Starting phenix.real_space_refine on Mon Jul 6 16:30:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7koo_22979/07_2026/7koo_22979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7koo_22979/07_2026/7koo_22979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7koo_22979/07_2026/7koo_22979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7koo_22979/07_2026/7koo_22979_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7koo_22979/07_2026/7koo_22979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7koo_22979/07_2026/7koo_22979.map" } resolution = 3.0 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 165 5.16 5 C 12210 2.51 5 N 3035 2.21 5 O 3500 1.98 5 H 18180 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37095 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 6285 Classifications: {'peptide': 392} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1041 Classifications: {'peptide': 71} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 63} Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, G, H, I, J, M, O, Q, S, N, P, R, T Time building chain proxies: 7.60, per 1000 atoms: 0.20 Number of scatterers: 37095 At special positions: 0 Unit cell: (130.559, 129.48, 167.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 165 16.00 O 3500 8.00 N 3035 7.00 C 12210 6.00 H 18180 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " 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 ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG B 501 " - " ASN B 67 " " NAG C 501 " - " ASN C 67 " " NAG D 501 " - " ASN D 67 " " NAG E 501 " - " ASN E 67 " " NAG K 1 " - " ASN A 110 " " NAG L 1 " - " ASN A 23 " " NAG M 1 " - " ASN B 110 " " NAG N 1 " - " ASN B 23 " " NAG O 1 " - " ASN C 110 " " NAG P 1 " - " ASN C 23 " " NAG Q 1 " - " ASN D 110 " " NAG R 1 " - " ASN D 23 " " NAG S 1 " - " ASN E 110 " " NAG T 1 " - " ASN E 23 " Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 944.1 milliseconds 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.3% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 removed outlier: 3.569A pdb=" N LYS A 5 " --> pdb=" O GLU A 1 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 84 " --> pdb=" O ASP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 465 removed outlier: 3.516A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.513A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 84' Processing helix chain 'B' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 3.520A pdb=" N SER B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.701A pdb=" N GLN C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 80 through 84' Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.066A pdb=" N LEU C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 227 Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.931A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 321 removed outlier: 3.647A pdb=" N ARG C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU C 416 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 removed outlier: 3.520A pdb=" N SER C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE D 84 " --> pdb=" O ASP D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing helix chain 'D' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 227 Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 321 removed outlier: 3.646A pdb=" N ARG D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 465 removed outlier: 3.516A pdb=" N GLU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU D 416 " --> pdb=" O LYS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.514A pdb=" N VAL E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.702A pdb=" N GLN E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE E 84 " --> pdb=" O ASP E 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 80 through 84' Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.065A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 227 Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 237 through 260 removed outlier: 3.932A pdb=" N LEU E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 321 removed outlier: 3.647A pdb=" N ARG E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 465 removed outlier: 3.517A pdb=" N GLU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 478 removed outlier: 3.521A pdb=" N SER E 475 " --> pdb=" O VAL E 471 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.011A 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: 3.503A pdb=" N ASN A 110 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 48 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP A 41 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR A 60 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.592A 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: 3.524A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.807A 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: 3.524A pdb=" N GLY A 146 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 21.375A pdb=" N ARG A 182 " --> pdb=" O CYS F 44 " (cutoff:3.500A) removed outlier: 18.350A pdb=" N CYS F 44 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 12.130A pdb=" N GLU A 184 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU F 42 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE A 186 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 22 