ( 6) link_ALPHA1-2 : angle 4.06647 / 2.00 ( 18) link_ALPHA1-4 : bond 0.01085 / 0.67 ( 6) link_ALPHA1-4 : angle 3.29539 / 1.63 ( 18) link_BETA1-4 : bond 0.02734 / 1.79 ( 12) link_BETA1-4 : angle 3.07109 / 1.70 ( 36) link_MAN-SER : bond 0.00319 / 0.19 ( 6) link_MAN-SER : angle 1.59627 / 0.85 ( 12) link_MAN-THR : bond 0.00408 / 0.23 ( 3) link_MAN-THR : angle 2.61836 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: C 254 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8318 (pp) REVERT: F 205 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7977 (tmm-80) outliers start: 37 outliers final: 19 residues processed: 173 average time/residue: 0.7522 time to fit residues: 142.2705 Evaluate side-chains 146 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 205 ARG Chi-restraints excluded: chain F residue 261 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 overall best weight: 0.2318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 ASN C 203 ASN C 341 ASN D 127 GLN D 144 GLN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 GLN ** F 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.059405 restraints weight = 33512.213| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.65 r_work: 0.2680 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17994 Z= 0.084 Angle : 0.464 7.907 24483 Z= 0.227 Chirality : 0.040 0.171 2640 Planarity : 0.003 0.036 3147 Dihedral : 7.652 95.269 3071 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.93 % Rotamer: Outliers : 2.11 % Allowed : 22.51 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.66 (0.19), residues: 2082 helix: 1.40 (0.25), residues: 483 sheet: -0.11 (0.30), residues: 273 loop : 0.30 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 149 TYR 0.011 0.001 TYR F 142 PHE 0.012 0.001 PHE C 306 TRP 0.013 0.001 TRP C 399 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.08 (17961) covalent geometry : angle 0.44874 / 0.22 (24393) hydrogen bonds : bond 0.03411 / 2.28 ( 497) hydrogen bonds : angle 4.99854 / 3.46 ( 1353) link_ALPHA1-2 : bond 0.00418 / 0.25 ( 6) link_ALPHA1-2 : angle 2.22334 / 1.14 ( 18) link_ALPHA1-4 : bond 0.00844 / 0.52 ( 6) link_ALPHA1-4 : angle 2.43754 / 1.21 ( 18) link_BETA1-4 : bond 0.00527 / 0.37 ( 12) link_BETA1-4 : angle 1.84714 / 1.06 ( 36) link_MAN-SER : bond 0.00027 / 0.02 ( 6) link_MAN-SER : angle 0.60057 / 0.30 ( 12) link_MAN-THR : bond 0.00430 / 0.25 ( 3) link_MAN-THR : angle 2.41955 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.718 Fit side-chains REVERT: A 65 GLU cc_start: 0.8123 (pm20) cc_final: 0.7664 (pp20) REVERT: B 144 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8499 (mm-40) REVERT: C 155 ILE cc_start: 0.8614 (tp) cc_final: 0.8325 (pp) REVERT: C 240 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9081 (tp) REVERT: D 57 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8069 (ptp90) REVERT: D 205 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6812 (ptp90) REVERT: E 474 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8325 (pp) REVERT: F 144 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8315 (mm110) outliers start: 39 outliers final: 16 residues processed: 155 average time/residue: 0.7582 time to fit residues: 129.0077 Evaluate side-chains 141 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 319 MET Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 205 ARG Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 138 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN D 127 GLN ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.054313 restraints weight = 34568.253| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.65 r_work: 0.2560 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 17994 Z= 0.323 Angle : 0.589 8.193 24483 Z= 0.288 Chirality : 0.046 0.223 2640 Planarity : 0.004 0.037 3147 Dihedral : 8.038 104.211 3051 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 3.46 % Allowed : 21.37 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.49 (0.19), residues: 2082 helix: 1.49 (0.25), residues: 465 sheet: -0.32 (0.30), residues: 285 loop : 0.13 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 149 TYR 0.013 0.001 TYR C 102 PHE 0.017 0.002 PHE E 306 TRP 0.012 0.001 TRP C 399 HIS 0.003 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00757 / 0.32 (17961) covalent geometry : angle 0.57081 / 0.28 (24393) hydrogen bonds : bond 0.04623 / 3.14 ( 497) hydrogen bonds : angle 5.38705 / 3.72 ( 1353) link_ALPHA1-2 : bond 0.00488 / 0.29 ( 6) link_ALPHA1-2 : angle 2.97179 / 1.49 ( 18) link_ALPHA1-4 : bond 0.00506 / 0.30 ( 6) link_ALPHA1-4 : angle 2.83529 / 1.41 ( 18) link_BETA1-4 : bond 0.00754 / 0.53 ( 12) link_BETA1-4 : angle 2.31472 / 1.32 ( 36) link_MAN-SER : bond 0.00672 / 0.41 ( 6) link_MAN-SER : angle 1.19473 / 0.64 ( 12) link_MAN-THR : bond 0.00422 / 0.24 ( 3) link_MAN-THR : angle 2.18138 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 117 time to evaluate : 0.735 Fit side-chains REVERT: A 90 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9238 (pt0) REVERT: C 149 ARG cc_start: 0.8703 (tpp80) cc_final: 0.8387 (tpp-160) REVERT: D 142 TYR cc_start: 0.8734 (t80) cc_final: 0.8520 (t80) REVERT: E 311 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (tp) REVERT: F 48 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9117 (mp) outliers start: 64 outliers final: 38 residues processed: 164 average time/residue: 0.7108 time to fit residues: 128.8192 Evaluate side-chains 160 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 454 SER Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 126 optimal weight: 0.6980 chunk 82 optimal weight: 0.0060 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN D 127 GLN D 144 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.056437 restraints weight = 33998.249| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.65 r_work: 0.2594 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17994 Z= 0.111 Angle : 0.478 7.409 24483 Z= 0.232 Chirality : 0.041 0.178 2640 Planarity : 0.003 0.041 3147 Dihedral : 7.387 99.725 3049 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 1.95 % Allowed : 22.62 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.69 (0.19), residues: 2082 helix: 1.78 (0.25), residues: 465 sheet: -0.28 (0.30), residues: 285 loop : 0.24 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 149 TYR 0.007 0.001 TYR C 102 PHE 0.010 0.001 PHE C 306 TRP 0.012 0.001 TRP C 399 HIS 0.002 0.000 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (17961) covalent geometry : angle 0.46100 / 0.23 (24393) hydrogen bonds : bond 0.03580 / 2.40 ( 497) hydrogen bonds : angle 4.98179 / 3.45 ( 1353) link_ALPHA1-2 : bond 0.00377 / 0.22 ( 6) link_ALPHA1-2 : angle 2.46642 / 1.26 ( 18) link_ALPHA1-4 : bond 0.00731 / 0.45 ( 6) link_ALPHA1-4 : angle 2.50433 / 1.25 ( 18) link_BETA1-4 : bond 0.00522 / 0.37 ( 12) link_BETA1-4 : angle 2.09162 / 1.21 ( 36) link_MAN-SER : bond 0.00116 / 0.07 ( 6) link_MAN-SER : angle 0.66929 / 0.35 ( 12) link_MAN-THR : bond 0.00332 / 0.19 ( 3) link_MAN-THR : angle 2.10980 / 1.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.717 Fit side-chains REVERT: A 64 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8972 (mmmm) REVERT: A 65 GLU cc_start: 0.8151 (pm20) cc_final: 0.7793 (pp20) REVERT: A 98 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9064 (tt0) REVERT: C 149 ARG cc_start: 0.8735 (tpp80) cc_final: 0.7871 (tpp80) REVERT: D 144 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8214 (mm110) REVERT: F 48 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9096 (mp) outliers start: 36 outliers final: 18 residues processed: 150 average time/residue: 0.7120 time to fit residues: 117.6078 Evaluate side-chains 145 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 118 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 127 GLN ** D 246 ASN ** 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 = 0.3169 r_free = 0.3169 target = 0.079281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.055106 restraints weight = 34146.185| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.64 r_work: 0.2583 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 17994 Z= 0.214 Angle : 0.523 7.388 24483 Z= 0.254 Chirality : 0.043 0.200 2640 Planarity : 0.003 0.043 3147 Dihedral : 7.458 101.406 3048 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 2.71 % Allowed : 21.75 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.66 (0.19), residues: 2082 helix: 1.78 (0.25), residues: 465 sheet: -0.27 (0.30), residues: 285 loop : 0.21 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 149 TYR 0.011 0.001 TYR A 102 PHE 0.013 0.001 PHE F 100 TRP 0.012 0.001 TRP C 399 HIS 0.002 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (17961) covalent geometry : angle 0.50536 / 0.25 (24393) hydrogen bonds : bond 0.03934 / 2.67 ( 497) hydrogen bonds : angle 5.08275 / 3.51 ( 1353) link_ALPHA1-2 : bond 0.00415 / 0.24 ( 6) link_ALPHA1-2 : angle 2.68335 / 1.36 ( 18) link_ALPHA1-4 : bond 0.00564 / 0.34 ( 6) link_ALPHA1-4 : angle 2.56583 / 1.28 ( 18) link_BETA1-4 : bond 0.00638 / 0.45 ( 12) link_BETA1-4 : angle 2.21308 / 1.28 ( 36) link_MAN-SER : bond 0.00408 / 0.25 ( 6) link_MAN-SER : angle 0.88478 / 0.46 ( 12) link_MAN-THR : bond 0.00129 / 0.07 ( 