Starting phenix.real_space_refine on Sat Mar 7 02:41:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7koo_22979/03_2026/7koo_22979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7koo_22979/03_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_22979/03_2026/7koo_22979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7koo_22979/03_2026/7koo_22979_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7koo_22979/03_2026/7koo_22979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7koo_22979/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 7.43, 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: 3.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.93 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: 7.93 Time building geometry restraints manager: 4.53 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: 0.04 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: 1.030 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: 0.140 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 covalent geometry : bond 0.00977 (19415) covalent geometry : angle 1.13539 (26450) SS BOND : bond 0.00386 ( 5) SS BOND : angle 1.11346 ( 10) hydrogen bonds : bond 0.13010 ( 910) hydrogen bonds : angle 6.39753 ( 2940) link_ALPHA1-3 : bond 0.00366 ( 5) link_ALPHA1-3 : angle 1.65730 ( 15) link_BETA1-4 : bond 0.01179 ( 15) link_BETA1-4 : angle 1.76512 ( 45) link_NAG-ASN : bond 0.00261 ( 15) link_NAG-ASN : angle 3.58812 ( 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 : 0.918 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: 0.7985 (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: 0.7957 time to fit residues: 278.9980 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 : 1.003 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 46 ASN C 38 GLN C 52 ASN D 38 GLN E 46 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.180149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126337 restraints weight = 57962.891| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.97 r_work: 0.3251 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1353 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= 0.142 Angle : 0.648 11.501 26565 Z= 0.321 Chirality : 0.081 1.737 3090 Planarity : 0.006 0.047 3250 Dihedral : 10.285 72.058 3223 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.58 % Allowed : 8.78 % Favored : 89.64 % 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: 1.32 (0.17), residues: 890 sheet: -0.88 (0.20), residues: 600 loop : -0.86 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 25 TYR 0.012 0.001 TYR B 419 PHE 0.014 0.001 PHE A 452 TRP 0.011 0.001 TRP E 59 HIS 0.002 0.001 HIS F 4 Details of bonding type rmsd covalent geometry : bond 0.00330 (19415) covalent geometry : angle 0.63340 (26450) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.49644 ( 10) hydrogen bonds : bond 0.05267 ( 910) hydrogen bonds : angle 4.97972 ( 2940) link_ALPHA1-3 : bond 0.00922 ( 5) link_ALPHA1-3 : angle 1.69138 ( 15) link_BETA1-4 : bond 0.00526 ( 15) link_BETA1-4 : angle 1.75410 ( 45) link_NAG-ASN : bond 0.00312 ( 15) link_NAG-ASN : angle 2.85628 ( 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 236 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8485 (tptt) cc_final: 0.8177 (tppt) REVERT: A 227 LEU cc_start: 0.8161 (tp) cc_final: 0.7902 (tp) REVERT: A 450 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.6069 (mtt) REVERT: A 472 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5623 (mp0) REVERT: B 45 LYS cc_start: 0.8574 (tptt) cc_final: 0.8300 (tppt) REVERT: B 239 ILE cc_start: 0.6872 (mm) cc_final: 0.6588 (mm) REVERT: B 437 TRP cc_start: 0.5513 (m100) cc_final: 0.4961 (m-10) REVERT: C 43 ASP cc_start: 0.8017 (t0) cc_final: 0.7800 (t0) REVERT: C 45 LYS cc_start: 0.8553 (tptt) cc_final: 0.8179 (tppt) REVERT: C 116 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: C 437 TRP cc_start: 0.5477 (m100) cc_final: 0.5130 (m-10) REVERT: D 288 THR cc_start: 0.7057 (OUTLIER) cc_final: 0.6788 (t) REVERT: D 437 TRP cc_start: 0.5574 (m100) cc_final: 0.5280 (m-10) REVERT: E 52 ASN cc_start: 0.8863 (t0) cc_final: 0.8597 (t0) outliers start: 33 outliers final: 11 residues processed: 218 average time/residue: 0.8263 time to fit residues: 215.7667 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 : 0.679 ------------------------------------------------------------------------------- 