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN B 110 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 48 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 41 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 60 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 29 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.807A 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: 3.523A pdb=" N GLY B 146 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 21.147A pdb=" N ARG B 182 " --> pdb=" O CYS G 44 " (cutoff:3.500A) removed outlier: 18.147A pdb=" N CYS G 44 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N GLU B 184 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N LEU G 42 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE B 186 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 22 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.011A 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: 3.503A pdb=" N ASN C 110 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 48 " --> pdb=" O ASP C 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP C 41 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR C 60 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 6.592A 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: 3.524A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.807A 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: 3.524A pdb=" N GLY C 146 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 21.090A pdb=" N ARG C 182 " --> pdb=" O CYS H 44 " (cutoff:3.500A) removed outlier: 18.140A pdb=" N CYS H 44 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 11.887A pdb=" N GLU C 184 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N LEU H 42 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE C 186 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU H 22 " --> pdb=" O ALA H 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.011A 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: 3.503A pdb=" N ASN D 110 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP D 41 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR D 60 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 29 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.524A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.807A 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: 3.524A pdb=" N GLY D 146 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 21.338A pdb=" N ARG D 182 " --> pdb=" O CYS I 44 " (cutoff:3.500A) removed outlier: 18.360A pdb=" N CYS I 44 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 12.052A pdb=" N GLU D 184 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LEU I 42 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE D 186 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU I 22 " --> pdb=" O ALA I 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 3.503A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.011A 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: 3.503A pdb=" N ASN E 110 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP E 41 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR E 60 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 29 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.807A 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: 3.523A pdb=" N GLY E 146 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 21.218A pdb=" N ARG E 182 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 18.273A pdb=" N CYS J 44 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N GLU E 184 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N LEU J 42 " --> pdb=" O GLU E 184 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE E 186 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU J 22 " --> pdb=" O ALA J 45 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2940 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: 8.34 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18135 1.03 - 1.23: 336 1.23 - 1.43: 7859 1.43 - 1.62: 11045 1.62 - 1.82: 220 Bond restraints: 37595 Sorted by residual: bond pdb=" C ALA E 101 " pdb=" N THR E 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.37e+01 bond pdb=" C ALA B 101 " pdb=" N THR B 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.37e+01 bond pdb=" C ALA A 101 " pdb=" N THR A 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.35e+01 bond pdb=" C ALA D 101 " pdb=" N THR D 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.35e+01 bond pdb=" C ALA C 101 " pdb=" N THR C 102 " ideal model delta sigma weight residual 1.329 1.240 0.090 1.36e-02 5.41e+03 4.33e+01 ... (remaining 37590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 67607 5.28 - 10.57: 183 10.57 - 15.85: 35 15.85 - 21.13: 5 21.13 - 26.41: 15 Bond angle restraints: 67845 Sorted by residual: angle pdb=" CB LEU D 292 " pdb=" CG LEU D 292 " pdb=" HG LEU D 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU B 292 " pdb=" CG LEU B 292 " pdb=" HG LEU B 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU A 292 " pdb=" CG LEU A 292 " pdb=" HG LEU A 292 " ideal model delta sigma weight residual 109.00 82.59 26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" CB LEU E 292 " pdb=" CG LEU E 292 " pdb=" HG LEU E 292 " ideal model delta sigma weight residual 109.00 82.61 26.39 3.00e+00 1.11e-01 7.74e+01 angle pdb=" CB LEU