Starting phenix.real_space_refine on Mon May 19 02:32:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzu_48769/05_2025/9mzu_48769_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzu_48769/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mzu_48769/05_2025/9mzu_48769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzu_48769/05_2025/9mzu_48769.map" model { file = "/net/cci-nas-00/data/ceres_data/9mzu_48769/05_2025/9mzu_48769_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzu_48769/05_2025/9mzu_48769_trim.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.40, per 1000 atoms: 0.65 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: 5.08 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.15 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: 4.57 Time building geometry restraints manager: 5.60 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: 0.03 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: 6.300 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: 0.440 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.660 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP E 399 HIS 0.002 0.001 HIS E 373 PHE 0.014 0.001 PHE C 306 TYR 0.010 0.001 TYR C 102 ARG 0.002 0.000 ARG D 261 Details of bonding type rmsd link_MAN-THR : bond 0.00408 ( 3) link_MAN-THR : angle 2.61836 ( 6) 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_ALPHA1-2 : bond 0.00725 ( 6) link_ALPHA1-2 : angle 4.06647 ( 18) hydrogen bonds : bond 0.14053 ( 497) hydrogen bonds : angle 5.93969 ( 1353) covalent geometry : bond 0.00264 (17961) covalent geometry : angle 0.49518 (24393) link_MAN-SER : bond 0.00319 ( 6) link_MAN-SER : angle 1.59627 ( 12) *********************** 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 : 2.055 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: 1.5433 time to fit residues: 293.1651 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 : 1.905 ------------------------------------------------------------------------------- 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 174 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 0.0040 chunk 187 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.081005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.056582 restraints weight = 33838.009| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.66 r_work: 0.2607 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17994 Z= 0.163 Angle : 0.507 7.309 24483 Z= 0.248 Chirality : 0.042 0.208 2640 Planarity : 0.003 0.042 3147 Dihedral : 8.020 100.540 3071 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.79 % Favored : 96.16 % Rotamer: Outliers : 3.08 % Allowed : 21.86 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2082 helix: 1.28 (0.25), residues: 483 sheet: -0.33 (0.30), residues: 285 loop : 0.21 (0.18), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 399 HIS 0.002 0.001 HIS E 373 PHE 0.014 0.001 PHE C 306 TYR 0.009 0.001 TYR C 102 ARG 0.007 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00070 ( 3) link_MAN-THR : angle 2.32378 ( 6) link_ALPHA1-4 : bond 0.00720 ( 6) link_ALPHA1-4 : angle 2.59436 ( 18) link_BETA1-4 : bond 0.00592 ( 12) link_BETA1-4 : angle 1.97116 ( 36) link_ALPHA1-2 : bond 0.00428 ( 6) link_ALPHA1-2 : angle 2.49671 ( 18) hydrogen bonds : bond 0.03925 ( 497) hydrogen bonds : angle 5.21276 ( 1353) covalent geometry : bond 0.00378 (17961) covalent geometry : angle 0.49053 (24393) link_MAN-SER : bond 0.00265 ( 6) link_MAN-SER : angle 0.80588 ( 12) *********************** 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 180 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 1.991 Fit side-chains REVERT: A 65 GLU cc_start: 0.8188 (pm20) cc_final: 0.7766 (pp20) REVERT: A 111 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8593 (mtt180) REVERT: A 442 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.8550 (pptt) REVERT: B 144 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8515 (mm-40) REVERT: C 240 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9169 (tp) REVERT: D 144 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8250 (mm110) outliers start: 57 outliers final: 27 residues processed: 162 average time/residue: 1.4415 time to fit residues: 258.9171 Evaluate side-chains 148 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 111 ARG 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 442 LYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 319 MET 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 130 ILE 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 415 ILE Chi-restraints excluded: chain E residue 474 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 127 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 chunk 196 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 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 = 0.3156 r_free = 0.3156 target = 0.078653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.054340 restraints weight = 34032.134| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.65 r_work: 0.2568 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 17994 Z= 0.263 Angle : 0.563 8.187 24483 Z= 0.274 Chirality : 0.045 0.219 2640 Planarity : 0.004 0.043 3147 Dihedral : 7.973 106.217 3047 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 3.90 % Allowed : 21.