3) link_MAN-THR : angle 1.89768 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8232 (pm20) cc_final: 0.7810 (pp20) REVERT: A 90 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9141 (pt0) REVERT: B 189 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.8839 (mm-40) REVERT: C 149 ARG cc_start: 0.8668 (tpp80) cc_final: 0.8278 (tpp80) REVERT: C 188 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7489 (mmt-90) REVERT: D 57 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7383 (ttp80) REVERT: D 144 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8267 (mm110) REVERT: E 311 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8288 (tp) REVERT: F 48 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9123 (mp) outliers start: 50 outliers final: 32 residues processed: 159 average time/residue: 0.7359 time to fit residues: 128.5907 Evaluate side-chains 162 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 294 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** 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 = 0.3193 r_free = 0.3193 target = 0.080761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.056611 restraints weight = 33765.158| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.64 r_work: 0.2614 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17994 Z= 0.110 Angle : 0.469 7.757 24483 Z= 0.226 Chirality : 0.041 0.175 2640 Planarity : 0.003 0.042 3147 Dihedral : 7.017 96.695 3048 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 1.79 % Allowed : 22.56 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.82 (0.19), residues: 2082 helix: 1.97 (0.25), residues: 465 sheet: -0.23 (0.30), residues: 285 loop : 0.30 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 149 TYR 0.007 0.001 TYR C 102 PHE 0.009 0.001 PHE C 306 TRP 0.013 0.001 TRP C 399 HIS 0.001 0.000 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17961) covalent geometry : angle 0.45214 / 0.22 (24393) hydrogen bonds : bond 0.03365 / 2.26 ( 497) hydrogen bonds : angle 4.81010 / 3.33 ( 1353) link_ALPHA1-2 : bond 0.00392 / 0.23 ( 6) link_ALPHA1-2 : angle 2.40785 / 1.23 ( 18) link_ALPHA1-4 : bond 0.00693 / 0.43 ( 6) link_ALPHA1-4 : angle 2.40435 / 1.20 ( 18) link_BETA1-4 : bond 0.00516 / 0.36 ( 12) link_BETA1-4 : angle 2.09760 / 1.21 ( 36) link_MAN-SER : bond 0.00114 / 0.07 ( 6) link_MAN-SER : angle 0.65830 / 0.33 ( 12) link_MAN-THR : bond 0.00301 / 0.17 ( 3) link_MAN-THR : angle 2.00742 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.742 Fit side-chains REVERT: A 65 GLU cc_start: 0.8236 (pm20) cc_final: 0.7788 (pp20) REVERT: A 98 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9070 (tt0) REVERT: A 209 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8384 (mmtm) REVERT: A 276 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8558 (mmm) REVERT: D 57 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7788 (ptp90) REVERT: D 144 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8365 (mm110) REVERT: F 48 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9095 (mp) outliers start: 33 outliers final: 20 residues processed: 150 average time/residue: 0.7326 time to fit residues: 121.1471 Evaluate side-chains 152 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 chunk 156 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 0.0770 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 127 GLN ** D 246 ASN ** 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 = 0.3214 r_free = 0.3214 target = 0.081921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057879 restraints weight = 33704.804| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.64 r_work: 0.2640 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 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 : 0.002 0.038 17994 Z= 0.089 Angle : 0.450 8.879 24483 Z= 0.216 Chirality : 0.040 0.162 2640 Planarity : 0.002 0.045 3147 Dihedral : 6.401 86.682 3046 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 22.94 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2082 helix: 2.18 (0.26), residues: 465 sheet: 0.06 (0.29), residues: 309 loop : 0.38 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 149 TYR 0.006 0.001 TYR C 102 PHE 0.010 0.001 PHE C 306 TRP 0.012 0.001 TRP C 399 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (17961) covalent geometry : angle 0.43436 / 0.21 (24393) hydrogen bonds : bond 0.03018 / 2.01 ( 497) hydrogen bonds : angle 4.55832 / 3.15 ( 1353) link_ALPHA1-2 : bond 0.00438 / 0.26 ( 6) link_ALPHA1-2 : angle 2.21613 / 1.14 ( 18) link_ALPHA1-4 : bond 0.00737 / 0.46 ( 6) link_ALPHA1-4 : angle 2.30865 / 1.16 ( 18) link_BETA1-4 : bond 0.00510 / 0.36 ( 12) link_BETA1-4 : angle 2.02676 / 1.17 ( 36) link_MAN-SER : bond 0.00043 / 0.03 ( 6) link_MAN-SER : angle 0.62529 / 0.31 ( 12) link_MAN-THR : bond 0.00382 / 0.22 ( 3) link_MAN-THR : angle 1.81685 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8294 (pm20) cc_final: 0.7785 (pp20) REVERT: A 98 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.9059 (tt0) REVERT: A 209 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8404 (mmtm) REVERT: A 276 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8549 (mmm) REVERT: D 57 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7510 (ptp90) REVERT: D 144 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8409 (mm110) REVERT: E 474 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (pp) REVERT: F 48 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9076 (mp) outliers start: 31 outliers final: 16 residues processed: 150 average time/residue: 0.6629 time to fit residues: 109.5384 Evaluate side-chains 149 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 7 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.054390 restraints weight = 34345.557| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.64 r_work: 0.2569 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2459 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 17994 Z= 0.297 Angle : 0.568 8.696 24483 Z= 0.276 Chirality : 0.045 0.210 2640 Planarity : 0.003 0.057 3147 Dihedral : 6.881 89.818 3044 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 2.38 % Allowed : 22.40 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.75 (0.19), residues: 2082 helix: 1.85 (0.25), residues: 465 sheet: -0.22 (0.31), residues: 285 loop : 0.26 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 149 TYR 0.013 0.001 TYR C 102 PHE 0.015 0.002 PHE F 100 TRP 0.010 0.001 TRP C 399 HIS 0.003 0.001 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00691 / 0.30 (17961) covalent geometry : angle 0.55175 / 0.27 (24393) hydrogen bonds : bond 0.04120 / 2.79 ( 497) hydrogen bonds : angle 5.07375 / 3.50 ( 1353) link_ALPHA1-2 : bond 0.00432 / 0.25 ( 6) link_ALPHA1-2 : angle 2.76170 / 1.39 ( 18) link_ALPHA1-4 : bond 0.00568 / 0.34 ( 6) link_ALPHA1-4 : angle 2.62023 / 1.31 ( 18) link_BETA1-4 : bond 0.00745 / 0.52 ( 12) link_BETA1-4 : angle 2.29986 / 1.33 ( 36) link_MAN-SER : bond 0.00614 / 0.37 ( 6) link_MAN-SER : angle 0.98839 / 0.53 ( 12) link_MAN-THR : bond 0.00419 / 0.24 ( 3) link_MAN-THR : angle 1.71892 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 98 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.9083 (tt0) REVERT: A 151 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7447 (p) REVERT: A 209 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8390 (mmtm) REVERT: C 188 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7516 (mmp80) REVERT: D 57 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7375 (ttp80) REVERT: D 144 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8455 (mm-40) REVERT: E 311 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8319 (tp) REVERT: F 48 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9128 (mp) outliers start: 44 outliers final: 35 residues processed: 157 average time/residue: 0.6337 time to fit residues: 109.6258 Evaluate side-chains 163 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.056321 restraints weight = 34066.257| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.65 r_work: 0.2586 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17994 Z= 0.108 Angle : 0.486 9.366 24483 Z= 0.235 Chirality : 0.041 0.176 2640 Planarity : 0.003 0.054 3147 Dihedral : 6.350 82.826 3044 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.06 % Allowed : 22.78 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.92 (0.19), residues: 2082 helix: 2.05 (0.25), residues: 465 sheet: -0.20 (0.31), residues: 285 loop : 0.37 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 149 TYR 0.007 0.001 TYR C 102 PHE 0.011 0.001 PHE C 306 TRP 0.012 0.001 TRP C 399 HIS 0.001 0.000 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17961) covalent geometry : angle 0.46950 / 0.23 (24393) hydrogen bonds : bond 0.03397 / 2.28 ( 497) hydrogen bonds : angle 4.79749 / 3.32 ( 1353) link_ALPHA1-2 : bond 0.00398 / 0.24 ( 6) link_ALPHA1-2 : angle 2.38955 / 1.22 ( 18) link_ALPHA1-4 : bond 0.00807 / 0.50 ( 6) link_ALPHA1-4 : angle 2.47609 / 1.24 ( 18) link_BETA1-4 : bond 0.00536 / 0.38 ( 12) link_BETA1-4 : angle 2.14256 / 1.24 ( 36) link_MAN-SER : bond 0.00111 / 0.07 ( 6) link_MAN-SER : angle 0.68570 / 0.35 ( 12) link_MAN-THR : bond 0.00266 / 0.15 ( 3) link_MAN-THR : angle 1.88765 / 0.