C 292 " pdb=" CG LEU C 292 " pdb=" HG LEU C 292 " ideal model delta sigma weight residual 109.00 82.61 26.39 3.00e+00 1.11e-01 7.74e+01 ... (remaining 67840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 17164 22.10 - 44.19: 866 44.19 - 66.29: 210 66.29 - 88.39: 58 88.39 - 110.49: 32 Dihedral angle restraints: 18330 sinusoidal: 10085 harmonic: 8245 Sorted by residual: dihedral pdb=" CB CYS D 127 " pdb=" SG CYS D 127 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 48.41 44.59 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CB CYS B 127 " pdb=" SG CYS B 127 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual 93.00 48.43 44.57 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" CB CYS A 127 " pdb=" SG CYS A 127 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 48.44 44.56 1 1.00e+01 1.00e-02 2.76e+01 ... (remaining 18327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 3080 0.347 - 0.694: 5 0.694 - 1.041: 0 1.041 - 1.388: 0 1.388 - 1.735: 5 Chirality restraints: 3090 Sorted by residual: chirality pdb=" CG LEU C 292 " pdb=" CB LEU C 292 " pdb=" CD1 LEU C 292 " pdb=" CD2 LEU C 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.74 2.00e-01 2.50e+01 7.53e+01 chirality pdb=" CG LEU E 292 " pdb=" CB LEU E 292 " pdb=" CD1 LEU E 292 " pdb=" CD2 LEU E 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU B 292 " pdb=" CB LEU B 292 " pdb=" CD1 LEU B 292 " pdb=" CD2 LEU B 292 " both_signs ideal model delta sigma weight residual False -2.59 -0.85 -1.73 2.00e-01 2.50e+01 7.52e+01 ... (remaining 3087 not shown) Planarity restraints: 5420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 469 " -0.075 2.00e-02 2.50e+03 7.63e-02 8.73e+01 pdb=" CG ASN C 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN C 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN C 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN C 469 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 469 " -0.075 2.00e-02 2.50e+03 7.61e-02 8.70e+01 pdb=" CG ASN B 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN B 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN B 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN B 469 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 469 " -0.075 2.00e-02 2.50e+03 7.61e-02 8.69e+01 pdb=" CG ASN E 469 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN E 469 " 0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN E 469 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN E 469 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN E 469 " 0.107 2.00e-02 2.50e+03 ... (remaining 5417 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 623 2.08 - 2.71: 60129 2.71 - 3.34: 102073 3.34 - 3.97: 131964 3.97 - 4.60: 212097 Nonbonded interactions: 506886 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O GLU E 97 " model vdw 1.447 2.450 nonbonded pdb=" OD1 ASP D 88 " pdb=" HG SER D 147 " model vdw 1.543 2.450 nonbonded pdb=" OD1 ASP A 88 " pdb=" HG SER A 147 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASP B 88 " pdb=" HG SER B 147 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASP C 88 " pdb=" HG SER C 147 " model vdw 1.544 2.450 ... (remaining 506881 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.240 Extract box with map and model: 0.580 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 32.780 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.120 19455 Z= 0.510 Angle : 1.146 17.285 26565 Z= 0.677 Chirality : 0.090 1.735 3090 Planarity : 0.007 0.043 3250 Dihedral : 15.631 110.487 7545 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.20 % Allowed : 1.44 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.67 (0.17), residues: 2285 helix: 0.55 (0.17), residues: 905 sheet: -0.78 (0.22), residues: 475 loop : -1.17 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG I 25 TYR 0.039 0.003 TYR C 187 PHE 0.068 0.004 PHE C 452 TRP 0.016 0.002 TRP C 59 HIS 0.014 0.002 HIS E 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.51 (19415) covalent geometry : angle 1.13539 / 0.68 (26450) SS BOND : bond 0.00386 / 0.21 ( 5) SS BOND : angle 1.11346 / 0.59 ( 10) hydrogen bonds : bond 0.13010 / 8.61 ( 910) hydrogen bonds : angle 6.39753 / 4.46 ( 2940) link_ALPHA1-3 : bond 0.00366 / 0.20 ( 5) link_ALPHA1-3 : angle 1.65730 / 0.95 ( 15) link_BETA1-4 : bond 0.01179 / 0.62 ( 15) link_BETA1-4 : angle 1.76512 / 1.11 ( 45) link_NAG-ASN : bond 0.00261 / 0.13 ( 15) link_NAG-ASN : angle 3.58812 / 2.33 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.849 Fit side-chains REVERT: A 93 ASN cc_start: 0.8732 (p0) cc_final: 0.8352 (p0) REVERT: A 227 LEU cc_start: 0.8357 (tp) cc_final: 0.7984 (tp) REVERT: B 43 ASP cc_start: 0.7726 (t0) cc_final: 0.7478 (t0) REVERT: B 465 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7178 (mmm) REVERT: C 193 PRO cc_start: 0.8900 (OUTLIER) cc_final: 0.8585 (Cg_endo) REVERT: D 193 PRO cc_start: 0.8868 (OUTLIER) cc_final: 0.8530 (Cg_endo) REVERT: E 52 ASN cc_start: 0.8347 (t0) cc_final: 0.8083 (t0) REVERT: E 193 PRO cc_start: 0.8723 (OUTLIER) cc_final: 0.8370 (Cg_endo) REVERT: F 58 THR cc_start: 0.7634 (m) cc_final: 0.7396 (m) outliers start: 25 outliers final: 9 residues processed: 291 average time/residue: 0.7089 time to fit residues: 251.7500 Evaluate side-chains 203 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 193 PRO Chi-restraints excluded: chain D residue 