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: 3.9990 chunk 119 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 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: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN E 38 GLN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.174816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115325 restraints weight = 57680.835| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.98 r_work: 0.3083 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19455 Z= 0.153 Angle : 0.612 11.368 26565 Z= 0.303 Chirality : 0.081 1.733 3090 Planarity : 0.005 0.045 3250 Dihedral : 7.994 59.466 3202 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.82 % Allowed : 9.54 % Favored : 88.63 % 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: 0.28 (0.17), residues: 2285 helix: 1.63 (0.17), residues: 880 sheet: -0.60 (0.21), residues: 595 loop : -0.70 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.016 0.001 TYR B 419 PHE 0.014 0.001 PHE A 452 TRP 0.014 0.001 TRP E 437 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00371 (19415) covalent geometry : angle 0.59780 (26450) SS BOND : bond 0.00355 ( 5) SS BOND : angle 0.77484 ( 10) hydrogen bonds : bond 0.04919 ( 910) hydrogen bonds : angle 4.74347 ( 2940) link_ALPHA1-3 : bond 0.01111 ( 5) link_ALPHA1-3 : angle 1.84340 ( 15) link_BETA1-4 : bond 0.00315 ( 15) link_BETA1-4 : angle 1.86734 ( 45) link_NAG-ASN : bond 0.00233 ( 15) link_NAG-ASN : angle 2.50327 ( 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: 38 poor density : 188 time to evaluate : 0.948 Fit side-chains REVERT: A 45 LYS cc_start: 0.8548 (tptt) cc_final: 0.8169 (tppt) REVERT: A 472 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5518 (mp0) REVERT: B 45 LYS cc_start: 0.8706 (tptt) cc_final: 0.7843 (tppt) REVERT: B 46 ASN cc_start: 0.8884 (m-40) cc_final: 0.8669 (m110) REVERT: B 239 ILE cc_start: 0.6761 (mm) cc_final: 0.6484 (OUTLIER) REVERT: B 437 TRP cc_start: 0.5611 (m100) cc_final: 0.4744 (m-10) REVERT: B 448 CYS cc_start: 0.6089 (m) cc_final: 0.5865 (t) REVERT: C 43 ASP cc_start: 0.8145 (t0) cc_final: 0.7846 (t0) REVERT: C 45 LYS cc_start: 0.8611 (tptt) cc_final: 0.8058 (tppt) REVERT: D 116 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: D 272 GLN cc_start: 0.7464 (mt0) cc_final: 0.7211 (mt0) REVERT: D 450 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5840 (mtm) REVERT: E 116 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: E 304 MET cc_start: 0.4323 (ttm) cc_final: 0.4105 (ttm) outliers start: 38 outliers final: 19 residues processed: 205 average time/residue: 0.8334 time to fit residues: 204.3232 Evaluate side-chains 198 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 472 GLU 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 448 CYS Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 116 GLN 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 450 MET 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 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 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: 2.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 83 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3924 r_free = 0.3924 target = 0.171609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112350 restraints weight = 57648.263| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.35 r_work: 0.3034 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19455 Z= 0.149 Angle : 0.592 11.194 26565 Z= 0.292 Chirality : 0.081 1.717 3090 Planarity : 0.005 0.044 3250 Dihedral : 6.379 56.771 3202 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.92 % Allowed : 10.41 % Favored : 87.67 % 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: 0.52 (0.17), residues: 2285 helix: 1.84 (0.17), residues: 880 sheet: -0.43 (0.21), residues: 595 loop : -0.62 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.011 0.001 TYR B 419 PHE 0.015 0.001 PHE A 452 TRP 0.015 0.001 TRP E 437 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00357 (19415) covalent geometry : angle 0.58005 (26450) SS BOND : bond 0.00404 ( 5) SS BOND : angle 0.82695 ( 10) hydrogen bonds : bond 0.04550 ( 910) hydrogen bonds : angle 4.56643 ( 2940) link_ALPHA1-3 : bond 0.01260 ( 5) link_ALPHA1-3 : angle 2.18235 ( 15) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.72832 ( 45) link_NAG-ASN : bond 0.00221 ( 15) link_NAG-ASN : angle 2.15730 ( 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 230 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.832 Fit side-chains REVERT: A 45 LYS cc_start: 0.8561 (tptt) cc_final: 0.8251 (tppt) REVERT: A 259 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6800 (tp) REVERT: A 472 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5559 (mp0) REVERT: B 45 LYS cc_start: 0.8524 (tptt) cc_final: 0.8152 (tppt) REVERT: B 437 TRP cc_start: 0.5868 (m100) cc_final: 0.5303 (m-10) REVERT: C 45 LYS cc_start: 0.8622 (tptt) cc_final: 0.8258 (tppt) REVERT: C 116 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: D 116 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: D 272 GLN cc_start: 0.7386 (mt0) cc_final: 0.7090 (mt0) REVERT: D 450 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5889 (mtm) REVERT: E 116 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: E 472 GLU cc_start: 0.5516 (mp0) cc_final: 0.5288 (mp0) REVERT: G 41 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8212 (mt-10) outliers start: 40 outliers final: 20 residues processed: 212 average time/residue: 0.8563 time to fit residues: 216.7219 Evaluate side-chains 209 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 472 GLU 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 116 GLN Chi-restraints excluded: chain D residue 163 ASP 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 E residue 111 SER Chi-restraints excluded: chain E residue 116 GLN Chi-restraints excluded: chain E residue 128 TYR 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 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: 1.9990 chunk 171 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 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: 0.9980 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN B 56 GLN D 56 GLN E 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.168477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108315 restraints weight = 57207.596| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.95 r_work: 0.2993 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19455 Z= 0.214 Angle : 0.653 11.079 26565 Z= 0.325 Chirality : 0.082 1.722 3090 Planarity : 0.005 0.048 3250 Dihedral : 6.189 51.925 3202 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.54 % Allowed : 10.22 % Favored : 87.24 % 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: 0.41 (0.17), residues: 2285 helix: 1.70 (0.17), residues: 880 sheet: -0.23 (0.21), residues: 575 loop : -0.84 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 98 TYR 0.012 0.002 TYR B 194 PHE 0.017 0.002 PHE A 99 TRP 0.019 0.001 TRP E 437 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00529 (19415) covalent geometry : angle 0.64146 (26450) SS BOND : bond 0.00644 ( 5) SS BOND : angle 1.22914 ( 10) hydrogen bonds : bond 0.04809 ( 910) hydrogen bonds : angle 4.68706 ( 2940) link_ALPHA1-3 : bond 0.00961 ( 5) link_ALPHA1-3 : angle 1.92989 ( 15) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.91542 ( 45) link_NAG-ASN : bond 0.00176 ( 15) link_NAG-ASN : angle 2.19422 ( 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 254 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8552 (tptt) cc_final: 0.8243 (tppt) REVERT: A 253 MET cc_start: 0.6441 (mmt) cc_final: 0.6100 (mmp) REVERT: A 259 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6687 (tp) REVERT: B 45 LYS cc_start: 0.8633 (tptt) cc_final: 0.8263 (tppt) REVERT: B 272 GLN cc_start: 0.6991 (mt0) cc_final: 0.6565 (mt0) REVERT: B 437 TRP cc_start: 0.5996 (m100) cc_final: 0.5465 (m-10) REVERT: C 45 LYS cc_start: 0.8627 (tptt) cc_final: 0.8282 (tppt) REVERT: C 116 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7927 (tm-30) REVERT: C 128 TYR cc_start: 0.7527 (t80) cc_final: 0.6635 (t80) REVERT: D 116 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: D 130 ASP cc_start: 0.8198 (t0) cc_final: 0.7960 (t70) REVERT: D 450 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6229 (mtm) REVERT: E 116 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: E 295 HIS cc_start: 0.4548 (t70) cc_final: 0.4219 (t-90) REVERT: E 304 MET cc_start: 0.4282 (ttm) cc_final: 0.3936 (ttm) REVERT: G 41 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 53 outliers final: 31 residues processed: 235 average