Starting phenix.real_space_refine on Tue May 5 15:33:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v8c_43034/05_2026/8v8c_43034_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v8c_43034/05_2026/8v8c_43034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v8c_43034/05_2026/8v8c_43034_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v8c_43034/05_2026/8v8c_43034_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v8c_43034/05_2026/8v8c_43034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v8c_43034/05_2026/8v8c_43034.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.020 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 113 5.16 5 Cl 10 4.86 5 C 10182 2.51 5 N 2483 2.21 5 O 2828 1.98 5 H 15011 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30630 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 5975 Classifications: {'peptide': 373} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 352} Chain breaks: 1 Chain: "B" Number of atoms: 5997 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5984 Classifications: {'peptide': 374} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 353} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 374, 5985 Classifications: {'peptide': 374} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 353} Chain breaks: 1 bond proxies already assigned to first conformer: 6055 Chain: "C" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "D" Number of atoms: 6080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 6068 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 bond proxies already assigned to first conformer: 6139 Chain: "E" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'EPJ': 1, 'I34': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.82, per 1000 atoms: 0.29 Number of scatterers: 30630 At special positions: 0 Unit cell: (89.925, 91.575, 146.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 Cl 10 17.00 S 113 16.00 O 2828 8.00 N 2483 7.00 C 10182 6.00 H 15011 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.02 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.08 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG A 602 " - " ASN A 23 " " NAG B 602 " - " ASN B 67 " " NAG B 603 " - " ASN B 23 " " NAG C 602 " - " ASN C 67 " " NAG C 603 " - " ASN C 23 " " NAG D 602 " - " ASN D 67 " " NAG D 603 " - " ASN D 23 " " NAG E 602 " - " ASN E 67 " " NAG E 603 " - " ASN E 23 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3586 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 42.2% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 3.585A pdb=" N CYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.509A pdb=" N LEU A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 466 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.643A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.629A pdb=" N THR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 426 through 465 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.828A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 3.519A pdb=" N CYS C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.727A pdb=" N GLY C 236 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.559A pdb=" N GLY C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.654A pdb=" N TRP C 318 " --> pdb=" O ASN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 466 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.778A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 3.561A pdb=" N VAL D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.909A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 307 through 312 Processing helix chain 'D' and resid 314 through 321 Processing helix chain 'D' and resid 425 through 466 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.655A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 3.747A pdb=" N CYS E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 236 Processing helix chain 'E' and resid 237 through 250 Processing helix chain 'E' and resid 250 through 258 Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 426 through 465 removed outlier: 3.568A pdb=" N GLU E 431 " --> pdb=" O GLN E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.555A pdb=" N PHE E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.726A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.726A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 