111 SER Chi-restraints excluded: chain D residue 193 PRO Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 193 PRO Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain I residue 62 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 46 ASN C 38 GLN C 52 ASN D 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.181777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127961 restraints weight = 57768.949| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.51 r_work: 0.3095 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19455 Z= 0.141 Angle : 0.651 11.498 26565 Z= 0.323 Chirality : 0.081 1.753 3090 Planarity : 0.006 0.048 3250 Dihedral : 10.387 72.877 3223 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.53 % Allowed : 8.73 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.10 (0.17), residues: 2285 helix: 1.31 (0.17), residues: 890 sheet: -0.88 (0.20), residues: 600 loop : -0.85 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.011 0.001 TYR B 419 PHE 0.014 0.001 PHE A 452 TRP 0.012 0.001 TRP E 437 HIS 0.003 0.001 HIS F 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (19415) covalent geometry : angle 0.63630 / 0.32 (26450) SS BOND : bond 0.00249 / 0.13 ( 5) SS BOND : angle 0.49622 / 0.23 ( 10) hydrogen bonds : bond 0.05246 / 3.38 ( 910) hydrogen bonds : angle 4.97531 / 3.47 ( 2940) link_ALPHA1-3 : bond 0.00831 / 0.45 ( 5) link_ALPHA1-3 : angle 1.78577 / 1.00 ( 15) link_BETA1-4 : bond 0.00550 / 0.34 ( 15) link_BETA1-4 : angle 1.79003 / 1.18 ( 45) link_NAG-ASN : bond 0.00364 / 0.22 ( 15) link_NAG-ASN : angle 2.84019 / 1.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8516 (tptt) cc_final: 0.8173 (tppt) REVERT: A 227 LEU cc_start: 0.8005 (tp) cc_final: 0.7762 (tp) REVERT: A 450 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.6045 (mtt) REVERT: A 472 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: B 45 LYS cc_start: 0.8603 (tptt) cc_final: 0.8283 (tppt) REVERT: B 239 ILE cc_start: 0.6706 (mm) cc_final: 0.6425 (mm) REVERT: B 437 TRP cc_start: 0.5366 (m100) cc_final: 0.4790 (m-10) REVERT: C 43 ASP cc_start: 0.7965 (t0) cc_final: 0.7734 (t0) REVERT: C 45 LYS cc_start: 0.8560 (tptt) cc_final: 0.8169 (tppt) REVERT: C 116 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: C 437 TRP cc_start: 0.5277 (m100) cc_final: 0.4916 (m-10) REVERT: D 288 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.6534 (t) REVERT: E 52 ASN cc_start: 0.8776 (t0) cc_final: 0.8546 (t0) outliers start: 32 outliers final: 11 residues processed: 220 average time/residue: 0.7507 time to fit residues: 200.4864 Evaluate side-chains 193 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 160 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 56 GLN D 56 GLN E 38 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.171279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112929 restraints weight = 57659.946| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.35 r_work: 0.3004 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19455 Z= 0.218 Angle : 0.667 11.529 26565 Z= 0.331 Chirality : 0.083 1.739 3090 Planarity : 0.006 0.045 3250 Dihedral : 7.941 56.809 3202 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.16 % Allowed : 9.54 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2285 helix: 1.42 (0.17), residues: 890 sheet: -0.66 (0.21), residues: 595 loop : -0.80 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 98 TYR 0.012 0.002 TYR A 194 PHE 0.016 0.002 PHE C 319 TRP 0.015 0.001 TRP E 437 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (19415) covalent geometry : angle 0.65281 / 0.33 (26450) SS BOND : bond 0.00572 / 0.31 ( 5) SS BOND : angle 1.19897 / 0.62 ( 10) hydrogen bonds : bond 0.05188 / 3.33 ( 910) hydrogen bonds : angle 4.87028 / 3.39 ( 2940) link_ALPHA1-3 : bond 0.01191 / 0.64 ( 5) link_ALPHA1-3 : angle 2.05109 / 1.13 ( 15) link_BETA1-4 : bond 0.00481 / 0.28 ( 15) link_BETA1-4 : angle 2.16567 / 1.43 ( 45) link_NAG-ASN : bond 0.00223 / 0.14 ( 15) link_NAG-ASN : angle 2.45990 / 1.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.078 Fit side-chains REVERT: A 45 LYS cc_start: 0.8546 (tptt) cc_final: 0.8154 (tppt) REVERT: A 448 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5697 (p) REVERT: B 45 LYS cc_start: 0.8768 (tptt) cc_final: 0.7974 (tppt) REVERT: B 46 ASN cc_start: 0.8914 (m-40) cc_final: 0.8703 (m110) REVERT: B 437 TRP cc_start: 0.5755 (m100) cc_final: 0.5188 (m-10) REVERT: C 45 LYS cc_start: 0.8630 (tptt) cc_final: 0.8273 (tppt) REVERT: C 437 TRP cc_start: 0.5457 (m100) cc_final: 0.4917 (m-10) REVERT: D 116 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: D 296 HIS cc_start: 0.6361 (m-70) cc_final: 0.6124 (m90) REVERT: D 450 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5714 (mtm) REVERT: E 116 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: E 304 MET cc_start: 0.4320 (ttm) cc_final: 0.4057 (ttm) REVERT: G 41 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8295 (mt-10) outliers start: 45 outliers final: 23 residues processed: 206 average time/residue: 0.8702 time to fit residues: 215.8723 Evaluate side-chains 202 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 133 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** 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 = 0.3900 r_free = 0.3900 target = 0.169488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110030 