time/residue: 0.7987 time to fit residues: 227.4264 Evaluate side-chains 231 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 B residue 128 TYR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 448 CYS 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 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 128 TYR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 208 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 = 0.3904 r_free = 0.3904 target = 0.169786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112401 restraints weight = 57401.227| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.39 r_work: 0.3000 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2934 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= 0.120 Angle : 0.565 11.260 26565 Z= 0.280 Chirality : 0.080 1.704 3090 Planarity : 0.005 0.045 3250 Dihedral : 5.790 52.677 3202 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.87 % Allowed : 11.75 % Favored : 86.38 % 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: 0.60 (0.18), residues: 2285 helix: 1.90 (0.17), residues: 880 sheet: -0.36 (0.21), residues: 605 loop : -0.60 (0.21), residues: 800 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 0.011 0.001 PHE C 99 TRP 0.015 0.001 TRP E 437 HIS 0.005 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00283 (19415) covalent geometry : angle 0.55512 (26450) SS BOND : bond 0.00332 ( 5) SS BOND : angle 0.69556 ( 10) hydrogen bonds : bond 0.04341 ( 910) hydrogen bonds : angle 4.47438 ( 2940) link_ALPHA1-3 : bond 0.01025 ( 5) link_ALPHA1-3 : angle 1.83432 ( 15) link_BETA1-4 : bond 0.00439 ( 15) link_BETA1-4 : angle 1.44442 ( 45) link_NAG-ASN : bond 0.00231 ( 15) link_NAG-ASN : angle 1.99956 ( 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 241 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8574 (tptt) cc_final: 0.8255 (tppt) REVERT: A 253 MET cc_start: 0.6449 (mmt) cc_final: 0.6128 (mmp) REVERT: A 472 GLU cc_start: 0.6131 (mt-10) cc_final: 0.5872 (mp0) REVERT: B 45 LYS cc_start: 0.8654 (tptt) cc_final: 0.8257 (tppt) REVERT: B 272 GLN cc_start: 0.6975 (mt0) cc_final: 0.6543 (mt0) REVERT: B 437 TRP cc_start: 0.6003 (m100) cc_final: 0.5432 (m-10) REVERT: B 444 VAL cc_start: 0.6873 (OUTLIER) cc_final: 0.6663 (p) REVERT: C 45 LYS cc_start: 0.8617 (tptt) cc_final: 0.8258 (tppt) REVERT: C 116 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: C 128 TYR cc_start: 0.7457 (t80) cc_final: 0.6582 (t80) REVERT: C 448 CYS cc_start: 0.6120 (t) cc_final: 0.5865 (p) REVERT: D 116 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8108 (tm-30) REVERT: D 296 HIS cc_start: 0.5623 (m-70) cc_final: 0.5398 (m170) REVERT: D 450 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6303 (mtm) REVERT: E 116 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8086 (tm-30) REVERT: G 41 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8311 (mt-10) outliers start: 39 outliers final: 24 residues processed: 224 average time/residue: 0.7904 time to fit residues: 214.1905 Evaluate side-chains 229 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU 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 B residue 448 CYS 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 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 128 TYR 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 31 VAL 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 61 SER 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: 7.9990 chunk 81 optimal weight: 0.8980 chunk 188 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 134 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.168808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110629 restraints weight = 57661.533| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.43 r_work: 0.2999 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19455 Z= 0.142 Angle : 0.577 11.102 26565 Z= 0.284 Chirality : 0.080 1.707 3090 Planarity : 0.005 0.044 3250 Dihedral : 5.685 52.839 3202 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.16 % Allowed : 12.04 % Favored : 85.80 % 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: 0.59 (0.17), residues: 2285 helix: 1.92 (0.17), residues: 880 sheet: -0.38 (0.21), residues: 605 loop : -0.63 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.010 0.001 TYR A 128 PHE 0.010 0.001 PHE C 274 TRP 0.018 0.001 TRP D 