29 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.641A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.641A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.859A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY B 113 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.859A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY B 113 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.637A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.637A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.847A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.847A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C 29 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.542A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.542A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.997A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.997A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 48 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL D 42 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR D 50 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TRP D 54 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU D 36 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN D 56 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU D 34 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER D 58 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE D 32 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N THR D 60 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL D 30 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.694A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.694A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.131A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.131A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL E 48 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL E 42 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR E 50 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP E 54 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU E 36 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN E 56 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU E 34 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 58 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE E 32 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N THR E 60 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL E 30 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.575A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.575A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2556 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: 7.21 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4871 1.04 - 1.24: 12138 1.24 - 1.45: 5140 1.45 - 1.65: 8750 1.65 - 1.85: 177 Bond restraints: 31076 Sorted by residual: bond pdb=" NE1 TRP A 173 " pdb=" HE1 TRP A 173 " ideal model delta sigma weight residual 0.860 1.083 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP B 153 " pdb=" HE1 TRP B 153 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 173 " pdb=" HE1 TRP D 173 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP A 307 " pdb=" HE1 TRP A 307 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 153 " pdb=" HE1 TRP C 153 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 ... (remaining 31071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.19: 56004 8.19 - 16.37: 10 16.37 - 24.56: 0 24.56 - 32.75: 0 32.75 - 40.93: 2 Bond angle restraints: 56016 Sorted by residual: angle pdb=" CA PHE D 424 " pdb=" N PHE D 424 " pdb=" H PHE D 424 " ideal model delta sigma weight residual 114.00 154.93 -40.93 3.00e+00 1.11e-01 1.86e+02 angle pdb=" CA ASP A 428 " pdb=" N ASP A 428 " pdb=" H ASP A 428 " ideal model delta sigma weight residual 114.00 151.60 -37.60 3.00e+00 1.11e-01 1.57e+02 angle pdb=" N LEU E 249 " pdb=" CA LEU E 249 " pdb=" C LEU E 249 " ideal model delta sigma weight residual 113.18 104.59 8.59 1.21e+00 6.83e-01 5.04e+01 angle pdb=" C SER C 149 " pdb=" CA SER C 149 " pdb=" CB SER C 149 " ideal model delta sigma weight residual 109.38 118.04 -8.66 1.68e+00 3.54e-01 2.66e+01 angle pdb=" N LEU D 247 " pdb=" CA LEU D 247 " pdb=" C LEU D 247 " ideal model delta sigma weight residual 112.90 107.26 5.64 1.31e+00 5.83e-01 1.85e+01 ... (remaining 