restraints weight = 57818.029| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.43 r_work: 0.2977 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19455 Z= 0.143 Angle : 0.594 11.293 26565 Z= 0.293 Chirality : 0.081 1.711 3090 Planarity : 0.005 0.045 3250 Dihedral : 6.654 55.870 3202 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.92 % Allowed : 10.74 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.44 (0.17), residues: 2285 helix: 1.75 (0.17), residues: 880 sheet: -0.43 (0.21), residues: 595 loop : -0.68 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.009 0.001 TYR E 273 PHE 0.011 0.001 PHE C 99 TRP 0.016 0.001 TRP E 437 HIS 0.003 0.001 HIS D 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (19415) covalent geometry : angle 0.58174 / 0.29 (26450) SS BOND : bond 0.00378 / 0.20 ( 5) SS BOND : angle 0.77511 / 0.40 ( 10) hydrogen bonds : bond 0.04658 / 3.01 ( 910) hydrogen bonds : angle 4.63712 / 3.22 ( 2940) link_ALPHA1-3 : bond 0.01185 / 0.64 ( 5) link_ALPHA1-3 : angle 2.17142 / 1.21 ( 15) link_BETA1-4 : bond 0.00449 / 0.27 ( 15) link_BETA1-4 : angle 1.61009 / 1.06 ( 45) link_NAG-ASN : bond 0.00241 / 0.15 ( 15) link_NAG-ASN : angle 2.20638 / 1.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8547 (tptt) cc_final: 0.8228 (tppt) REVERT: A 448 CYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5859 (p) REVERT: A 472 GLU cc_start: 0.6112 (mt-10) cc_final: 0.5777 (mp0) REVERT: B 45 LYS cc_start: 0.8526 (tptt) cc_final: 0.8142 (tppt) REVERT: B 437 TRP cc_start: 0.5964 (m100) cc_final: 0.5422 (m-10) REVERT: B 448 CYS cc_start: 0.6169 (m) cc_final: 0.5939 (t) REVERT: B 450 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5791 (mtt) REVERT: C 45 LYS cc_start: 0.8623 (tptt) cc_final: 0.8250 (tppt) REVERT: C 116 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: C 437 TRP cc_start: 0.5604 (m100) cc_final: 0.5012 (m-10) REVERT: D 116 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: D 450 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5745 (mtm) REVERT: E 116 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: E 295 HIS cc_start: 0.4460 (t70) cc_final: 0.4109 (t-90) REVERT: E 304 MET cc_start: 0.4345 (ttm) cc_final: 0.4114 (ttm) REVERT: E 464 LEU cc_start: 0.7123 (mp) cc_final: 0.6813 (mm) REVERT: G 41 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8279 (mt-10) outliers start: 40 outliers final: 19 residues processed: 215 average time/residue: 0.8027 time to fit residues: 208.8464 Evaluate side-chains 210 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 123 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN E 272 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.169918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110247 restraints weight = 57984.571| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.10 r_work: 0.2993 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 19455 Z= 0.249 Angle : 0.688 11.009 26565 Z= 0.342 Chirality : 0.082 1.715 3090 Planarity : 0.006 0.052 3250 Dihedral : 6.468 51.827 3202 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.64 % Allowed : 10.65 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2285 helix: 1.54 (0.17), residues: 880 sheet: -0.35 (0.21), residues: 575 loop : -0.95 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 36 TYR 0.012 0.002 TYR B 194 PHE 0.017 0.002 PHE A 99 TRP 0.017 0.001 TRP E 437 HIS 0.005 0.002 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.25 (19415) covalent geometry : angle 0.67546 / 0.34 (26450) SS BOND : bond 0.00730 / 0.39 ( 5) SS BOND : angle 1.39912 / 0.72 ( 10) hydrogen bonds : bond 0.05032 / 3.26 ( 910) hydrogen bonds : angle 4.81165 / 3.35 ( 2940) link_ALPHA1-3 : bond 0.00942 / 0.51 ( 5) link_ALPHA1-3 : angle 2.07446 / 1.14 ( 15) link_BETA1-4 : bond 0.00424 / 0.26 ( 15) link_BETA1-4 : angle 2.08607 / 1.37 ( 45) link_NAG-ASN : bond 0.00193 / 0.10 ( 15) link_NAG-ASN : angle 2.22409 / 1.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8552 (tptt) cc_final: 0.8286 (tppt) REVERT: A 253 MET cc_start: 0.6680 (mmp) cc_final: 0.6410 (mmp) REVERT: A 259 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6725 (tp) REVERT: B 45 LYS cc_start: 0.8655 (tptt) cc_final: 0.8332 (tppt) REVERT: B 272 GLN cc_start: 0.7188 (mt0) cc_final: 0.6716 (mt0) REVERT: B 437 TRP cc_start: 0.6226 (m100) cc_final: 0.5696 (m-10) REVERT: C 45 LYS cc_start: 0.8599 (tptt) cc_final: 0.8308 (tppt) REVERT: C 116 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: C 128 TYR cc_start: 0.7616 (t80) cc_final: 0.6758 (t80) REVERT: C 161 GLU cc_start: 0.8497 (mp0) cc_final: 0.8095 (mp0) REVERT: C 437 TRP cc_start: 0.6216 (m100) cc_final: 0.5847 (m-10) REVERT: D 116 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: D 450 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.6062 (mtm) REVERT: E 116 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: E 304 MET cc_start: 0.4597 (ttm) cc_final: 0.4385 (ttm) REVERT: E 444 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.7124 (p) REVERT: G 41 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8327 (mt-10) outliers start: 55 outliers final: 33 residues processed: 232 average time/residue: 0.7091 time to fit residues: 201.0810 Evaluate side-chains 231 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 192 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 448 