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 2082 helix: 1.48 (0.25), residues: 465 sheet: -0.34 (0.30), residues: 285 loop : 0.07 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 399 HIS 0.002 0.001 HIS C 373 PHE 0.015 0.002 PHE F 100 TYR 0.012 0.001 TYR C 102 ARG 0.007 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00249 ( 3) link_MAN-THR : angle 2.17601 ( 6) link_ALPHA1-4 : bond 0.00546 ( 6) link_ALPHA1-4 : angle 2.78773 ( 18) link_BETA1-4 : bond 0.00679 ( 12) link_BETA1-4 : angle 2.29339 ( 36) link_ALPHA1-2 : bond 0.00427 ( 6) link_ALPHA1-2 : angle 2.93784 ( 18) hydrogen bonds : bond 0.04510 ( 497) hydrogen bonds : angle 5.32068 ( 1353) covalent geometry : bond 0.00613 (17961) covalent geometry : angle 0.54495 (24393) link_MAN-SER : bond 0.00541 ( 6) link_MAN-SER : angle 1.14669 ( 12) *********************** 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 192 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 120 time to evaluate : 2.099 Fit side-chains REVERT: A 111 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8670 (mtt180) REVERT: A 311 ILE cc_start: 0.8682 (mp) cc_final: 0.8450 (mp) REVERT: A 442 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.8481 (pptt) REVERT: D 57 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7615 (ttp80) REVERT: D 144 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8472 (mm110) REVERT: E 311 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8349 (tp) REVERT: F 48 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9116 (mp) outliers start: 72 outliers final: 43 residues processed: 173 average time/residue: 1.4945 time to fit residues: 285.8001 Evaluate side-chains 168 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 111 ARG 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 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 A residue 442 LYS 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 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 208 ILE 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 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 130 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 298 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 130 optimal weight: 0.0270 chunk 80 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 0.0370 chunk 126 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.056647 restraints weight = 33797.589| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.64 r_work: 0.2643 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17994 Z= 0.102 Angle : 0.469 7.339 24483 Z= 0.227 Chirality : 0.041 0.170 2640 Planarity : 0.003 0.040 3147 Dihedral : 7.293 100.538 3047 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 1.89 % Allowed : 22.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 2082 helix: 1.82 (0.25), residues: 465 sheet: -0.27 (0.30), residues: 285 loop : 0.24 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 399 HIS 0.001 0.000 HIS E 373 PHE 0.010 0.001 PHE C 306 TYR 0.007 0.001 TYR E 102 ARG 0.009 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00381 ( 3) link_MAN-THR : angle 2.17889 ( 6) link_ALPHA1-4 : bond 0.00756 ( 6) link_ALPHA1-4 : angle 2.45415 ( 18) link_BETA1-4 : bond 0.00526 ( 12) link_BETA1-4 : angle 2.07514 ( 36) link_ALPHA1-2 : bond 0.00396 ( 6) link_ALPHA1-2 : angle 2.44458 ( 18) hydrogen bonds : bond 0.03425 ( 497) hydrogen bonds : angle 4.88943 ( 1353) covalent geometry : bond 0.00234 (17961) covalent geometry : angle 0.45152 (24393) link_MAN-SER : bond 0.00074 ( 6) link_MAN-SER : angle 0.68000 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 2.155 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8163 (pm20) cc_final: 0.7734 (pp20) REVERT: A 98 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9062 (tt0) REVERT: A 111 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8499 (mtt180) REVERT: A 442 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.8424 (pptt) REVERT: B 144 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8475 (mm-40) REVERT: D 57 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.7516 (ttp80) REVERT: D 142 TYR cc_start: 0.8508 (t80) cc_final: 0.8308 (t80) REVERT: D 144 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8463 (mm110) REVERT: F 48 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9096 (mp) outliers start: 35 outliers final: 18 residues processed: 148 average time/residue: 1.5277 time to fit residues: 249.6458 Evaluate side-chains 149 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 130 PHE 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 A residue 442 LYS Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain C residue 42 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 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 130 optimal weight: 0.0770 chunk 145 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 GLN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.056380 restraints weight = 34172.476| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.66 r_work: 0.2627 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17994 Z= 0.123 Angle : 0.469 7.624 24483 Z= 0.226 Chirality : 0.041 0.174 2640 Planarity : 0.003 0.043 3147 Dihedral : 7.097 98.252 3046 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 2.49 % Allowed : 22.