Starting phenix.real_space_refine on Thu Nov 20 14:57:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tu6_26127/11_2025/7tu6_26127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tu6_26127/11_2025/7tu6_26127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tu6_26127/11_2025/7tu6_26127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tu6_26127/11_2025/7tu6_26127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tu6_26127/11_2025/7tu6_26127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tu6_26127/11_2025/7tu6_26127.map" } resolution = 2.7 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= 0.004 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19278 atoms to isotropic. 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 P 36 5.49 5 Mg 6 5.21 5 S 48 5.16 5 C 12756 2.51 5 N 3444 2.21 5 O 3738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20028 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "D" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3277 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 417} Chain breaks: 3 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 9, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'DTP': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'DTP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, E, F Time building chain proxies: 5.65, per 1000 atoms: 0.28 Number of scatterers: 20028 At special positions: 0 Unit cell: (130.48, 137.004, 97.86, 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) S 48 16.00 P 36 15.00 Mg 6 11.99 O 3738 8.00 N 3444 7.00 C 12756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 256 " distance=0.00 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 384 " distance=0.00 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 420 " distance=0.00 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 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 958.5 milliseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4812 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.561A pdb=" N LEU A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 8' Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 24 " --> pdb=" O ARG A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 24' Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 50 Processing helix chain 'A' and resid 64 through 91 removed outlier: 3.508A pdb=" N SER A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 Processing helix chain 'A' and resid 148 through 157 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 243 through 268 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.602A pdb=" N ALA A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR A 287 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 288 " --> pdb=" O GLY A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 288' Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 345 through 359 Processing helix chain 'A' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.734A pdb=" N MET A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 439 Processing helix chain 'B' and resid 4 through 8 removed outlier: 3.591A pdb=" N LEU B 8 " --> pdb=" O TRP B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4 through 8' Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 24 " --> pdb=" O ARG B 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 20 through 24' Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 64 through 91 removed outlier: 3.509A pdb=" N SER B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 removed outlier: 4.255A pdb=" N PHE B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 144 Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 182 through 190 Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 243 through 268 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.602A pdb=" N ALA B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR B 287 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 288 " --> pdb=" O GLY B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 284 through 288' Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 Processing helix chain 'B' and resid 345 through 359 Processing helix chain 'B' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.733A pdb=" N MET B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 439 Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.592A pdb=" N LEU C 8 " --> pdb=" O TRP C 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 8' Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 24' Processing helix chain 'C' and resid 29 through 41 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 47 through 50 Processing helix chain 'C' and resid 64 through 91 removed outlier: 3.509A pdb=" N SER C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 129 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 135 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 144 Processing helix chain 'C' and resid 148 through 157 Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 228 