CYS Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 15 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 208 optimal weight: 0.3980 chunk 229 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN E 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.175807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121141 restraints weight = 57456.722| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.78 r_work: 0.3049 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19455 Z= 0.116 Angle : 0.566 11.275 26565 Z= 0.281 Chirality : 0.080 1.706 3090 Planarity : 0.005 0.048 3250 Dihedral : 5.892 52.603 3202 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.77 % Allowed : 12.13 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.58 (0.18), residues: 2285 helix: 1.84 (0.17), residues: 880 sheet: -0.16 (0.21), residues: 575 loop : -0.73 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 185 TYR 0.010 0.001 TYR A 128 PHE 0.010 0.001 PHE C 99 TRP 0.011 0.001 TRP E 437 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (19415) covalent geometry : angle 0.55590 / 0.28 (26450) SS BOND : bond 0.00292 / 0.15 ( 5) SS BOND : angle 0.65315 / 0.34 ( 10) hydrogen bonds : bond 0.04398 / 2.84 ( 910) hydrogen bonds : angle 4.50754 / 3.13 ( 2940) link_ALPHA1-3 : bond 0.01095 / 0.58 ( 5) link_ALPHA1-3 : angle 1.90398 / 1.06 ( 15) link_BETA1-4 : bond 0.00437 / 0.27 ( 15) link_BETA1-4 : angle 1.38526 / 0.90 ( 45) link_NAG-ASN : bond 0.00250 / 0.16 ( 15) link_NAG-ASN : angle 2.04575 / 1.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8521 (tptt) cc_final: 0.8291 (tppt) REVERT: B 45 LYS cc_start: 0.8644 (tptt) cc_final: 0.8318 (tppt) REVERT: B 272 GLN cc_start: 0.7155 (mt0) cc_final: 0.6689 (mt0) REVERT: B 437 TRP cc_start: 0.6186 (m100) cc_final: 0.5678 (m-10) REVERT: B 448 CYS cc_start: 0.6466 (m) cc_final: 0.6198 (t) REVERT: C 116 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: C 128 TYR cc_start: 0.7484 (t80) cc_final: 0.6675 (t80) REVERT: C 437 TRP cc_start: 0.6142 (m100) cc_final: 0.5721 (m-10) REVERT: D 116 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: D 450 MET cc_start: 0.6289 (ttm) cc_final: 0.6011 (mtm) REVERT: E 116 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: E 295 HIS cc_start: 0.4824 (t70) cc_final: 0.4533 (t-90) REVERT: E 304 MET cc_start: 0.4598 (ttm) cc_final: 0.4394 (ttm) REVERT: E 444 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.7070 (p) REVERT: G 41 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8296 (mt-10) REVERT: H 23 CYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7911 (m) REVERT: J 63 ASP cc_start: 0.5966 (p0) cc_final: 0.5712 (m-30) outliers start: 37 outliers final: 24 residues processed: 224 average time/residue: 0.7173 time to fit residues: 198.0976 Evaluate side-chains 225 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain E residue 450 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 177 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 216 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** 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 = 0.3968 r_free = 0.3968 target = 0.174265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116072 restraints weight = 57715.687| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.23 r_work: 0.3064 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19455 Z= 0.119 Angle : 0.560 11.139 26565 Z= 0.275 Chirality : 0.079 1.708 3090 Planarity : 0.005 0.047 3250 Dihedral : 5.662 53.383 3202 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.92 % Allowed : 12.18 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.67 (0.17), residues: 2285 helix: 1.94 (0.17), residues: 880 sheet: -0.14 (0.21), residues: 575 loop : -0.70 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.009 0.001 TYR A 128 PHE 0.008 0.001 PHE C 274 TRP 0.011 0.001 TRP E 437 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (19415) covalent geometry : angle 0.55023 / 0.27 (26450) SS BOND : bond 0.00314 / 0.16 ( 5) SS BOND : angle 0.72946 / 0.38 ( 10) hydrogen bonds : bond 0.04232 / 2.74 ( 910) hydrogen bonds : angle 4.41746 / 3.07 ( 2940) link_ALPHA1-3 : bond 0.00870 / 0.47 ( 5) link_ALPHA1-3 : angle 1.72488 / 0.97 ( 15) link_BETA1-4 : bond 0.00367 / 0.22 ( 15) link_BETA1-4 : angle 1.55696 / 1.03 ( 45) link_NAG-ASN : bond 0.00182 / 0.12 ( 15) link_NAG-ASN : angle 1.98525 / 1.21 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8545 (tptt) cc_final: 0.8328 (tppt) REVERT: A 116 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: A 259 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6754 (tp) REVERT: B 45 LYS cc_start: 0.8667 (tptt) cc_final: 0.8342 (tppt) REVERT: B 272 GLN cc_start: 0.7259 (mt0) cc_final: 0.6778 (mt0) REVERT: B 437 TRP cc_start: 0.6363 (m100) cc_final: 0.5700 (m-10) REVERT: B 444 VAL cc_start: 0.7138 (p) cc_final: 0.6919 (p) REVERT: B 448 CYS cc_start: 0.6397 (m) cc_final: 0.6190 (t) REVERT: C 116 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: C 128 TYR cc_start: 0.7529 (t80) cc_final: 0.6722 (t80) REVERT: C 437 TRP cc_start: 0.6134 (m100) cc_final: 0.5669 (m-10) REVERT: D 116 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: D 450 MET cc_start: 0.6317 (ttm) cc_final: 0.6055 (mtm) REVERT: E 304 MET cc_start: 0.4565 (ttm) cc_final: 0.4325 (ttm) REVERT: E 444 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.7061 (p) REVERT: E 464 