Starting phenix.real_space_refine on Thu Sep 18 15:20:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzu_48769/09_2025/9mzu_48769_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzu_48769/09_2025/9mzu_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_48769/09_2025/9mzu_48769_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzu_48769/09_2025/9mzu_48769_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzu_48769/09_2025/9mzu_48769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzu_48769/09_2025/9mzu_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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: 3.88, per 1000 atoms: 0.22 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: 1.63 Conformation dependent library (CDL) restraints added in 521.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 2.80 Time building geometry restraints manager: 2.03 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 2.390 nonbonded pdb="CA CA C 501 " pdb=" O HOH C 601 " model vdw 2.086 2.390 nonbonded pdb="CA CA A 501 " pdb=" O HOH A 601 " model vdw 2.093 2.390 nonbonded pdb=" OE2 GLU C 90 " pdb="CA CA C 501 " model vdw 2.169 2.390 nonbonded pdb=" O ASP C 391 " pdb="CA CA C 501 " model vdw 2.176 2.390 ... (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: 12.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.000 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 aren 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 covalent geometry : bond 0.00264 (17961) covalent geometry : angle 0.49518 (24393) hydrogen bonds : bond 0.14053 ( 497) hydrogen bonds : angle 5.93969 ( 1353) link_ALPHA1-2 : bond 0.00725 ( 6) link_ALPHA1-2 : angle 4.06647 ( 18) link_ALPHA1-4 : bond 0.01085 ( 6) link_ALPHA1-4 : angle 3.29539 ( 18) link_BETA1-4 : bond 0.02734 ( 12) link_BETA1-4 : angle 3.07109 ( 36) link_MAN-SER : bond 0.00319 ( 6) link_MAN-SER : angle 1.59627 ( 12) link_MAN-THR : bond 0.00408 ( 3) link_MAN-THR : angle 2.61836 ( 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 : 0.571 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: 0.7662 time to fit residues: 144.5609 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 : 0.638 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3229 r_free = 0.3229 target = 0.083493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.059193 restraints weight = 33536.351| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.65 r_work: 0.2670 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.0949 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= 0.082 Angle : 0.462 7.926 24483 Z= 0.225 Chirality : 0.040 0.177 2640 Planarity : 0.003 0.041 3147 Dihedral : 7.654 95.159 3071 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 2.11 % Allowed : 22.67 % 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 aren not related in a simple way. whole: 0.66 (0.19), residues: 2082 helix: 1.39 (0.25), residues: 483 sheet: -0.26 (0.30), residues: 279 loop : 0.34 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 149 TYR 0.013 0.001 TYR F 142 PHE 0.012 0.001 PHE C 306 TRP 0.014 0.001 TRP C 399 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00186 (17961) covalent geometry : angle 0.44693 (24393) hydrogen bonds : bond 0.03509 ( 497) hydrogen bonds : angle 4.99354 ( 1353) link_ALPHA1-2 : bond 0.00425 ( 6) link_ALPHA1-2 : angle 2.24795 ( 18) link_ALPHA1-4 : bond 0.00862 ( 6) link_ALPHA1-4 : angle 2.42860 ( 18) link_BETA1-4 : bond 0.00531 ( 12) link_BETA1-4 : angle 1.86126 ( 36) link_MAN-SER : bond 0.00030 ( 6) link_MAN-SER : angle 0.61347 ( 12) link_MAN-THR : bond 0.00446 ( 3) link_MAN-THR : angle 2.34294 ( 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 167 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.649 Fit side-chains REVERT: A 65 GLU cc_start: 0.8115 (pm20) cc_final: 0.7676 (pp20) REVERT: B 144 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8513 (mm-40) REVERT: C 155 ILE cc_start: 0.8622 (tp) cc_final: 0.8339 (pp) REVERT: C 240 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9085 (tp) REVERT: D 57 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8076 (ptp90) REVERT: D 144 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8350 (mm110) REVERT: D 205 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6810 (ptp90) REVERT: E 474 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8325 (pp) REVERT: F 144 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8316 (mm110) outliers start: 39 outliers final: 16 residues processed: 154 average time/residue: 0.6867 time to fit residues: 115.5243 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 : 0.455 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.0000 chunk 2 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3157 r_free = 0.3157 target = 0.078762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.054370 restraints weight = 34557.235| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.67 r_work: 0.2582 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 17994 Z= 0.313 Angle : 0.580 8.023 24483 Z= 0.283 Chirality : 0.046 0.223 2640 Planarity : 0.004 0.038 3147 Dihedral : 7.974 102.922 3051 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 3.63 % Allowed : 21.16 % 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 aren not related in a simple way. whole: 0.50 (0.19), residues: 2082 helix: 1.53 (0.25), residues: 465 sheet: -0.31 (0.30), residues: 285 loop : 0.13 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 149 TYR 0.013 0.001 TYR C 102 PHE 0.016 0.002 PHE E 306 TRP 0.013 0.001 TRP C 399 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00727 (17961) covalent geometry : angle 0.56277 (24393) hydrogen bonds : bond 0.04577 ( 497) hydrogen bonds : angle 5.34548 ( 1353) link_ALPHA1-2 : bond 0.00468 ( 6) link_ALPHA1-2 : angle 2.89742 ( 18) link_ALPHA1-4 : bond 0.00508 ( 6) link_ALPHA1-4 : angle 2.76582 ( 18) link_BETA1-4 : bond 0.00710 ( 12) link_BETA1-4 : angle 2.27062 ( 36) link_MAN-SER : bond 0.00703 ( 6) link_MAN-SER : angle 1.12892 ( 12) link_MAN-THR : bond 0.00428 ( 3) link_MAN-THR : angle 2.11444 ( 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 186 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 119 time to evaluate : 0.692 Fit side-chains REVERT: C 149 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8414 (tpp-160) REVERT: D 144 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8402 (mm110) REVERT: E 311 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8292 (tp) REVERT: F 48 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9115 (mp) outliers start: 67 outliers final: 39 residues processed: 165 average time/residue: 0.6613 time to fit residues: 120.5746 Evaluate side-chains 162 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 275 MET 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 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: 0.0970 chunk 34 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN 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 = 0.3193 r_free = 0.3193 target = 0.080880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.056653 restraints weight = 33958.994| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.65 r_work: 0.2587 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17994 Z= 0.107 Angle : 0.470 7.673 24483 Z= 0.228 Chirality : 0.041 0.173 2640 Planarity : 0.003 0.044 3147 Dihedral : 7.292 98.146 3049 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 1.79 % Allowed : 22.84 % 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 aren not related in a simple way. whole: 0.72 (0.19), residues: 2082 helix: 1.81 (0.25), residues: 465 sheet: -0.27 (0.30), residues: 285 loop : 0.26 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 149 TYR 0.007 0.001 TYR E 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 covalent geometry : bond 0.00245 (17961) covalent geometry : angle 0.45323 (24393) hydrogen bonds : bond 0.03484 ( 497) hydrogen bonds : angle 4.91721 ( 1353) link_ALPHA1-2 : bond 0.00380 ( 6) link_ALPHA1-2 : angle 2.42162 ( 18) link_ALPHA1-4 : bond 0.00737 ( 6) link_ALPHA1-4 : angle 2.46119 ( 18) link_BETA1-4 : bond 0.00521 ( 12) link_BETA1-4 : angle 2.06504 ( 36) link_MAN-SER : bond 0.00101 ( 6) link_MAN-SER : angle 0.62270 ( 12) link_MAN-THR : bond 0.00383 ( 3) link_MAN-THR : angle 2.17401 ( 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 158 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.722 Fit side-chains REVERT: A 64 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8954 (mmmm) REVERT: A 65 GLU cc_start: 0.8158 (pm20) cc_final: 0.7730 (pp20) REVERT: A 98 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.9063 (tt0) REVERT: A 311 ILE cc_start: 0.8568 (mp) cc_final: 0.8349 (mp) REVERT: C 149 ARG cc_start: 0.8767 (tpp80) cc_final: 0.8003 (tpp80) REVERT: D 144 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8423 (mm110) REVERT: F 48 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9091 (mp) outliers start: 33 outliers final: 15 residues processed: 148 average time/residue: 0.7293 time to fit residues: 118.3419 Evaluate side-chains 141 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS 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 318 ILE Chi-restraints excluded: chain A residue 339 SER 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 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU 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: 0.6980 chunk 15 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 204 optimal weight: 0.2980 chunk 183 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3171 r_free = 0.3171 target = 0.079475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.055219 restraints weight = 34164.342| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.64 r_work: 0.2584 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17994 Z= 0.210 Angle : 0.517 7.314 24483 Z= 0.251 Chirality : 0.043 0.195 2640 Planarity : 0.003 0.049 3147 Dihedral : 7.355 99.604 3044 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 2.44 % Allowed : 22.02 % 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 aren not related in a simple way. whole: 0.70 (0.19), residues: 2082 helix: 1.83 (0.25), residues: 465 sheet: -0.26 (0.30), residues: 285 loop : 0.23 (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 C 306 TRP 0.012 0.001 TRP C 399 HIS 0.002 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00489 (17961) covalent geometry : angle 0.50022 (24393) hydrogen bonds : bond 0.03874 ( 497) hydrogen bonds : angle 5.03455 ( 1353) link_ALPHA1-2 : bond 0.00425 ( 6) link_ALPHA1-2 : angle 2.65873 ( 18) link_ALPHA1-4 : bond 0.00574 ( 6) link_ALPHA1-4 : angle 2.54541 ( 18) link_BETA1-4 : bond 0.00622 ( 12) link_BETA1-4 : angle 2.19143 ( 36) link_MAN-SER : bond 0.00405 ( 6) link_MAN-SER : angle 0.86925 ( 12) link_MAN-THR : bond 0.00125 ( 3) link_MAN-THR : angle 1.87529 ( 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 168 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8179 (pm20) cc_final: 0.7745 (pp20) REVERT: A 98 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9062 (tt0) REVERT: A 311 ILE cc_start: 0.8556 (mp) cc_final: 0.8329 (mp) REVERT: A 454 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9273 (m) REVERT: C 149 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8252 (tpp80) REVERT: C 188 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7488 (mmt-90) REVERT: D 57 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7613 (ttp80) REVERT: D 144 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8517 (mm110) REVERT: E 311 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8277 (tp) REVERT: F 48 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9118 (mp) outliers start: 45 outliers final: 29 residues processed: 154 average time/residue: 0.7052 time to fit residues: 119.0927 Evaluate side-chains 157 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 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 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 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 255 THR Chi-restraints excluded: chain E residue 130 PHE 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 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: 2.9990 chunk 117 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3170 r_free = 0.3170 target = 0.079251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.055041 restraints weight = 34045.881| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.64 r_work: 0.2566 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17994 Z= 0.211 Angle : 0.519 7.416 24483 Z= 0.252 Chirality : 0.043 0.205 2640 Planarity : 0.003 0.046 3147 Dihedral : 7.344 100.525 3044 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 2.71 % Allowed : 22.02 % Favored : 75.27 % 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 aren not related in a simple way. whole: 0.68 (0.19), residues: 2082 helix: 1.80 (0.25), residues: 465 sheet: -0.25 (0.30), residues: 285 loop : 0.21 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 149 TYR 0.010 0.001 TYR C 102 PHE 0.012 0.001 PHE F 100 TRP 0.012 0.001 TRP C 399 HIS 0.002 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00489 (17961) covalent geometry : angle 0.50145 (24393) hydrogen bonds : bond 0.03881 ( 497) hydrogen bonds : angle 5.05694 ( 1353) link_ALPHA1-2 : bond 0.00372 ( 6) link_ALPHA1-2 : angle 2.64075 ( 18) link_ALPHA1-4 : bond 0.00598 ( 6) link_ALPHA1-4 : angle 2.53787 ( 18) link_BETA1-4 : bond 0.00617 ( 12) link_BETA1-4 : angle 2.24646 ( 36) link_MAN-SER : bond 0.00404 ( 6) link_MAN-SER : angle 0.83829 ( 12) link_MAN-THR : bond 0.00112 ( 3) link_MAN-THR : angle 1.90241 ( 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 172 