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 2082 helix: 1.97 (0.25), residues: 465 sheet: -0.26 (0.30), residues: 285 loop : 0.28 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 399 HIS 0.001 0.000 HIS E 373 PHE 0.012 0.001 PHE C 306 TYR 0.011 0.001 TYR B 128 ARG 0.011 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00246 ( 3) link_MAN-THR : angle 1.88730 ( 6) link_ALPHA1-4 : bond 0.00649 ( 6) link_ALPHA1-4 : angle 2.41618 ( 18) link_BETA1-4 : bond 0.00526 ( 12) link_BETA1-4 : angle 2.07146 ( 36) link_ALPHA1-2 : bond 0.00409 ( 6) link_ALPHA1-2 : angle 2.43751 ( 18) hydrogen bonds : bond 0.03410 ( 497) hydrogen bonds : angle 4.79709 ( 1353) covalent geometry : bond 0.00285 (17961) covalent geometry : angle 0.45185 (24393) link_MAN-SER : bond 0.00145 ( 6) link_MAN-SER : angle 0.70798 ( 12) *********************** 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 171 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 1.945 Fit side-chains REVERT: A 65 GLU cc_start: 0.8179 (pm20) cc_final: 0.7769 (pp20) REVERT: A 98 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.9016 (tt0) REVERT: A 111 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8573 (mtt180) REVERT: A 311 ILE cc_start: 0.8515 (mp) cc_final: 0.8289 (mp) REVERT: A 442 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.8419 (pptt) REVERT: A 454 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9268 (m) REVERT: C 188 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7446 (mmp80) REVERT: D 57 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7923 (ptp90) REVERT: D 142 TYR cc_start: 0.8523 (t80) cc_final: 0.8322 (t80) REVERT: D 144 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8491 (mm110) REVERT: E 311 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (tp) REVERT: F 48 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9083 (mp) outliers start: 46 outliers final: 28 residues processed: 156 average time/residue: 1.4899 time to fit residues: 256.7201 Evaluate side-chains 161 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 111 ARG Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 215 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 442 LYS 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 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 313 LEU Chi-restraints excluded: chain C residue 319 MET 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 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 151 THR Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 172 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.077986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.053728 restraints weight = 34750.900| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.66 r_work: 0.2552 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 17994 Z= 0.315 Angle : 0.585 8.384 24483 Z= 0.285 Chirality : 0.046 0.229 2640 Planarity : 0.004 0.045 3147 Dihedral : 7.663 105.312 3042 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 3.19 % Allowed : 21.48 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 2082 helix: 1.63 (0.25), residues: 465 sheet: -0.29 (0.30), residues: 285 loop : 0.10 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 399 HIS 0.002 0.001 HIS C 373 PHE 0.016 0.002 PHE F 100 TYR 0.014 0.001 TYR C 102 ARG 0.011 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00451 ( 3) link_MAN-THR : angle 1.88247 ( 6) link_ALPHA1-4 : bond 0.00517 ( 6) link_ALPHA1-4 : angle 2.70534 ( 18) link_BETA1-4 : bond 0.00779 ( 12) link_BETA1-4 : angle 2.39960 ( 36) link_ALPHA1-2 : bond 0.00406 ( 6) link_ALPHA1-2 : angle 2.87635 ( 18) hydrogen bonds : bond 0.04415 ( 497) hydrogen bonds : angle 5.28872 ( 1353) covalent geometry : bond 0.00732 (17961) covalent geometry : angle 0.56780 (24393) link_MAN-SER : bond 0.00668 ( 6) link_MAN-SER : angle 1.08763 ( 12) *********************** 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 178 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 119 time to evaluate : 2.141 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8326 (pm20) cc_final: 0.7909 (pp20) REVERT: A 98 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9062 (tt0) REVERT: A 111 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8684 (mtt180) REVERT: A 311 ILE cc_start: 0.8617 (mp) cc_final: 