Processing helix chain 'C' and resid 243 through 268 Processing helix chain 'C' and resid 272 through 280 removed outlier: 3.601A pdb=" N ALA C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR C 287 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE C 288 " --> pdb=" O GLY C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 288' Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 345 through 359 Processing helix chain 'C' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.734A pdb=" N MET C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 439 Processing helix chain 'D' and resid 4 through 8 removed outlier: 3.591A pdb=" N LEU D 8 " --> pdb=" O TRP D 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 8' Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU D 23 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 24 " --> pdb=" O ARG D 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 20 through 24' Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 64 through 91 removed outlier: 3.508A pdb=" N SER D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 135 removed outlier: 4.262A pdb=" N GLU D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 159 through 169 Processing helix chain 'D' and resid 182 through 190 Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 216 through 228 Processing helix chain 'D' and resid 243 through 268 Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.602A pdb=" N ALA D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR D 287 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE D 288 " --> pdb=" O GLY D 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 284 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 298 through 325 removed outlier: 3.753A pdb=" N ARG D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 411 through 426 removed outlier: 3.735A pdb=" N MET D 426 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 439 Processing helix chain 'E' and resid 4 through 8 removed outlier: 3.592A pdb=" N LEU E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 4 through 8' Processing helix chain 'E' and resid 20 through 24 removed outlier: 3.548A pdb=" N GLU E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 24 " --> pdb=" O ARG E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 24' Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 47 through 50 Processing helix chain 'E' and resid 64 through 91 removed outlier: 3.509A pdb=" N SER E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 4.255A pdb=" N PHE E 105 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 135 removed outlier: 4.262A pdb=" N GLU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS E 129 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE E 135 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 182 through 190 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 228 Processing helix chain 'E' and resid 243 through 268 Processing helix chain 'E' and resid 272 through 280 removed outlier: 3.601A pdb=" N ALA E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 288 removed outlier: 3.893A pdb=" N THR E 287 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 288 " --> pdb=" O GLY E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 288' Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 331 Processing helix chain 'E' and resid 345 through 359 Processing helix chain 'E' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN E 389 " --> pdb=" O ARG E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 403 Processing helix chain 'E' and resid 411 through 426 removed outlier: 3.734A pdb=" N MET E 426 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 439 Processing helix chain 'F' and resid 4 through 8 removed outlier: 3.591A pdb=" N LEU F 8 " --> pdb=" O TRP F 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 4 through 8' Processing helix chain 'F' and resid 20 through 24 removed outlier: 3.547A pdb=" N GLU F 23 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN F 24 " --> pdb=" O ARG F 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 20 through 24' Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 64 through 91 removed outlier: 3.508A pdb=" N SER F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 115 removed outlier: 4.256A pdb=" N PHE F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 115 " --> pdb=" O ALA F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 135 removed outlier: 4.261A pdb=" N GLU F 128 " --> pdb=" O GLY F 124 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE F 135 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 148 through 157 Processing helix chain 'F' and resid 159 through 169 Processing helix chain 'F' and resid 182 through 190 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 216 through 228 Processing helix chain 'F' and resid 243 through 268 Processing helix chain 'F' and resid 272 through 280 removed outlier: 3.601A pdb=" N ALA F 276 " --> pdb=" O PRO F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 