LEU cc_start: 0.7584 (mp) cc_final: 0.7304 (mm) REVERT: F 23 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7598 (p) REVERT: H 23 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7927 (m) outliers start: 40 outliers final: 24 residues processed: 230 average time/residue: 0.7009 time to fit residues: 198.4954 Evaluate side-chains 232 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 204 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN ** B 295 HIS ** 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 = 0.3979 r_free = 0.3979 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115819 restraints weight = 57270.612| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.92 r_work: 0.3028 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19455 Z= 0.148 Angle : 0.578 11.111 26565 Z= 0.286 Chirality : 0.080 1.705 3090 Planarity : 0.005 0.046 3250 Dihedral : 5.677 52.950 3202 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.87 % Allowed : 12.28 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2285 helix: 1.92 (0.17), residues: 880 sheet: -0.14 (0.22), residues: 550 loop : -0.61 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.009 0.001 TYR A 128 PHE 0.014 0.001 PHE A 99 TRP 0.013 0.001 TRP E 437 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (19415) covalent geometry : angle 0.56850 / 0.28 (26450) SS BOND : bond 0.00424 / 0.22 ( 5) SS BOND : angle 0.88888 / 0.45 ( 10) hydrogen bonds : bond 0.04288 / 2.78 ( 910) hydrogen bonds : angle 4.43958 / 3.09 ( 2940) link_ALPHA1-3 : bond 0.00850 / 0.46 ( 5) link_ALPHA1-3 : angle 1.72812 / 0.97 ( 15) link_BETA1-4 : bond 0.00399 / 0.24 ( 15) link_BETA1-4 : angle 1.56644 / 1.03 ( 45) link_NAG-ASN : bond 0.00159 / 0.11 ( 15) link_NAG-ASN : angle 1.92489 / 1.16 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8557 (tptt) cc_final: 0.8296 (tppt) REVERT: A 116 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: A 253 MET cc_start: 0.6651 (mmp) cc_final: 0.6154 (mmp) REVERT: A 259 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6471 (tp) REVERT: A 260 MET cc_start: 0.6080 (mtp) cc_final: 0.5752 (mtp) REVERT: B 45 LYS cc_start: 0.8680 (tptt) cc_final: 0.8318 (tppt) REVERT: B 272 GLN cc_start: 0.7317 (mt0) cc_final: 0.6706 (mt0) REVERT: B 437 TRP cc_start: 0.6295 (m100) cc_final: 0.5629 (m-10) REVERT: B 444 VAL cc_start: 0.7057 (OUTLIER) cc_final: 0.6823 (p) REVERT: B 448 CYS cc_start: 0.6395 (m) cc_final: 0.6175 (t) REVERT: C 116 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: C 128 TYR cc_start: 0.7495 (t80) cc_final: 0.6690 (t80) REVERT: C 437 TRP cc_start: 0.6193 (m100) cc_final: 0.5706 (m-10) REVERT: D 116 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: D 450 MET cc_start: 0.6311 (ttm) cc_final: 0.6054 (mtm) REVERT: E 304 MET cc_start: 0.4507 (ttm) cc_final: 0.4261 (ttm) REVERT: E 444 VAL cc_start: 0.7290 (OUTLIER) cc_final: 0.7064 (p) REVERT: E 464 LEU cc_start: 0.7499 (mp) cc_final: 0.7230 (mm) REVERT: H 23 CYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7953 (m) REVERT: J 63 ASP cc_start: 0.5879 (p0) cc_final: 0.5662 (m-30) outliers start: 39 outliers final: 28 residues processed: 235 average time/residue: 0.8054 time to fit residues: 233.6230 Evaluate side-chains 237 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 104 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 163 optimal weight: 0.3980 chunk 168 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN ** A 295 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.172977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113491 restraints weight = 58106.730| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.05 r_work: 0.3061 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19455 Z= 0.115 Angle : 0.550 11.167 26565 Z= 0.270 Chirality : 0.079 1.705 3090 Planarity : 0.004 0.047 3250 Dihedral : 5.502 53.238 3202 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.73 % Allowed : 12.81 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.17), residues: 2285 helix: 2.03 (0.17), residues: 880 sheet: -0.01 (0.21), residues: 585 loop : -0.64 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.009 0.001 TYR A 128 PHE 0.008 0.001 PHE A 99 TRP 0.016 0.001 TRP A 437 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (19415) covalent geometry : angle 0.54097 / 0.27 (26450) SS BOND : bond 0.00314 / 0.17 ( 5) SS BOND : angle 0.66987 / 0.35 ( 10) hydrogen bonds : bond 0.04066 / 2.64 ( 910) hydrogen bonds : angle 4.31652 / 3.00 ( 2940) link_ALPHA1-3 : bond 0.00794 / 0.43 ( 5) link_ALPHA1-3 : angle 1.61704 / 0.91 ( 15) link_BETA1-4 : bond 0.00425 / 0.25 ( 15) link_BETA1-4 : angle 1.42267 / 0.93 ( 45) link_NAG-ASN : bond 0.00190 / 0.12 ( 15) link_NAG-ASN : angle 1.88129 / 1.