0.8409 (mp) REVERT: A 442 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.8525 (pptt) REVERT: B 189 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.8833 (mm-40) REVERT: C 188 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7507 (mmt-90) REVERT: D 57 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7691 (ttp80) REVERT: D 142 TYR cc_start: 0.8596 (t80) cc_final: 0.8386 (t80) REVERT: D 144 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8557 (mm110) REVERT: E 311 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8374 (tp) REVERT: F 48 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9144 (mp) outliers start: 59 outliers final: 41 residues processed: 165 average time/residue: 1.5162 time to fit residues: 276.8783 Evaluate side-chains 166 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 2.161 ------------------------------------------------------------------------------- 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 111 ARG Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 215 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 442 LYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 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 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 454 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 D residue 294 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 151 THR 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 118 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 147 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 11 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN 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 = 0.3194 r_free = 0.3194 target = 0.080749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.056615 restraints weight = 33868.997| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 2.65 r_work: 0.2616 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17994 Z= 0.094 Angle : 0.470 7.585 24483 Z= 0.227 Chirality : 0.041 0.171 2640 Planarity : 0.003 0.043 3147 Dihedral : 6.912 98.398 3042 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.57 % Allowed : 23.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 2082 helix: 2.00 (0.25), residues: 465 sheet: -0.24 (0.30), residues: 285 loop : 0.30 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 399 HIS 0.001 0.000 HIS A 169 PHE 0.011 0.001 PHE C 306 TYR 0.008 0.001 TYR B 142 ARG 0.011 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00472 ( 3) link_MAN-THR : angle 2.18713 ( 6) link_ALPHA1-4 : bond 0.00743 ( 6) link_ALPHA1-4 : angle 2.39733 ( 18) link_BETA1-4 : bond 0.00527 ( 12) link_BETA1-4 : angle 2.13738 ( 36) link_ALPHA1-2 : bond 0.00385 ( 6) link_ALPHA1-2 : angle 2.36840 ( 18) hydrogen bonds : bond 0.03289 ( 497) hydrogen bonds : angle 4.77759 ( 1353) covalent geometry : bond 0.00217 (17961) covalent geometry : angle 0.45343 (24393) link_MAN-SER : bond 0.00054 ( 6) link_MAN-SER : angle 0.66676 ( 12) *********************** 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 152 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 2.037 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8342 (pm20) cc_final: 0.7812 (pp20) REVERT: A 98 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.9078 (tt0) REVERT: A 111 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8516 (mtt180) REVERT: A 209 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8433 (mmtm) REVERT: A 311 ILE cc_start: 0.8535 (mp) cc_final: 0.8309 (mp) REVERT: A 442 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.8417 (pptt) REVERT: B 127 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8975 (tm-30) REVERT: C 148 LYS cc_start: 0.8736 (pptt) cc_final: 0.8440 (pptt) REVERT: D 57 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7614 (ttp80) REVERT: D 142 TYR cc_start: 0.8547 (t80) cc_final: 0.8343 (t80) REVERT: D 144 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8443 (mm110) REVERT: F 48 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9100 (mp) outliers start: 29 outliers final: 20 residues processed: 145 average time/residue: 1.5344 time to fit residues: 245.1895 Evaluate side-chains 147 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 111 ARG 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 A residue 442 LYS 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 349 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 130 PHE 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 118 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 82 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.078412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.054304 restraints weight = 34502.772| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 2.64 r_work: 0.2551 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 : 0.006 0.112 17994 Z= 0.278 Angle : 0.561 8.121 24483 Z= 0.272 Chirality : 0.045 0.212 2640 Planarity : 0.003 0.051 3147 Dihedral : 7.340 103.607 3042 