288 removed outlier: 3.894A pdb=" N THR F 287 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE F 288 " --> pdb=" O GLY F 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 284 through 288' Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 298 through 325 removed outlier: 3.754A pdb=" N ARG F 302 " --> pdb=" O GLU F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 331 Processing helix chain 'F' and resid 345 through 359 Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.960A pdb=" N ASN F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 403 Processing helix chain 'F' and resid 411 through 426 removed outlier: 3.733A pdb=" N MET F 426 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 439 1182 hydrogen bonds defined for protein. 3456 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: 3.38 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3216 1.31 - 1.43: 5461 1.43 - 1.56: 11603 1.56 - 1.68: 66 1.68 - 1.81: 78 Bond restraints: 20424 Sorted by residual: bond pdb=" CA GLN E 52 " pdb=" C GLN E 52 " ideal model delta sigma weight residual 1.526 1.569 -0.043 9.20e-03 1.18e+04 2.14e+01 bond pdb=" CA GLN C 52 " pdb=" C GLN C 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.12e+01 bond pdb=" CA GLN F 52 " pdb=" C GLN F 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.10e+01 bond pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.10e+01 bond pdb=" CA GLN D 52 " pdb=" C GLN D 52 " ideal model delta sigma weight residual 1.526 1.568 -0.042 9.20e-03 1.18e+04 2.06e+01 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 26128 1.47 - 2.93: 1193 2.93 - 4.40: 267 4.40 - 5.87: 78 5.87 - 7.33: 66 Bond angle restraints: 27732 Sorted by residual: angle pdb=" N LEU B 412 " pdb=" CA LEU B 412 " pdb=" C LEU B 412 " ideal model delta sigma weight residual 111.71 118.90 -7.19 1.15e+00 7.56e-01 3.91e+01 angle pdb=" N LEU C 412 " pdb=" CA LEU C 412 " pdb=" C LEU C 412 " ideal model delta sigma weight residual 111.71 118.89 -7.18 1.15e+00 7.56e-01 3.89e+01 angle pdb=" N LEU F 412 " pdb=" CA LEU F 412 " pdb=" C LEU F 412 " ideal model delta sigma weight residual 111.71 118.88 -7.17 1.15e+00 7.56e-01 3.89e+01 angle pdb=" N LEU A 412 " pdb=" CA LEU A 412 " pdb=" C LEU A 412 " ideal model delta sigma weight residual 111.71 118.87 -7.16 1.15e+00 7.56e-01 3.88e+01 angle pdb=" N LEU D 412 " pdb=" CA LEU D 412 " pdb=" C LEU D 412 " ideal model delta sigma weight residual 111.71 118.86 -7.15 1.15e+00 7.56e-01 3.87e+01 ... (remaining 27727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 11186 17.72 - 35.44: 764 35.44 - 53.16: 260 53.16 - 70.88: 24 70.88 - 88.61: 60 Dihedral angle restraints: 12294 sinusoidal: 4788 harmonic: 7506 Sorted by residual: dihedral pdb=" C TYR B 257 " pdb=" N TYR B 257 " pdb=" CA TYR B 257 " pdb=" CB TYR B 257 " ideal model delta harmonic sigma weight residual -122.60 -132.57 9.97 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C TYR F 257 " pdb=" N TYR F 257 " pdb=" CA TYR F 257 " pdb=" CB TYR F 257 " ideal model delta harmonic sigma weight residual -122.60 -132.56 9.96 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C TYR C 257 " pdb=" N TYR C 257 " pdb=" CA TYR C 257 " pdb=" CB TYR C 257 " ideal model delta harmonic sigma weight residual -122.60 -132.55 9.95 0 2.50e+00 1.60e-01 1.59e+01 ... (remaining 12291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2885 0.085 - 0.169: 163 0.169 - 0.254: 54 0.254 - 0.339: 12 0.339 - 0.423: 12 Chirality restraints: 3126 Sorted by residual: chirality pdb=" CA TYR B 257 " pdb=" N TYR B 257 " pdb=" C TYR B 257 " pdb=" CB TYR B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA TYR E 257 " pdb=" N TYR E 257 " pdb=" C TYR E 257 " pdb=" CB TYR E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA TYR C 257 " pdb=" N TYR C 257 " pdb=" C TYR C 257 " pdb=" CB TYR C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 3123 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 269 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.10e+00 pdb=" C GLY B 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY B 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C GLY A 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 269 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C GLY F 269 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY F 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU F 270 " -0.013 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 42 2.49 - 3.10: 13784 3.10 - 3.70: 29177 3.70 - 4.30: 43361 4.30 - 4.90: 73256 Nonbonded interactions: 159620 Sorted by model distance: nonbonded pdb=" NE2 HIS F 116 " pdb="MG MG F 503 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS C 116 " pdb="MG MG C 502 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS A 116 " pdb="MG MG A 503 " model vdw 1.892 2.250 nonbonded pdb=" NE2 HIS D 116 " pdb="MG MG D 503 " model vdw 1.893 2.250 nonbonded pdb=" NE2 HIS E 116 " pdb="MG MG E 502 " model vdw 1.893 2.250 ... (remaining 