56011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 13784 17.41 - 34.83: 905 34.83 - 52.24: 265 52.24 - 69.65: 78 69.65 - 87.06: 25 Dihedral angle restraints: 15057 sinusoidal: 8208 harmonic: 6849 Sorted by residual: dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual 180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 15054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2244 0.090 - 0.180: 229 0.180 - 0.269: 16 0.269 - 0.359: 11 0.359 - 0.449: 3 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CB VAL E 256 " pdb=" CA VAL E 256 " pdb=" CG1 VAL E 256 " pdb=" CG2 VAL E 256 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA SER C 149 " pdb=" N SER C 149 " pdb=" C SER C 149 " pdb=" CB SER C 149 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C1 EPJ B 604 " pdb=" C2 EPJ B 604 " pdb=" C6 EPJ B 604 " pdb=" C7 EPJ B 604 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2500 not shown) Planarity restraints: 4465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG E 602 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " 0.132 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.332 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG A 601 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.506 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 213 " -0.128 2.00e-02 2.50e+03 1.38e-01 2.87e+02 pdb=" CG ASN B 213 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 213 " 0.124 2.00e-02 2.50e+03 pdb=" ND2 ASN B 213 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 213 " 0.202 2.00e-02 2.50e+03 pdb="HD22 ASN B 213 " -0.205 2.00e-02 2.50e+03 ... (remaining 4462 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 471 2.01 - 2.66: 40038 2.66 - 3.30: 89135 3.30 - 3.95: 119928 3.95 - 4.60: 183411 Nonbonded interactions: 432983 Sorted by model distance: nonbonded pdb=" HE2 TYR D 209 " pdb=" HE1 TYR D 210 " model vdw 1.362 2.100 nonbonded pdb="HD11 LEU C 215 " pdb="HD21 LEU C 464 " model vdw 1.410 2.440 nonbonded pdb="HG22 ILE A 221 " pdb="HG13 VAL A 245 " model vdw 1.421 2.440 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.425 2.100 nonbonded pdb="HD12 LEU B 231 " pdb=" HD2 PRO B 232 " model vdw 1.433 2.440 ... (remaining 432978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 425 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.50 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: 1.280 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: 0.170 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.410 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 : 0.007 0.106 16095 Z= 0.339 Angle : 1.033 14.299 21987 Z= 0.552 Chirality : 0.061 0.449 2503 Planarity : 0.011 0.295 2685 Dihedral : 14.047 87.064 6112 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.18), residues: 1863 helix: -0.83 (0.18), residues: 701 sheet: -1.29 (0.22), residues: 453 loop : -1.16 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 98 TYR 0.031 0.003 TYR D 209 PHE 0.022 0.002 PHE E 134 TRP 0.032 0.002 TRP C 307 HIS 0.006 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00728 (16065) covalent geometry : angle 1.01078 (21907) SS BOND : bond 0.01665 ( 10) SS BOND : angle 2.45907 ( 20) hydrogen bonds : bond 0.15865 ( 775) hydrogen bonds : angle 7.36263 ( 2556) link_BETA1-4 : bond 0.00196 ( 5) link_BETA1-4 : angle 2.36966 ( 15) link_NAG-ASN : bond 0.02994 ( 15) link_NAG-ASN : angle 4.37009 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 TRP cc_start: 0.7042 (m-10) cc_final: 0.6523 (t60) REVERT: E 253 MET cc_start: 0.6716 (tpt) cc_final: 0.6368 (tpt) outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.2653 time to fit residues: 101.0457 Evaluate side-chains 191 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN E 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105686 restraints weight = 99526.486| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.42 r_work: 0.3548 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 16095 Z= 0.150 Angle : 0.633 10.607 21987 Z= 0.324 Chirality : 0.042 0.187 2503 Planarity : 0.005 0.062 2685 Dihedral : 9.391 88.125 2562 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.94 % Allowed : 4.46 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.19), residues: 1863 helix: 0.49 (0.19), residues: 692 sheet: -1.19 (0.21), residues: 452 loop : -0.95 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 