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.704 Fit side-chains REVERT: A 65 GLU cc_start: 0.8203 (pm20) cc_final: 0.7932 (pp20) REVERT: A 98 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9073 (tt0) REVERT: A 151 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7391 (p) REVERT: A 209 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8389 (mmtm) REVERT: A 276 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8570 (mmm) REVERT: D 57 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7505 (ttp80) REVERT: D 144 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8488 (mm110) REVERT: E 474 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (pp) REVERT: F 48 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9108 (mp) outliers start: 38 outliers final: 25 residues processed: 150 average time/residue: 0.6555 time to fit residues: 108.9418 Evaluate side-chains 154 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN D 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.077213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.053028 restraints weight = 34539.872| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 2.65 r_work: 0.2542 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.164 17994 Z= 0.421 Angle : 0.658 9.110 24483 Z= 0.320 Chirality : 0.049 0.240 2640 Planarity : 0.004 0.063 3147 Dihedral : 7.211 92.882 3044 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 2.27 % Allowed : 22.56 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.48 (0.19), residues: 2082 helix: 1.54 (0.25), residues: 465 sheet: -0.28 (0.31), residues: 285 loop : 0.10 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 149 TYR 0.015 0.001 TYR C 102 PHE 0.018 0.002 PHE D 100 TRP 0.012 0.002 TRP E 399 HIS 0.004 0.001 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00982 / 0.42 (17961) covalent geometry : angle 0.64025 / 0.32 (24393) hydrogen bonds : bond 0.04717 / 3.21 ( 497) hydrogen bonds : angle 5.40653 / 3.73 ( 1353) link_ALPHA1-2 : bond 0.00433 / 0.25 ( 6) link_ALPHA1-2 : angle 3.04374 / 1.52 ( 18) link_ALPHA1-4 : bond 0.00579 / 0.35 ( 6) link_ALPHA1-4 : angle 2.86606 / 1.44 ( 18) link_BETA1-4 : bond 0.00940 / 0.66 ( 12) link_BETA1-4 : angle 2.59925 / 1.49 ( 36) link_MAN-SER : bond 0.00915 / 0.55 ( 6) link_MAN-SER : angle 1.26680 / 0.70 ( 12) link_MAN-THR : bond 0.00750 / 0.42 ( 3) link_MAN-THR : angle 1.84036 / 0.90 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.472 Fit side-chains REVERT: A 98 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.9098 (tt0) REVERT: A 209 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (mmtm) REVERT: B 189 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.8840 (mm-40) REVERT: D 57 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7801 (ttp80) REVERT: D 144 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8600 (mm110) REVERT: F 48 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9161 (mp) outliers start: 42 outliers final: 32 residues processed: 151 average time/residue: 0.6697 time to fit residues: 111.8339 Evaluate side-chains 153 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 chunk 93 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.055344 restraints weight = 34179.554| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.66 r_work: 0.2587 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17994 Z= 0.134 Angle : 0.508 9.636 24483 Z= 0.246 Chirality : 0.041 0.196 2640 Planarity : 0.003 0.037 3147 Dihedral : 6.489 87.303 3044 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.73 % Allowed : 23.27 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 2082 helix: 1.88 (0.25), residues: 465 sheet: -0.21 (0.31), residues: 285 loop : 0.27 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 149 TYR 0.007 0.001 TYR C 102 PHE 0.011 0.001 PHE C 306 TRP 0.012 0.001 TRP E 399 HIS 0.001 0.000 HIS E 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (17961) covalent geometry : angle 0.49038 / 0.24 (24393) hydrogen bonds : bond 0.03594 / 2.42 ( 497) hydrogen bonds : angle 4.96591 / 3.43 ( 1353) link_ALPHA1-2 : bond 0.00356 / 0.21 ( 6) link_ALPHA1-2 : angle 2.50362 / 1.28 ( 18) link_ALPHA1-4 : bond 0.00846 / 0.52 ( 6) link_ALPHA1-4 : angle 2.57916 / 1.29 ( 18) link_BETA1-4 : bond 0.00556 / 0.39 ( 12) link_BETA1-4 : angle 2.26053 / 1.31 ( 36) link_MAN-SER : bond 0.00213 / 0.13 ( 6) link_MAN-SER : angle 0.72739 / 0.37 ( 12) link_MAN-THR : bond 0.00213 / 0.12 ( 3) link_MAN-THR : angle 1.96128 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6577.45 seconds wall clock time: 112 minutes 57.16 seconds (6777.16 seconds total)