159615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 501) selection = (chain 'B' and resid 3 through 501) selection = (chain 'C' and resid 3 through 501) selection = (chain 'D' and resid 3 through 501) selection = (chain 'E' and resid 3 through 501) selection = (chain 'F' and resid 3 through 501) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.550 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20424 Z= 0.448 Angle : 0.790 7.332 27735 Z= 0.532 Chirality : 0.058 0.423 3126 Planarity : 0.005 0.078 3474 Dihedral : 15.187 88.605 7476 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.90 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.33 % 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: 0.38 (0.17), residues: 2532 helix: 1.23 (0.13), residues: 1674 sheet: None (None), residues: 0 loop : -1.75 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 45 TYR 0.014 0.002 TYR C 305 PHE 0.006 0.001 PHE C 61 TRP 0.006 0.001 TRP B 4 HIS 0.007 0.002 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00691 (20424) covalent geometry : angle 0.79027 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.19349 ( 1182) hydrogen bonds : angle 6.14249 ( 3456) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 523 time to evaluate : 0.707 Fit side-chains REVERT: A 102 PHE cc_start: 0.8226 (p90) cc_final: 0.7942 (p90) REVERT: A 253 ASP cc_start: 0.7549 (t70) cc_final: 0.7157 (t0) REVERT: B 28 ARG cc_start: 0.8132 (ttt-90) cc_final: 0.7866 (mmm160) REVERT: B 65 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7240 (tpt170) REVERT: B 117 ASP cc_start: 0.6763 (m-30) cc_final: 0.6531 (m-30) REVERT: B 153 GLN cc_start: 0.8322 (tp40) cc_final: 0.8082 (mm-40) REVERT: B 226 GLU cc_start: 0.6998 (tp30) cc_final: 0.6782 (tp30) REVERT: B 270 LEU cc_start: 0.8442 (mt) cc_final: 0.8214 (mt) REVERT: B 354 LEU cc_start: 0.7965 (tp) cc_final: 0.7749 (tt) REVERT: C 28 ARG cc_start: 0.8145 (ttt-90) cc_final: 0.7927 (mmm160) REVERT: C 65 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7263 (tpt170) REVERT: C 253 ASP cc_start: 0.7473 (t70) cc_final: 0.7227 (t70) REVERT: C 270 LEU cc_start: 0.8229 (mt) cc_final: 0.8014 (mt) REVERT: D 253 ASP cc_start: 0.7660 (t70) cc_final: 0.7207 (t0) REVERT: D 270 LEU cc_start: 0.8634 (mt) cc_final: 0.8393 (mt) REVERT: D 326 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 20 LEU cc_start: 0.8548 (mt) cc_final: 0.8276 (mt) REVERT: E 45 ARG cc_start: 0.8420 (ttm170) cc_final: 0.8184 (ttp80) REVERT: E 86 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7895 (mtmt) REVERT: E 207 ASP cc_start: 0.7376 (p0) cc_final: 0.7086 (p0) REVERT: E 214 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8305 (mm-40) REVERT: E 326 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 20 LEU cc_start: 0.8727 (mt) cc_final: 0.8450 (mt) REVERT: F 45 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8123 (ttp80) REVERT: F 270 LEU cc_start: 0.8460 (mt) cc_final: 0.8248 (mp) REVERT: F 326 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7512 (tm-30) outliers start: 12 outliers final: 1 residues processed: 532 average time/residue: 0.8134 time to fit residues: 476.1394 Evaluate side-chains 435 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 432 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain E residue 411 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 48 GLN A 153 GLN A 343 ASN A 389 ASN A 395 ASN B 3 ASN B 24 GLN B 48 GLN B 52 GLN B 120 ASN B 199 HIS B 267 ASN B 343 ASN B 345 GLN B 389 ASN B 395 ASN C 24 GLN C 48 GLN C 52 GLN C 199 HIS C 267 ASN C 345 GLN C 389 ASN C 395 ASN D 13 GLN D 24 GLN D 48 GLN D 153 GLN D 389 ASN D 395 ASN E 24 GLN E 52 GLN E 120 ASN E 153 GLN E 389 ASN E 395 ASN F 13 GLN F 24 GLN F 48 GLN F 52 GLN F 120 ASN F 137 ASN F 343 ASN F 389 ASN F 395 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115721 restraints weight = 25552.419| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.81 r_work: 0.3315 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20424 Z= 0.222 Angle : 0.581 6.191 27735 Z= 0.317 Chirality : 0.041 0.165 3126 Planarity : 0.004 0.042 3474 Dihedral : 11.751 80.859 3183 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.41 % Allowed : 11.20 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.62 (0.16), residues: 2532 helix: 1.52 (0.12), residues: 1692 sheet: None (None), residues: 0 loop : -2.00 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 77 TYR 0.032 0.002 TYR B 257 PHE 0.022 0.002 PHE F 220 TRP 0.011 0.002 TRP D 240 HIS 0.008 0.002 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00518 (20424) covalent geometry : angle 0.58088 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.08404 ( 1182) hydrogen bonds : angle 4.02092 ( 3456) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 537 time to evaluate : 0.770 Fit side-chains REVERT: A 101 LYS cc_start: 0.8311 (mttp) cc_final: 0.8089 (mttm) REVERT: A 102 PHE cc_start: 0.8629 (p90) cc_final: 0.8353 (p90) REVERT: A 260 ILE cc_start: 0.8384 (mm) cc_final: 0.8174 (mp) REVERT: B 