185 TYR 0.013 0.001 TYR C 209 PHE 0.019 0.001 PHE E 99 TRP 0.018 0.001 TRP C 307 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00331 (16065) covalent geometry : angle 0.61391 (21907) SS BOND : bond 0.00752 ( 10) SS BOND : angle 1.41796 ( 20) hydrogen bonds : bond 0.05013 ( 775) hydrogen bonds : angle 5.72351 ( 2556) link_BETA1-4 : bond 0.00201 ( 5) link_BETA1-4 : angle 1.35972 ( 15) link_NAG-ASN : bond 0.00401 ( 15) link_NAG-ASN : angle 3.28200 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7301 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 445 ASP cc_start: 0.7483 (m-30) cc_final: 0.7279 (m-30) REVERT: A 450 MET cc_start: 0.6703 (mmt) cc_final: 0.6491 (ttp) REVERT: B 315 TRP cc_start: 0.7614 (m-10) cc_final: 0.6636 (t60) REVERT: D 137 ASP cc_start: 0.7980 (p0) cc_final: 0.7392 (p0) REVERT: E 253 MET cc_start: 0.6698 (tpt) cc_final: 0.6170 (tpt) outliers start: 16 outliers final: 14 residues processed: 212 average time/residue: 0.2604 time to fit residues: 83.9605 Evaluate side-chains 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 172 optimal weight: 0.4980 chunk 6 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.119277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105777 restraints weight = 99713.728| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.41 r_work: 0.3551 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16095 Z= 0.125 Angle : 0.562 9.628 21987 Z= 0.287 Chirality : 0.041 0.175 2503 Planarity : 0.004 0.057 2685 Dihedral : 8.702 84.963 2562 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.82 % Allowed : 5.40 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1863 helix: 1.05 (0.19), residues: 693 sheet: -1.06 (0.21), residues: 460 loop : -0.69 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.019 0.001 TYR D 209 PHE 0.020 0.001 PHE E 319 TRP 0.013 0.001 TRP C 307 HIS 0.003 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00267 (16065) covalent geometry : angle 0.54526 (21907) SS BOND : bond 0.00701 ( 10) SS BOND : angle 1.23489 ( 20) hydrogen bonds : bond 0.04312 ( 775) hydrogen bonds : angle 5.33117 ( 2556) link_BETA1-4 : bond 0.00200 ( 5) link_BETA1-4 : angle 1.20897 ( 15) link_NAG-ASN : bond 0.00380 ( 15) link_NAG-ASN : angle 2.90157 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7033 (mt-10) REVERT: A 305 PRO cc_start: 0.6854 (Cg_exo) cc_final: 0.6632 (Cg_endo) REVERT: B 61 ASP cc_start: 0.7575 (t0) cc_final: 0.7255 (t0) REVERT: B 315 TRP cc_start: 0.7567 (m-10) cc_final: 0.6616 (t60) REVERT: C 460 THR cc_start: 0.7455 (m) cc_final: 0.7180 (m) REVERT: C 465 MET cc_start: 0.7090 (ttp) cc_final: 0.6854 (mtp) REVERT: D 137 ASP cc_start: 0.7917 (p0) cc_final: 0.7320 (p0) REVERT: E 40 MET cc_start: 0.8691 (mtp) cc_final: 0.8468 (mpp) REVERT: E 231 LEU cc_start: 0.8421 (mp) cc_final: 0.8106 (mp) REVERT: E 253 MET cc_start: 0.6577 (tpt) cc_final: 0.5922 (tpt) outliers start: 14 outliers final: 10 residues processed: 208 average time/residue: 0.2525 time to fit residues: 80.4796 Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 84 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 GLN E 170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.116960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103517 restraints weight = 97716.543| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.32 r_work: 0.3516 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16095 Z= 0.216 Angle : 0.604 9.030 21987 Z= 0.310 Chirality : 0.041 0.188 2503 Planarity : 0.005 0.057 2685 Dihedral : 8.237 88.142 2562 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.94 % Allowed : 5.99 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.19), residues: 1863 helix: 1.14 (0.19), residues: 691 sheet: -1.14 (0.22), residues: 459 loop : -0.61 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 309 TYR 0.036 0.002 TYR E 209 PHE 0.025 0.002 PHE E 319 TRP 0.013 0.001 TRP D 307 HIS 0.007 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00482 (16065) covalent geometry : angle 0.58638 (21907) SS BOND : bond 0.00758 ( 10) SS BOND : angle 1.29494 ( 20) hydrogen bonds : bond 0.04314 ( 775) hydrogen bonds : angle 5.22399 ( 2556) link_BETA1-4 : bond 0.00175 ( 5) link_BETA1-4 : angle 1.75908 ( 15) link_NAG-ASN : bond 0.00295 ( 15) link_NAG-ASN : angle 2.97101 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: A 277 THR cc_start: 0.8333 (m) cc_final: 0.8090 (t) REVERT: A 459 CYS cc_start: 0.7152 (m) cc_final: 0.6775 (p) REVERT: B 57 MET cc_start: 0.8327 (mtt) cc_final: 0.8069 (mtt) REVERT: B 315 TRP cc_start: 0.7709 (m-10) cc_final: 0.6766 (t60) REVERT: C 460 THR cc_start: 0.7552 (m) cc_final: 0.7313 (m) REVERT: E 40 MET cc_start: 0.8775 (mtp) cc_final: 0.8572 (mpp) REVERT: E 231 LEU cc_start: 0.8503 (mp) cc_final: 0.8229 (mp) outliers start: 16 outliers final: 14 residues processed: 199 average time/residue: 0.2746 time to fit residues: 81.8436 Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 431 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 125 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 150 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** E 26 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 = 0.3836 r_free = 0.3836 target = 0.117671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104006 restraints weight = 103097.990| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.42 r_work: 0.3516 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16095 Z= 0.169 Angle : 0.558 9.112 21987 Z= 0.285 Chirality : 0.040 0.153 2503 Planarity : 0.004 0.056 2685 Dihedral : 7.907 84.273 2562 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.94 % Allowed : 6.69 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 1863 helix: 1.24 (0.19), residues: 694 sheet: -1.17 (0.22), residues: 460 loop : -0.58 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 309 TYR 0.016 0.001 TYR E 209 PHE 0.024 0.001 PHE E 319 TRP 0.011 0.001 TRP D 307 HIS 0.006 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00375 (16065) covalent geometry : angle 0.54159 (21907) SS BOND : bond 0.00693 ( 10) SS BOND : angle 1.30226 ( 20) hydrogen bonds : bond 0.04026 ( 775) hydrogen bonds : angle 5.10206 ( 2556) link_BETA1-4 : bond 0.00097 ( 5) link_BETA1-4 : angle 1.22578 ( 15) link_NAG-ASN : bond 0.00302 ( 15) link_NAG-ASN : angle 2.88543 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: A 456 THR cc_start: 0.7142 (m) cc_final: 0.6799 (p) REVERT: A 459 CYS cc_start: 0.7159 (m) cc_final: 0.6827 (p) REVERT: B 57 MET cc_start: 0.8332 (mtt) cc_final: 0.8066 (mtt) REVERT: B 315 TRP cc_start: 0.7688 (m-10) cc_final: 0.6732 (t60) REVERT: C 188 GLU cc_start: 0.6450 (mm-30) cc_final: 0.6149 (tp30) REVERT: C 460 THR cc_start: 0.7564 (m) cc_final: 0.7312 (m) REVERT: C 465 MET cc_start: 0.7138 (ttp) cc_final: 0.6877 (mtp) REVERT: E 231 LEU cc_start: 0.8498 (mp) cc_final: 0.8227 (mp) outliers start: 16 outliers final: 14 residues processed: 198 average time/residue: 0.2635 time to fit residues: 79.2609 Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 9 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 157 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.118242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104687 restraints weight = 102216.258| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.39 r_work: 0.3529 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16095 Z= 0.133 Angle : 0.536 8.966 21987 Z= 0.273 Chirality : 0.040 0.167 2503 Planarity : 0.004 0.058 2685 Dihedral : 7.622 80.720 2562 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.00 % Allowed : 7.11 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1863 helix: 1.37 (0.19), residues: 703 sheet: -1.05 (0.22), residues: 460 loop : -0.47 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 309 TYR 0.020 0.001 TYR A 209 PHE 0.019 0.001 PHE E 319 TRP 0.011 0.001 TRP C 307 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00299 (16065) covalent geometry : angle 0.51871 (21907) SS BOND : bond 0.00685 ( 10) SS BOND : angle 1.27315 ( 20) hydrogen bonds : bond 0.03846 ( 775) hydrogen bonds : angle 4.96024 ( 2556) link_BETA1-4 : bond 0.00183 ( 5) link_BETA1-4 : angle 1.23086 ( 15) link_NAG-ASN : bond 0.00308 ( 15) link_NAG-ASN : angle 2.81616 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7813 (mp10) REVERT: A 456 THR cc_start: 0.7068 (m) cc_final: 0.6664 (p) REVERT: A 459 CYS cc_start: 0.7174 (m) cc_final: 0.6902 (p) REVERT: B 57 MET cc_start: 0.8329 (mtt) cc_final: 0.8054 (mtt) REVERT: B 315 TRP cc_start: 0.7686 (m-10) cc_final: 0.6764 (t60) REVERT: B 445 ASP cc_start: 0.6702 (m-30) cc_final: 0.6494 (m-30) REVERT: B 455 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6136 (t80) REVERT: C 188 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6131 (tp30) REVERT: E 231 LEU cc_start: 0.8465 (mp) cc_final: 0.8222 (mp) REVERT: E 431 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7413 (mp0) outliers start: 17 outliers final: 12 residues processed: 196 average time/residue: 0.2707 time to fit residues: 80.7578 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 128 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 148 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.116484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102697 restraints weight = 106828.717| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.46 r_work: 0.3490 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16095 Z= 0.228 Angle : 0.591 8.753 21987 Z= 0.304 Chirality : 0.041 0.284 2503 Planarity : 0.004 0.056 2685 Dihedral : 7.739 83.858 2562 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.23 % Allowed : 6.93 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1863 helix: 1.18 (0.19), residues: 705 sheet: -1.12 (0.22), residues: 461 loop : -0.57 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 309 TYR 0.024 0.002 TYR E 209 PHE 0.027 0.002 PHE E 319 TRP 0.012 0.001 TRP D 307 HIS 0.008 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00520 (16065) covalent geometry : angle 0.57470 (21907) SS BOND : bond 0.00707 ( 10) SS BOND : angle 1.31770 ( 20) hydrogen bonds : bond 0.04115 ( 775) hydrogen bonds : angle 5.10361 ( 2556) link_BETA1-4 : bond 0.00101 ( 5) link_BETA1-4 : angle 1.23074 ( 15) link_NAG-ASN : bond 0.00287 ( 15) link_NAG-ASN : angle 2.95318 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: A 277 THR cc_start: 0.8327 (m) cc_final: 0.8111 (t) REVERT: A 456 THR cc_start: 0.7049 (m) cc_final: 0.6573 (p) REVERT: A 459 CYS cc_start: 0.7174 (m) cc_final: 0.6902 (p) REVERT: B 57 MET cc_start: 0.8381 (mtt) cc_final: 0.8097 (mtt) REVERT: B 315 TRP cc_start: 0.7693 (m-10) cc_final: 0.6757 (t60) REVERT: B 455 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6132 (t80) REVERT: C 188 GLU cc_start: 0.6458 (mm-30) cc_final: 0.6034 (tp30) REVERT: E 231 LEU cc_start: 0.8525 (mp) cc_final: 0.8279 (mp) outliers start: 21 outliers final: 16 residues processed: 193 average time/residue: 0.2792 time to fit residues: 82.0191 Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.116427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102234 restraints weight = 113686.645| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.61 r_work: 0.3478 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16095 Z= 0.212 Angle : 0.584 8.914 21987 Z= 0.300 Chirality : 0.041 0.287 2503 Planarity : 0.004 0.056 2685 Dihedral : 7.742 86.776 2562 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.06 % Allowed : 7.46 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1863 helix: 1.12 (0.19), residues: 712 sheet: -1.23 (0.22), residues: 461 loop : -0.53 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 309 TYR 0.020 0.001 TYR E 209 PHE 0.022 0.001 PHE E 319 TRP 0.012 0.001 TRP D 307 HIS 0.007 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00483 (16065) covalent geometry : angle 0.56707 (21907) SS BOND : bond 0.00676 ( 10) SS BOND : angle 1.34705 ( 20) hydrogen bonds : bond 0.04092 ( 775) hydrogen bonds : angle 5.10355 ( 2556) link_BETA1-4 : bond 0.00086 ( 5) link_BETA1-4 : angle 1.25633 ( 15) link_NAG-ASN : bond 0.00284 ( 15) link_NAG-ASN : angle 2.91352 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: A 277 THR cc_start: 0.8305 (m) cc_final: 0.8104 (t) REVERT: B 57 MET cc_start: 0.8376 (mtt) cc_final: 0.8131 (mtt) REVERT: B 315 TRP cc_start: 0.7690 (m-10) cc_final: 0.6740 (t60) REVERT: B 455 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6213 (t80) REVERT: C 188 GLU cc_start: 0.6457 (mm-30) cc_final: 0.5996 (tp30) REVERT: E 231 LEU cc_start: 0.8588 (mp) cc_final: 0.8366 (mp) outliers start: 18 outliers final: 15 residues processed: 192 average time/residue: 0.2741 time to fit residues: 79.3613 Evaluate side-chains 192 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102178 restraints weight = 104478.510| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.41 r_work: 0.3485 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16095 Z= 0.240 Angle : 0.599 8.810 21987 Z= 0.310 Chirality : 0.041 0.169 2503 Planarity : 0.005 