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8302 (pm20) cc_final: 0.7857 (pp20) REVERT: A 98 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.9064 (tt0) REVERT: A 209 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8389 (mmtm) REVERT: A 311 ILE cc_start: 0.8557 (mp) cc_final: 0.8314 (mp) REVERT: D 57 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.7603 (ttp80) REVERT: D 142 TYR cc_start: 0.8590 (t80) cc_final: 0.8384 (t80) REVERT: D 144 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8552 (mm110) REVERT: E 311 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8319 (tp) REVERT: F 48 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9131 (mp) outliers start: 50 outliers final: 35 residues processed: 158 average time/residue: 0.6563 time to fit residues: 113.9708 Evaluate side-chains 161 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 48 LEU 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 215 VAL 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 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 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 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 Chi-restraints excluded: chain F residue 294 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 102 optimal weight: 0.0000 chunk 123 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3191 r_free = 0.3191 target = 0.080556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.056374 restraints weight = 33829.597| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.64 r_work: 0.2610 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17994 Z= 0.114 Angle : 0.468 7.863 24483 Z= 0.226 Chirality : 0.041 0.176 2640 Planarity : 0.003 0.039 3147 Dihedral : 6.858 95.495 3044 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 1.95 % Allowed : 22.84 % 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 aren not related in a simple way. whole: 0.88 (0.19), residues: 2082 helix: 2.06 (0.25), residues: 465 sheet: -0.22 (0.30), residues: 285 loop : 0.33 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 149 TYR 0.006 0.001 TYR E 102 PHE 0.010 0.001 PHE C 306 TRP 0.013 0.001 TRP E 399 HIS 0.001 0.000 HIS A 373 Details of bonding type rmsd covalent geometry : bond 0.00262 (17961) covalent geometry : angle 0.45111 (24393) hydrogen bonds : bond 0.03343 ( 497) hydrogen bonds : angle 4.76789 ( 1353) link_ALPHA1-2 : bond 0.00388 ( 6) link_ALPHA1-2 : angle 2.40516 ( 18) link_ALPHA1-4 : bond 0.00677 ( 6) link_ALPHA1-4 : angle 2.38221 ( 18) link_BETA1-4 : bond 0.00520 ( 12) link_BETA1-4 : angle 2.12644 ( 36) link_MAN-SER : bond 0.00119 ( 6) link_MAN-SER : angle 0.68191 ( 12) link_MAN-THR : bond 0.00271 ( 3) link_MAN-THR : angle 1.94790 ( 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: 36 poor density : 126 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8315 (pm20) cc_final: 0.7773 (pp20) REVERT: A 98 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9072 (tt0) REVERT: A 209 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8386 (mmtm) REVERT: A 311 ILE cc_start: 0.8511 (mp) cc_final: 0.8274 (mp) REVERT: B 127 GLN cc_start: 0.9276 (tm-30) cc_final: 0.9052 (tm-30) REVERT: D 57 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7856 (ptp90) REVERT: D 142 TYR cc_start: 0.8533 (t80) cc_final: 0.8332 (t80) REVERT: D 144 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8529 (mm110) REVERT: F 48 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9101 (mp) outliers start: 36 outliers final: 31 residues processed: 152 average time/residue: 0.6600 time to fit residues: 110.4853 Evaluate side-chains 158 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 240 LEU 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 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 274 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 276 MET 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=2.00 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 118 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.078595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.054432 restraints weight = 34227.723| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.63 r_work: 0.2569 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 17994 Z= 0.261 Angle : 0.549 7.934 24483 Z= 0.267 Chirality : 0.044 0.210 2640 Planarity : 0.003 0.049 3147 Dihedral : 7.221 99.701 3044 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.92 % Rotamer: Outliers : 2.81 % Allowed : 22.29 % Favored : 74.89 % 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 aren not related in a simple way. whole: 0.70 (0.19), residues: 2082 helix: 1.83 (0.25), residues: 465 sheet: -0.25 (0.30), residues: 285 loop : 0.22 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 149 TYR 0.013 0.001 TYR C 102 PHE 0.015 0.001 PHE F 100 TRP 0.012 0.001 TRP C 399 HIS 0.002 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00607 (17961) covalent geometry : angle 0.53217 (24393) hydrogen bonds : bond 0.04075 ( 497) hydrogen bonds : angle 5.09733 ( 1353) link_ALPHA1-2 : bond 0.00393 ( 6) link_ALPHA1-2 : angle 2.72244 ( 18) link_ALPHA1-4 : bond 0.00528 ( 6) link_ALPHA1-4 : angle 2.57557 ( 18) link_BETA1-4 : bond 0.00698 ( 12) link_BETA1-4 : angle 2.31948 ( 36) link_MAN-SER : bond 0.00529 ( 6) link_MAN-SER : angle 0.96323 ( 12) link_MAN-THR : bond 0.00293 ( 3) link_MAN-THR : angle 1.74186 ( 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 172 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 120 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 98 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.9089 (tt0) REVERT: A 209 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8385 (mmtm) REVERT: A 311 ILE cc_start: 0.8567 (mp) cc_final: 0.8340 (mp) REVERT: A 454 SER cc_start: 0.9535 (OUTLIER) cc_final: 0.9281 (m) REVERT: B 127 GLN cc_start: 0.9242 (tm-30) cc_final: 0.9000 (tm-30) REVERT: C 188 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7520 (mmp80) REVERT: D 57 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7696 (ttp80) REVERT: D 144 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8550 (mm110) REVERT: E 311 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8351 (tp) REVERT: F 48 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9129 (mp) outliers start: 52 outliers final: 35 residues processed: 156 average time/residue: 0.6669 time to fit residues: 114.2867 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 : 0.484 ------------------------------------------------------------------------------- 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 184 VAL 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 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 319 MET 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 170 ASP 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 111 SER 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: 2.9990 chunk 178 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 87 optimal weight: 0.0030 chunk 43 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3185 r_free = 0.3185 target = 0.080124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.055933 restraints weight = 34110.024| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.65 r_work: 0.2602 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1590 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= 0.117 Angle : 0.481 8.024 24483 Z= 0.233 Chirality : 0.041 0.181 2640 Planarity : 0.003 0.050 3147 Dihedral : 6.737 95.153 3044 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 1.95 % Allowed : 23.11 % Favored : 74.95 % 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 aren not related in a simple way. whole: 0.87 (0.19), residues: 2082 helix: 2.04 (0.25), residues: 465 sheet: -0.23 (0.30), residues: 285 loop : 0.33 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 149 TYR 0.006 0.001 TYR E 102 PHE 0.011 0.001 PHE C 306 TRP 0.014 0.001 TRP E 399 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00273 (17961) covalent geometry : angle 0.46389 (24393) hydrogen bonds : bond 0.03399 ( 497) hydrogen bonds : angle 4.79650 ( 1353) link_ALPHA1-2 : bond 0.00402 ( 6) link_ALPHA1-2 : angle 2.41603 ( 18) link_ALPHA1-4 : bond 0.00695 ( 6) link_ALPHA1-4 : angle 2.41321 ( 18) link_BETA1-4 : bond 0.00530 ( 12) link_BETA1-4 : angle 2.18191 ( 36) link_MAN-SER : bond 0.00124 ( 6) link_MAN-SER : angle 0.69228 ( 12) link_MAN-THR : bond 0.00274 ( 3) link_MAN-THR : angle 1.96277 ( 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 159 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8244 (pm20) cc_final: 0.7956 (pp20) REVERT: A 98 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.9080 (tt0) REVERT: A 209 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8373 (mmtm) REVERT: A 311 ILE cc_start: 0.8568 (mp) cc_final: 0.8329 (mp) REVERT: C 188 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7508 (mmp80) REVERT: D 57 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7935 (ptp90) REVERT: D 144 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8531 (mm110) REVERT: F 48 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9107 (mp) outliers start: 36 outliers final: 28 