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 2.44 % Allowed : 22.89 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 2082 helix: 1.79 (0.25), residues: 465 sheet: -0.25 (0.31), residues: 285 loop : 0.18 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 399 HIS 0.002 0.001 HIS E 373 PHE 0.016 0.002 PHE F 100 TYR 0.013 0.001 TYR C 102 ARG 0.013 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00334 ( 3) link_MAN-THR : angle 1.70098 ( 6) link_ALPHA1-4 : bond 0.00508 ( 6) link_ALPHA1-4 : angle 2.60178 ( 18) link_BETA1-4 : bond 0.00727 ( 12) link_BETA1-4 : angle 2.35676 ( 36) link_ALPHA1-2 : bond 0.00404 ( 6) link_ALPHA1-2 : angle 2.74815 ( 18) hydrogen bonds : bond 0.04166 ( 497) hydrogen bonds : angle 5.13491 ( 1353) covalent geometry : bond 0.00649 (17961) covalent geometry : angle 0.54440 (24393) link_MAN-SER : bond 0.00585 ( 6) link_MAN-SER : angle 1.02520 ( 12) *********************** 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 162 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 2.229 Fit side-chains revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8335 (pm20) cc_final: 0.7934 (pp20) REVERT: A 98 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.9093 (tt0) REVERT: A 111 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8648 (mtt180) REVERT: A 209 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8417 (mmtm) REVERT: A 311 ILE cc_start: 0.8528 (mp) cc_final: 0.8289 (mp) REVERT: A 442 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.8519 (pptt) REVERT: B 57 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8308 (ptp90) REVERT: C 188 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7518 (mmp80) REVERT: D 57 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.7527 (ttp80) REVERT: D 144 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8496 (mm110) REVERT: E 111 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7425 (mtt-85) REVERT: E 311 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8378 (tp) REVERT: F 48 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9132 (mp) outliers start: 45 outliers final: 34 residues processed: 152 average time/residue: 1.6694 time to fit residues: 278.8124 Evaluate side-chains 159 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 2.069 ------------------------------------------------------------------------------- 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 111 ARG Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 57 ARG 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 184 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 111 ARG 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 118 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 174 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** 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 = 0.3188 r_free = 0.3188 target = 0.080302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.056039 restraints weight = 34261.071| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.67 r_work: 0.2602 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17994 Z= 0.114 Angle : 0.480 7.475 24483 Z= 0.232 Chirality : 0.041 0.182 2640 Planarity : 0.003 0.048 3147 Dihedral : 6.802 98.327 3042 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer: Outliers : 1.79 % Allowed : 23.48 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 2082 helix: 2.00 (0.25), residues: 465 sheet: -0.25 (0.31), residues: 285 loop : 0.31 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 399 HIS 0.001 0.000 HIS A 169 PHE 0.011 0.001 PHE C 306 TYR 0.006 0.001 TYR E 102 ARG 0.012 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00289 ( 3) link_MAN-THR : angle 1.98772 ( 6) link_ALPHA1-4 : bond 0.00685 ( 6) link_ALPHA1-4 : angle 2.38706 ( 18) link_BETA1-4 : bond 0.00524 ( 12) link_BETA1-4 : angle 2.19142 ( 36) link_ALPHA1-2 : bond 0.00369 ( 6) link_ALPHA1-2 : angle 2.41957 ( 18) hydrogen bonds : bond 0.03363 ( 497) hydrogen bonds : angle 4.79885 ( 1353) covalent geometry : bond 0.00265 (17961) covalent geometry : angle 0.46259 (24393) link_MAN-SER : bond 0.00115 ( 6) link_MAN-SER : angle 0.67694 ( 12) *********************** 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 155 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.958 Fit side-chains REVERT: A 65 GLU cc_start: 0.8382 (pm20) cc_final: 0.7871 (pp20) REVERT: A 98 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.9071 (tt0) REVERT: A 111 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8446 (mtt180) REVERT: A 311 ILE cc_start: 0.8585 (mp) cc_final: 0.8355 (mp) REVERT: A 442 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.8417 (pptt) REVERT: C 188 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7515 (mmp80) REVERT: D 57 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7627 (ttp80) REVERT: D 142 TYR cc_start: 0.8558 (t80) cc_final: 0.8348 (t80) REVERT: D 144 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8536 (mm110) REVERT: F 48 