0.056 2685 Dihedral : 7.812 87.251 2562 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.06 % Allowed : 7.46 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1863 helix: 1.05 (0.19), residues: 713 sheet: -1.30 (0.22), residues: 464 loop : -0.60 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 309 TYR 0.020 0.002 TYR E 209 PHE 0.021 0.002 PHE E 319 TRP 0.013 0.001 TRP D 307 HIS 0.007 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00546 (16065) covalent geometry : angle 0.58254 (21907) SS BOND : bond 0.00696 ( 10) SS BOND : angle 1.36818 ( 20) hydrogen bonds : bond 0.04198 ( 775) hydrogen bonds : angle 5.15424 ( 2556) link_BETA1-4 : bond 0.00129 ( 5) link_BETA1-4 : angle 1.28307 ( 15) link_NAG-ASN : bond 0.00279 ( 15) link_NAG-ASN : angle 2.95861 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: A 277 THR cc_start: 0.8327 (m) cc_final: 0.8105 (t) REVERT: B 57 MET cc_start: 0.8363 (mtt) cc_final: 0.8110 (mtt) REVERT: B 315 TRP cc_start: 0.7684 (m-10) cc_final: 0.6818 (t60) REVERT: B 455 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.6171 (t80) REVERT: C 188 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5930 (tp30) REVERT: E 231 LEU cc_start: 0.8601 (mp) cc_final: 0.8380 (mp) outliers start: 18 outliers final: 14 residues processed: 190 average time/residue: 0.2672 time to fit residues: 77.3899 Evaluate side-chains 191 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 431 GLU Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 136 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104304 restraints weight = 106320.097| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.44 r_work: 0.3524 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16095 Z= 0.112 Angle : 0.529 9.168 21987 Z= 0.270 Chirality : 0.040 0.172 2503 Planarity : 0.004 0.055 2685 Dihedral : 7.378 86.982 2562 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.76 % Allowed : 7.87 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1863 helix: 1.37 (0.19), residues: 716 sheet: -1.20 (0.22), residues: 458 loop : -0.33 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 309 TYR 0.019 0.001 TYR A 209 PHE 0.024 0.001 PHE E 319 TRP 0.015 0.001 TRP C 307 HIS 0.004 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00253 (16065) covalent geometry : angle 0.51320 (21907) SS BOND : bond 0.00684 ( 10) SS BOND : angle 1.29571 ( 20) hydrogen bonds : bond 0.03747 ( 775) hydrogen bonds : angle 4.86443 ( 2556) link_BETA1-4 : bond 0.00267 ( 5) link_BETA1-4 : angle 1.21581 ( 15) link_NAG-ASN : bond 0.00304 ( 15) link_NAG-ASN : angle 2.73029 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: B 57 MET cc_start: 0.8267 (mtt) cc_final: 0.8023 (mtt) REVERT: B 315 TRP cc_start: 0.7669 (m-10) cc_final: 0.6793 (t60) REVERT: B 455 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6142 (t80) REVERT: C 188 GLU cc_start: 0.6364 (mm-30) cc_final: 0.5953 (tp30) REVERT: E 231 LEU cc_start: 0.8523 (mp) cc_final: 0.8290 (mp) outliers start: 13 outliers final: 10 residues processed: 187 average time/residue: 0.2671 time to fit residues: 74.9763 Evaluate side-chains 186 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103298 restraints weight = 111856.018| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.52 r_work: 0.3503 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16095 Z= 0.152 Angle : 0.537 8.757 21987 Z= 0.274 Chirality : 0.040 0.168 2503 Planarity : 0.004 0.055 2685 Dihedral : 7.298 85.611 2562 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.70 % Allowed : 7.87 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1863 helix: 1.39 (0.19), residues: 716 sheet: -1.17 (0.22), residues: 458 loop : -0.30 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 309 TYR 0.014 0.001 TYR E 209 PHE 0.013 0.001 PHE E 134 TRP 0.012 0.001 TRP D 307 HIS 0.005 0.001 HIS E 295 Details of bonding type rmsd covalent geometry : bond 0.00351 (16065) covalent geometry : angle 0.52086 (21907) SS BOND : bond 0.00688 ( 10) SS BOND : angle 1.26027 ( 20) hydrogen bonds : bond 0.03778 ( 775) hydrogen bonds : angle 4.86172 ( 2556) link_BETA1-4 : bond 0.00113 ( 5) link_BETA1-4 : angle 1.22300 ( 15) link_NAG-ASN : bond 0.00238 ( 15) link_NAG-ASN : angle 2.74161 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7627.73 seconds wall clock time: 129 minutes 46.55 seconds (7786.55 seconds total)