437 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00348 (19415) covalent geometry : angle 0.56632 (26450) SS BOND : bond 0.00384 ( 5) SS BOND : angle 0.85353 ( 10) hydrogen bonds : bond 0.04281 ( 910) hydrogen bonds : angle 4.44715 ( 2940) link_ALPHA1-3 : bond 0.00940 ( 5) link_ALPHA1-3 : angle 1.80733 ( 15) link_BETA1-4 : bond 0.00359 ( 15) link_BETA1-4 : angle 1.60502 ( 45) link_NAG-ASN : bond 0.00155 ( 15) link_NAG-ASN : angle 1.98324 ( 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 252 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8575 (tptt) cc_final: 0.8271 (tppt) REVERT: A 253 MET cc_start: 0.6456 (mmt) cc_final: 0.6087 (mmp) REVERT: A 259 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.6292 (tp) REVERT: A 472 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5958 (mp0) REVERT: B 45 LYS cc_start: 0.8678 (tptt) cc_final: 0.8247 (tppt) REVERT: B 272 GLN cc_start: 0.6972 (mt0) cc_final: 0.6348 (mt0) REVERT: B 437 TRP cc_start: 0.6060 (m100) cc_final: 0.5369 (m-10) REVERT: B 444 VAL cc_start: 0.6875 (OUTLIER) cc_final: 0.6658 (p) REVERT: C 116 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: C 128 TYR cc_start: 0.7439 (t80) cc_final: 0.6588 (t80) REVERT: D 116 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: D 272 GLN cc_start: 0.7670 (mt0) cc_final: 0.7456 (pt0) REVERT: D 296 HIS cc_start: 0.5663 (m-70) cc_final: 0.5462 (m170) REVERT: D 450 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6356 (mtm) REVERT: F 3 CYS cc_start: 0.7977 (m) cc_final: 0.7723 (m) REVERT: G 41 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8354 (mt-10) REVERT: J 63 ASP cc_start: 0.5862 (p0) cc_final: 0.5626 (m-30) outliers start: 45 outliers final: 31 residues processed: 234 average time/residue: 0.7705 time to fit residues: 218.5372 Evaluate side-chains 239 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 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 B residue 448 CYS Chi-restraints excluded: chain C residue 76 THR 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 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 128 TYR 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 31 VAL Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain G residue 62 THR 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=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: 0.8980 chunk 183 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 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 = 0.3887 r_free = 0.3887 target = 0.168292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108074 restraints weight = 57409.451| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.34 r_work: 0.2962 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19455 Z= 0.153 Angle : 0.580 11.165 26565 Z= 0.286 Chirality : 0.080 1.705 3090 Planarity : 0.005 0.045 3250 Dihedral : 5.682 52.337 3202 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.16 % Allowed : 12.28 % Favored : 85.56 % 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: 1.93 (0.17), residues: 880 sheet: -0.15 (0.22), residues: 550 loop : -0.61 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.010 0.001 TYR A 128 PHE 0.013 0.001 PHE A 99 TRP 0.020 0.001 TRP D 437 HIS 0.007 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00376 (19415) covalent geometry : angle 0.57025 (26450) SS BOND : bond 0.00448 ( 5) SS BOND : angle 0.87347 ( 10) hydrogen bonds : bond 0.04300 ( 910) hydrogen bonds : angle 4.44583 ( 2940) link_ALPHA1-3 : bond 0.00829 ( 5) link_ALPHA1-3 : angle 1.72175 ( 15) link_BETA1-4 : bond 0.00404 ( 15) link_BETA1-4 : angle 1.54529 ( 45) link_NAG-ASN : bond 0.00158 ( 15) link_NAG-ASN : angle 1.93606 ( 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 255 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8601 (tptt) cc_final: 0.8287 (tppt) REVERT: A 253 MET cc_start: 0.6480 (mmt) cc_final: 0.6039 (mmp) REVERT: A 259 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6283 (tp) REVERT: A 472 GLU cc_start: 0.6139 (mt-10) cc_final: 0.5895 (mp0) REVERT: B 45 LYS cc_start: 0.8694 (tptt) cc_final: 0.8247 (tppt) REVERT: B 272 GLN cc_start: 0.7094 (mt0) cc_final: 0.6465 (mt0) REVERT: B 437 TRP cc_start: 0.6068 (m100) cc_final: 0.5358 (m-10) REVERT: B 444 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6582 (p) REVERT: C 116 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7983 (tm-30) REVERT: C 128 TYR cc_start: 0.7455 (t80) cc_final: 0.6604 (t80) REVERT: D 116 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: D 272 GLN cc_start: 0.7852 (mt0) cc_final: 0.7613 (pt0) REVERT: D 450 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6383 (mtm) REVERT: E 444 VAL cc_start: 0.6995 (OUTLIER) cc_final: 0.6783 (p) REVERT: F 3 CYS cc_start: 0.7938 (m) cc_final: 0.7690 (m) REVERT: G 41 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8412 (mt-10) REVERT: H 23 CYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7871 (m) REVERT: J 63 ASP cc_start: 0.5801 (p0) cc_final: 0.5575 (m-30) outliers start: 45 outliers final: 33 residues processed: 238 average time/residue: 0.7651 time to fit residues: 221.6753 Evaluate side-chains 246 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR 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 B residue 448 CYS 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 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 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 61 SER 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: 5.9990 chunk 135 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 163 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 186 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.172477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113769 restraints weight = 58083.810| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.32 r_work: 0.3071 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3242 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= 0.122 Angle : 0.556 11.164 26565 Z= 0.274 Chirality : 0.079 1.704 3090 Planarity : 0.005 0.044 3250 Dihedral : 5.541 52.424 3202 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.30 % Allowed : 12.18 % Favored : 85.52 % 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: 0.85 (0.17), residues: 2285 helix: 2.23 (0.17), residues: 850 sheet: -0.02 (0.22), residues: 560 loop : -0.68 (0.20), residues: 875 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 0.009 0.001 PHE A 99 TRP 0.024 0.001 TRP D 437 HIS 0.004 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00293 (19415) covalent geometry : angle 0.54688 (26450) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.70592 ( 10) hydrogen bonds : bond 0.04117 ( 910) hydrogen bonds : angle 4.34709 ( 2940) link_ALPHA1-3 : bond 0.00787 ( 5) link_ALPHA1-3 : angle 1.62763 ( 15) link_BETA1-4 : bond 0.00438 ( 15) link_BETA1-4 : angle 1.43332 ( 45) link_NAG-ASN : bond 0.00186 ( 15) link_NAG-ASN : angle 1.89632 ( 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 263 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8578 (tptt) cc_final: 0.8306 (tppt) REVERT: A 259 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6487 (tp) REVERT: A 437 TRP cc_start: 0.6477 (m100) cc_final: 0.6014 (m-10) REVERT: B 45 LYS cc_start: 0.8674 (tptt) cc_final: 0.8299 (tppt) REVERT: B 272 GLN cc_start: 0.7304 (mt0) cc_final: 0.6696 (mt0) REVERT: B 437 TRP cc_start: 0.6061 (m100) cc_final: 0.5386 (m-10) REVERT: B 444 VAL cc_start: 0.6932 (OUTLIER) cc_final: 0.6694 (p) REVERT: C 116 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: C 128 TYR cc_start: 0.7468 (t80) cc_final: 0.6660 (t80) REVERT: D 116 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: D 450 MET cc_start: 0.6750 (OUTLIER) cc_final: 0.6435 (mtm) REVERT: E 444 VAL cc_start: 0.7123 (OUTLIER) cc_final: 0.6907 (p) REVERT: F 3 CYS cc_start: 0.8093 (m) cc_final: 0.7879 (m) REVERT: G 41 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8372 (mt-10) REVERT: H 23 CYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8082 (m) REVERT: J 63 ASP cc_start: 0.5862 (p0) cc_final: 0.5609 (m-30) outliers start: 48 outliers final: 26 residues processed: 241 average time/residue: 0.7777 time to fit residues: 227.9054 Evaluate side-chains 244 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 444 VAL Chi-restraints excluded: chain B residue 448 CYS Chi-restraints excluded: chain C residue 76 THR 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 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 163 ASP 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 75 optimal weight: 7.9990 chunk 138 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 209 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN E 