residues processed: 149 average time/residue: 0.7101 time to fit residues: 116.1007 Evaluate side-chains 156 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 318 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 48 LEU 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 C residue 36 THR Chi-restraints excluded: chain C residue 42 SER 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 347 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 383 SER 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: 3.9990 chunk 122 optimal weight: 2.9990 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: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3126 r_free = 0.3126 target = 0.076547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.052389 restraints weight = 34779.982| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 2.64 r_work: 0.2521 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.188 17994 Z= 0.505 Angle : 0.706 9.799 24483 Z= 0.345 Chirality : 0.052 0.260 2640 Planarity : 0.005 0.062 3147 Dihedral : 8.033 110.262 3044 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 2.44 % Allowed : 22.73 % Favored : 74.84 % 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 aren not related in a simple way. whole: 0.35 (0.18), residues: 2082 helix: 1.37 (0.24), residues: 465 sheet: -0.21 (0.30), residues: 279 loop : -0.01 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 149 TYR 0.015 0.002 TYR C 102 PHE 0.020 0.002 PHE D 100 TRP 0.013 0.002 TRP E 399 HIS 0.004 0.001 HIS B 259 Details of bonding type rmsd covalent geometry : bond 0.01178 (17961) covalent geometry : angle 0.68810 (24393) hydrogen bonds : bond 0.05053 ( 497) hydrogen bonds : angle 5.56154 ( 1353) link_ALPHA1-2 : bond 0.00436 ( 6) link_ALPHA1-2 : angle 3.17352 ( 18) link_ALPHA1-4 : bond 0.00501 ( 6) link_ALPHA1-4 : angle 2.93119 ( 18) link_BETA1-4 : bond 0.01066 ( 12) link_BETA1-4 : angle 2.77362 ( 36) link_MAN-SER : bond 0.01096 ( 6) link_MAN-SER : angle 1.44530 ( 12) link_MAN-THR : bond 0.00914 ( 3) link_MAN-THR : angle 1.98939 ( 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 164 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 119 time to evaluate : 0.597 Fit side-chains REVERT: A 65 GLU cc_start: 0.8344 (pm20) cc_final: 0.8139 (pp20) REVERT: A 98 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9105 (tt0) REVERT: A 209 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8392 (mmtm) REVERT: C 188 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7462 (mmp80) REVERT: D 57 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.7870 (ttp80) REVERT: D 144 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8674 (mm110) REVERT: F 48 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9172 (mp) outliers start: 45 outliers final: 36 residues processed: 156 average time/residue: 0.6645 time to fit residues: 114.0944 Evaluate side-chains 158 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 275 MET 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 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 111 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3169 r_free = 0.3169 target = 0.079108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054930 restraints weight = 34331.680| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.65 r_work: 0.2577 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17994 Z= 0.138 Angle : 0.517 7.456 24483 Z= 0.252 Chirality : 0.042 0.196 2640 Planarity : 0.003 0.038 3147 Dihedral : 7.340 104.964 3044 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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 aren not related in a simple way. whole: 0.64 (0.19), residues: 2082 helix: 1.76 (0.25), residues: 465 sheet: -0.27 (0.30), residues: 285 loop : 0.18 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 223 TYR 0.007 0.001 TYR C 102 PHE 0.012 0.001 PHE C 306 TRP 0.015 0.001 TRP E 399 HIS 0.002 0.000 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00321 (17961) covalent geometry : angle 0.49961 (24393) hydrogen bonds : bond 0.03787 ( 497) hydrogen bonds : angle 5.08351 ( 1353) link_ALPHA1-2 : bond 0.00340 ( 6) link_ALPHA1-2 : angle 2.57453 ( 18) link_ALPHA1-4 : bond 0.00682 ( 6) link_ALPHA1-4 : angle 2.57374 ( 18) link_BETA1-4 : bond 0.00569 ( 12) link_BETA1-4 : angle 2.31747 ( 36) link_MAN-SER : bond 0.00207 ( 6) link_MAN-SER : angle 0.77576 ( 12) link_MAN-THR : bond 0.00185 ( 3) link_MAN-THR : angle 1.97732 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6573.23 seconds wall clock time: 112 minutes 37.40 seconds (6757.40 seconds total)