45 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8059 (ttp80) REVERT: B 226 GLU cc_start: 0.8074 (tp30) cc_final: 0.7799 (tp30) REVERT: B 280 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: B 358 ARG cc_start: 0.8334 (ptp-110) cc_final: 0.8119 (ptm160) REVERT: C 24 GLN cc_start: 0.8075 (mt0) cc_final: 0.7706 (tt0) REVERT: C 45 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7915 (ttp80) REVERT: C 65 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7966 (tpt170) REVERT: C 117 ASP cc_start: 0.7899 (m-30) cc_final: 0.7665 (m-30) REVERT: C 280 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6778 (mtp) REVERT: D 101 LYS cc_start: 0.8259 (mttp) cc_final: 0.7856 (mttp) REVERT: D 216 GLU cc_start: 0.7551 (mp0) cc_final: 0.7220 (mp0) REVERT: D 260 ILE cc_start: 0.8414 (mm) cc_final: 0.8207 (mp) REVERT: D 293 TYR cc_start: 0.7715 (t80) cc_final: 0.7494 (t80) REVERT: D 326 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7176 (tm-30) REVERT: E 45 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8601 (ttp80) REVERT: E 260 ILE cc_start: 0.8011 (mm) cc_final: 0.7802 (mp) REVERT: E 270 LEU cc_start: 0.8567 (mt) cc_final: 0.8284 (mp) REVERT: E 415 ASN cc_start: 0.8390 (m-40) cc_final: 0.8116 (m-40) REVERT: F 45 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8602 (ttp80) REVERT: F 155 LEU cc_start: 0.8674 (mt) cc_final: 0.8434 (mm) REVERT: F 270 LEU cc_start: 0.8581 (mt) cc_final: 0.8324 (mp) REVERT: F 326 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7683 (tm-30) outliers start: 66 outliers final: 38 residues processed: 559 average time/residue: 0.7489 time to fit residues: 464.9933 Evaluate side-chains 534 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 491 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 280 MET Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 280 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 24 GLN A 48 GLN A 267 ASN B 3 ASN B 13 GLN B 52 GLN B 345 GLN C 52 GLN C 345 GLN D 13 GLN D 24 GLN D 343 ASN E 52 GLN E 137 ASN E 267 ASN F 48 GLN F 52 GLN F 137 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118022 restraints weight = 25658.726| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.73 r_work: 0.3355 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.154 Angle : 0.482 5.669 27735 Z= 0.265 Chirality : 0.037 0.157 3126 Planarity : 0.003 0.036 3474 Dihedral : 11.047 88.170 3178 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.46 % Allowed : 14.86 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.98 (0.17), residues: 2532 helix: 1.85 (0.13), residues: 1692 sheet: None (None), residues: 0 loop : -1.97 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 358 TYR 0.027 0.001 TYR B 257 PHE 0.014 0.001 PHE F 220 TRP 0.009 0.001 TRP D 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00341 (20424) covalent geometry : angle 0.48203 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.06857 ( 1182) hydrogen bonds : angle 3.85847 ( 3456) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 491 time to evaluate : 0.760 Fit side-chains REVERT: A 102 PHE cc_start: 0.8568 (p90) cc_final: 0.8301 (p90) REVERT: B 45 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8021 (ttp80) REVERT: B 65 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7667 (tpt170) REVERT: B 117 ASP cc_start: 0.7801 (m-30) cc_final: 0.7550 (m-30) REVERT: B 136 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7668 (ttmm) REVERT: B 154 ASP cc_start: 0.8335 (m-30) cc_final: 0.8124 (m-30) REVERT: B 226 GLU cc_start: 0.8065 (tp30) cc_final: 0.7776 (tp30) REVERT: B 373 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 24 GLN cc_start: 0.8089 (mt0) cc_final: 0.7744 (tt0) REVERT: C 45 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7900 (ttp80) REVERT: C 373 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7038 (t80) REVERT: D 216 GLU cc_start: 0.7582 (mp0) cc_final: 0.7228 (mp0) REVERT: D 326 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7647 (tm-30) REVERT: E 11 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7957 (tttt) REVERT: E 45 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8609 (ttp80) REVERT: E 48 GLN cc_start: 0.8744 (pt0) cc_final: 0.8529 (pt0) REVERT: E 260 ILE cc_start: 0.7970 (mm) cc_final: 0.7726 (mp) REVERT: E 270 LEU cc_start: 0.8442 (mt) cc_final: 0.8209 (mp) REVERT: E 415 ASN cc_start: 0.8356 (m-40) cc_final: 0.8078 (m-40) REVERT: F 45 ARG cc_start: 0.8824 (ttm170) cc_final: 0.8547 (ttp80) REVERT: F 270 LEU cc_start: 0.8523 (mt) cc_final: 0.8284 (mp) REVERT: F 326 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7604 (tm-30) outliers start: 67 outliers final: 35 residues processed: 517 average time/residue: 0.6939 time to fit residues: 401.1019 Evaluate side-chains 530 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 490 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 157 LYS Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 74 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 