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9107 (mp) outliers start: 33 outliers final: 25 residues processed: 147 average time/residue: 1.6359 time to fit residues: 266.6520 Evaluate side-chains 153 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 2.132 ------------------------------------------------------------------------------- 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 111 ARG 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 A residue 442 LYS 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 42 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 130 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 113 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 135 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 33 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 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 = 0.3210 r_free = 0.3210 target = 0.081630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.057520 restraints weight = 33991.032| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.65 r_work: 0.2624 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17994 Z= 0.088 Angle : 0.456 8.824 24483 Z= 0.219 Chirality : 0.040 0.163 2640 Planarity : 0.003 0.050 3147 Dihedral : 6.067 87.005 3042 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.41 % Allowed : 23.97 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2082 helix: 2.23 (0.26), residues: 465 sheet: 0.04 (0.29), residues: 309 loop : 0.40 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 399 HIS 0.001 0.000 HIS A 169 PHE 0.009 0.001 PHE C 306 TYR 0.006 0.001 TYR C 102 ARG 0.011 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00355 ( 3) link_MAN-THR : angle 1.74807 ( 6) link_ALPHA1-4 : bond 0.00720 ( 6) link_ALPHA1-4 : angle 2.24310 ( 18) link_BETA1-4 : bond 0.00510 ( 12) link_BETA1-4 : angle 2.09374 ( 36) link_ALPHA1-2 : bond 0.00432 ( 6) link_ALPHA1-2 : angle 2.19772 ( 18) hydrogen bonds : bond 0.02975 ( 497) hydrogen bonds : angle 4.48670 ( 1353) covalent geometry : bond 0.00210 (17961) covalent geometry : angle 0.44008 (24393) link_MAN-SER : bond 0.00053 ( 6) link_MAN-SER : angle 0.64414 ( 12) ********************** 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 151 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 2.009 Fit side-chains REVERT: A 65 GLU cc_start: 0.8368 (pm20) cc_final: 0.7867 (pp20) REVERT: A 98 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.9052 (tt0) REVERT: A 111 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8400 (mtt180) REVERT: A 311 ILE cc_start: 0.8435 (mp) cc_final: 0.8217 (mp) REVERT: B 57 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8139 (ptp90) REVERT: C 149 ARG cc_start: 0.8852 (ttp80) cc_final: 0.7927 (tmm160) REVERT: D 57 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7695 (ptp90) REVERT: D 142 TYR cc_start: 0.8495 (t80) cc_final: 0.8289 (t80) REVERT: D 144 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8443 (mm110) outliers start: 26 outliers final: 18 residues processed: 144 average time/residue: 1.6606 time to fit residues: 262.2546 Evaluate side-chains 143 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 111 ARG 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 57 ARG Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain C residue 184 VAL 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 269 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 474 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 204 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 0.4980 chunk 174 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.057478 restraints weight = 33844.672| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.65 r_work: 0.2623 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 17994 Z= 0.145 Angle : 0.699 59.039 24483 Z= 0.385 Chirality : 0.045 0.969 2640 Planarity : 0.003 0.047 3147 Dihedral : 6.060 86.967 3039 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.41 % Allowed : 24.03 % Favored : 74.57 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2082 helix: 2.23 (0.26), residues: 465 sheet: 0.05 (0.29), residues: 309 loop : 0.40 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 399 HIS 0.001 0.000 HIS A 169 PHE 0.009 0.001 PHE C 306 TYR 0.006 0.001 TYR C 102 ARG 0.005 0.000 ARG A 149 Details of bonding type rmsd link_MAN-THR : bond 0.00262 ( 3) link_MAN-THR : angle 1.86864 ( 6) link_ALPHA1-4 : bond 0.00635 ( 6) link_ALPHA1-4 : angle 2.24977 ( 18) link_BETA1-4 : bond 0.00507 ( 12) link_BETA1-4 : angle 2.09248 ( 36) link_ALPHA1-2 : bond 0.00378 ( 6) link_ALPHA1-2 : angle 2.26205 ( 18) hydrogen bonds : bond 0.03032 ( 497) hydrogen bonds : angle 4.49720 ( 1353) covalent geometry : bond 0.00314 (17961) covalent geometry : angle 0.68921 (24393) link_MAN-SER : bond 0.00167 ( 6) link_MAN-SER : angle 0.68746 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13076.47 seconds wall clock time: 226 minutes 6.12 seconds (13566.12 seconds total)