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8617 (tptt) cc_final: 0.8357 (tppt) REVERT: A 116 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: A 260 MET cc_start: 0.6030 (mtp) cc_final: 0.5740 (mtp) REVERT: B 45 LYS cc_start: 0.8723 (tptt) cc_final: 0.8368 (tppt) REVERT: B 272 GLN cc_start: 0.7407 (mt0) cc_final: 0.6770 (mt0) REVERT: B 437 TRP cc_start: 0.6298 (m100) cc_final: 0.5659 (m-10) REVERT: B 444 VAL cc_start: 0.7216 (OUTLIER) cc_final: 0.6991 (p) REVERT: B 472 GLU cc_start: 0.5665 (mp0) cc_final: 0.5429 (mp0) REVERT: C 116 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: C 128 TYR cc_start: 0.7516 (t80) cc_final: 0.6721 (t80) REVERT: C 437 TRP cc_start: 0.6296 (m100) cc_final: 0.5799 (m-10) REVERT: D 116 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: E 304 MET cc_start: 0.4504 (ttm) cc_final: 0.4253 (ttm) REVERT: E 444 VAL cc_start: 0.7397 (OUTLIER) cc_final: 0.7166 (p) REVERT: E 464 LEU cc_start: 0.7575 (mp) cc_final: 0.7316 (mm) REVERT: H 23 CYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8047 (m) REVERT: J 63 ASP cc_start: 0.5861 (p0) cc_final: 0.5628 (m-30) outliers start: 36 outliers final: 22 residues processed: 230 average time/residue: 0.8153 time to fit residues: 230.1593 Evaluate side-chains 231 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 75 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 209 optimal weight: 0.0050 chunk 219 optimal weight: 2.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.173794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114745 restraints weight = 57496.989| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.90 r_work: 0.2977 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19455 Z= 0.176 Angle : 0.595 11.093 26565 Z= 0.293 Chirality : 0.080 1.707 3090 Planarity : 0.005 0.044 3250 Dihedral : 5.671 52.138 3202 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.58 % Allowed : 13.00 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.64 (0.17), residues: 2285 helix: 1.91 (0.17), residues: 880 sheet: -0.12 (0.21), residues: 575 loop : -0.74 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.009 0.001 TYR D 31 PHE 0.015 0.001 PHE A 99 TRP 0.020 0.001 TRP A 437 HIS 0.009 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (19415) covalent geometry : angle 0.58514 / 0.29 (26450) SS BOND : bond 0.00516 / 0.27 ( 5) SS BOND : angle 1.01330 / 0.51 ( 10) hydrogen bonds : bond 0.04301 / 2.80 ( 910) hydrogen bonds : angle 4.44123 / 3.09 ( 2940) link_ALPHA1-3 : bond 0.00698 / 0.38 ( 5) link_ALPHA1-3 : angle 1.70408 / 0.96 ( 15) link_BETA1-4 : bond 0.00401 / 0.24 ( 15) link_BETA1-4 : angle 1.62877 / 1.06 ( 45) link_NAG-ASN : bond 0.00144 / 0.09 ( 15) link_NAG-ASN : angle 1.91354 / 1.16 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8596 (tptt) cc_final: 0.8315 (tppt) REVERT: A 116 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: B 45 LYS cc_start: 0.8689 (tptt) cc_final: 0.8311 (tppt) REVERT: B 272 GLN cc_start: 0.7395 (mt0) cc_final: 0.6733 (mt0) REVERT: B 437 TRP cc_start: 0.6344 (m100) cc_final: 0.5626 (m-10) REVERT: B 444 VAL cc_start: 0.7038 (OUTLIER) cc_final: 0.6799 (p) REVERT: B 472 GLU cc_start: 0.5663 (mp0) cc_final: 0.5432 (mp0) REVERT: C 116 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: C 128 TYR cc_start: 0.7505 (t80) cc_final: 0.6698 (t80) REVERT: C 437 TRP cc_start: 0.6212 (m100) cc_final: 0.5711 (m-10) REVERT: D 116 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: E 116 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7691 (tm130) REVERT: E 304 MET cc_start: 0.4466 (ttm) cc_final: 0.4225 (ttm) REVERT: E 444 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6999 (p) REVERT: E 464 LEU cc_start: 0.7521 (mp) cc_final: 0.7251 (mm) REVERT: H 23 CYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7973 (m) REVERT: J 63 ASP cc_start: 0.5883 (p0) cc_final: 0.5673 (m-30) outliers start: 33 outliers final: 22 residues processed: 231 average time/residue: 0.7753 time to fit residues: 222.0367 Evaluate side-chains 239 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 116 GLN Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 444 VAL Chi-restraints excluded: chain E residue 448 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain J residue 61 SER Chi-restraints excluded: chain J residue 62 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 76 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 272 GLN ** A 295 HIS ** 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 = 0.3946 r_free = 0.3946 target = 0.172300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117041 restraints weight = 57633.484| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.85 r_work: 0.2967 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.296 19455 Z= 0.216 Angle : 0.764 59.136 26565 Z= 0.416 Chirality : 0.080 1.706 3090 Planarity : 0.005 0.044 3250 Dihedral : 5.669 51.920 3202 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.58 % Allowed : 12.95 % Favored : 85.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 7.41 % 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: 0.63 (0.17), residues: 2285 helix: 1.91 (0.17), residues: 880 sheet: -0.13 (0.21), residues: 575 loop : -0.74 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.008 0.001 TYR A 128 PHE 0.014 0.001 PHE A 99 TRP 0.016 0.001 TRP A 437 HIS 0.008 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (19415) covalent geometry : angle 0.75732 / 0.41 (26450) SS BOND : bond 0.00417 / 0.22 ( 5) SS BOND : angle 0.97522 / 0.49 ( 10) hydrogen bonds : bond 0.04262 / 2.77 ( 910) hydrogen bonds : angle 4.44269 / 3.10 ( 2940) link_ALPHA1-3 : bond 0.00867 / 0.46 ( 5) link_ALPHA1-3 : angle 1.81853 / 1.03 ( 15) link_BETA1-4 : bond 0.00367 / 0.22 ( 15) link_BETA1-4 : angle 1.62532 / 1.05 ( 45) link_NAG-ASN : bond 0.00129 / 0.08 ( 15) link_NAG-ASN : angle 1.90822 / 1.15 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10885.92 seconds wall clock time: 185 minutes 9.84 seconds (11109.84 seconds total)