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113747 restraints weight = 57900.940| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.15 r_work: 0.2965 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19455 Z= 0.140 Angle : 0.570 11.159 26565 Z= 0.280 Chirality : 0.080 1.750 3090 Planarity : 0.005 0.044 3250 Dihedral : 5.554 52.161 3202 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.63 % Allowed : 13.09 % Favored : 85.28 % 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: 0.78 (0.17), residues: 2285 helix: 2.19 (0.17), residues: 850 sheet: -0.10 (0.22), residues: 550 loop : -0.71 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.008 0.001 TYR A 128 PHE 0.012 0.001 PHE A 99 TRP 0.029 0.001 TRP D 437 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00342 (19415) covalent geometry : angle 0.56037 (26450) SS BOND : bond 0.00390 ( 5) SS BOND : angle 0.84897 ( 10) hydrogen bonds : bond 0.04149 ( 910) hydrogen bonds : angle 4.36605 ( 2940) link_ALPHA1-3 : bond 0.00767 ( 5) link_ALPHA1-3 : angle 1.65753 ( 15) link_BETA1-4 : bond 0.00454 ( 15) link_BETA1-4 : angle 1.52905 ( 45) link_NAG-ASN : bond 0.00161 ( 15) link_NAG-ASN : angle 1.89059 ( 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 254 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8606 (tptt) cc_final: 0.8318 (tppt) REVERT: A 437 TRP cc_start: 0.6511 (m100) cc_final: 0.6049 (m-10) REVERT: B 45 LYS cc_start: 0.8692 (tptt) cc_final: 0.8296 (tppt) REVERT: B 272 GLN cc_start: 0.7319 (mt0) cc_final: 0.6658 (mt0) REVERT: B 437 TRP cc_start: 0.6261 (m100) cc_final: 0.5558 (m-10) REVERT: B 444 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6699 (p) REVERT: B 472 GLU cc_start: 0.5542 (mp0) cc_final: 0.5317 (mp0) REVERT: C 116 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: C 128 TYR cc_start: 0.7484 (t80) cc_final: 0.6674 (t80) REVERT: D 116 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: D 450 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6462 (mtm) REVERT: F 3 CYS cc_start: 0.8109 (m) cc_final: 0.7883 (m) REVERT: G 41 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8402 (mt-10) REVERT: H 23 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8057 (m) REVERT: J 63 ASP cc_start: 0.5875 (p0) cc_final: 0.5573 (m-30) outliers start: 34 outliers final: 27 residues processed: 241 average time/residue: 0.7499 time to fit residues: 221.2623 Evaluate side-chains 246 residues out of total 2090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 GLU 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 B residue 448 CYS Chi-restraints excluded: chain C residue 76 THR 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 450 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 128 TYR 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 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: 0.7980 chunk 28 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 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 = 0.3976 r_free = 0.3976 target = 0.174938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115457 restraints weight = 57475.337| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.91 r_work: 0.3129 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3416 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= 0.108 Angle : 0.551 11.378 26565 Z= 0.271 Chirality : 0.079 1.701 3090 Planarity : 0.004 0.044 3250 Dihedral : 5.422 52.223 3202 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.63 % Allowed : 13.14 % Favored : 85.23 % 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: 0.91 (0.17), residues: 2285 helix: 2.26 (0.17), residues: 850 sheet: 0.02 (0.22), residues: 560 loop : -0.63 (0.20), residues: 875 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 C 99 TRP 0.031 0.001 TRP D 437 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00254 (19415) covalent geometry : angle 0.54258 (26450) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.61774 ( 10) hydrogen bonds : bond 0.03983 ( 910) hydrogen bonds : angle 4.26139 ( 2940) link_ALPHA1-3 : bond 0.00742 ( 5) link_ALPHA1-3 : angle 1.54138 ( 15) link_BETA1-4 : bond 0.00428 ( 15) link_BETA1-4 : angle 1.37483 ( 45) link_NAG-ASN : bond 0.00212 ( 15) link_NAG-ASN : angle 1.84624 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11167.56 seconds wall clock time: 189 minutes 19.82 seconds (11359.82 seconds total)