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 13 GLN A 24 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 345 GLN D 24 GLN D 214 GLN D 267 ASN D 343 ASN D 400 GLN D 434 ASN E 24 GLN E 52 GLN E 137 ASN F 48 GLN F 52 GLN F 137 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114648 restraints weight = 25582.493| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.79 r_work: 0.3295 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20424 Z= 0.224 Angle : 0.548 5.440 27735 Z= 0.299 Chirality : 0.041 0.157 3126 Planarity : 0.004 0.035 3474 Dihedral : 10.946 89.077 3174 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.23 % Allowed : 15.84 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.72 (0.17), residues: 2532 helix: 1.65 (0.13), residues: 1692 sheet: None (None), residues: 0 loop : -2.08 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 65 TYR 0.020 0.002 TYR B 257 PHE 0.021 0.002 PHE F 220 TRP 0.010 0.002 TRP A 240 HIS 0.006 0.002 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00532 (20424) covalent geometry : angle 0.54767 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.08504 ( 1182) hydrogen bonds : angle 4.03166 ( 3456) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 528 time to evaluate : 0.813 Fit side-chains REVERT: A 102 PHE cc_start: 0.8637 (p90) cc_final: 0.8367 (p90) REVERT: A 229 LEU cc_start: 0.8364 (mt) cc_final: 0.8132 (mp) REVERT: A 326 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 65 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7652 (tpt170) REVERT: B 117 ASP cc_start: 0.7888 (m-30) cc_final: 0.7539 (m-30) REVERT: B 136 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7719 (ttmm) REVERT: B 226 GLU cc_start: 0.8069 (tp30) cc_final: 0.7765 (tp30) REVERT: B 373 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7504 (t80) REVERT: C 24 GLN cc_start: 0.8161 (mt0) cc_final: 0.7893 (tt0) REVERT: C 373 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7146 (t80) REVERT: D 214 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8527 (tp40) REVERT: D 216 GLU cc_start: 0.7693 (mp0) cc_final: 0.7337 (mp0) REVERT: D 326 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7770 (tm-30) REVERT: E 11 LYS cc_start: 0.8271 (ptmt) cc_final: 0.8047 (tttt) REVERT: E 45 ARG cc_start: 0.8854 (ttm170) cc_final: 0.8579 (ttp80) REVERT: E 260 ILE cc_start: 0.8032 (mm) cc_final: 0.7770 (mt) REVERT: E 270 LEU cc_start: 0.8471 (mt) cc_final: 0.8228 (mp) REVERT: E 354 LEU cc_start: 0.8463 (tp) cc_final: 0.8149 (tp) REVERT: E 415 ASN cc_start: 0.8388 (m-40) cc_final: 0.8122 (m-40) REVERT: F 45 ARG cc_start: 0.8856 (ttm170) cc_final: 0.8519 (ttp80) REVERT: F 202 SER cc_start: 0.8340 (m) cc_final: 0.8066 (t) REVERT: F 326 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7723 (tm-30) outliers start: 82 outliers final: 51 residues processed: 556 average time/residue: 0.7034 time to fit residues: 435.4367 Evaluate side-chains 567 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 513 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 430 LYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 153 GLN Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Chi-restraints excluded: chain F residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 236 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 52 GLN B 345 GLN C 52 GLN C 345 GLN D 24 GLN D 343 ASN E 48 GLN E 52 GLN E 137 ASN F 137 ASN F 343 ASN F 400 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119525 restraints weight = 25509.062| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.71 r_work: 0.3377 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20424 Z= 0.125 Angle : 0.450 5.118 27735 Z= 0.249 Chirality : 0.036 0.146 3126 Planarity : 0.003 0.034 3474 Dihedral : 10.201 85.799 3174 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.30 % Allowed : 18.11 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2532 helix: 2.00 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.91 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.020 0.001 TYR D 257 PHE 0.012 0.001 PHE F 220 TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00259 (20424) covalent geometry : angle 0.45037 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.05921 ( 1182) hydrogen bonds : angle 3.76708 ( 3456) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 498 time to evaluate : 0.772 Fit side-chains REVERT: A 102 PHE cc_start: 0.8595 (p90) cc_final: 0.8319 (p90) REVERT: A 151 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 326 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 45 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8021 (ttp80) REVERT: B 65 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7410 (tpt170) REVERT: B 117 ASP cc_start: 0.7875 (m-30) cc_final: 0.7546 (m-30) REVERT: B 136 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7709 (ttmm) REVERT: B 226 GLU cc_start: 0.7967 (tp30) cc_final: 0.7677 (tp30) REVERT: B 373 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7188 (t80) REVERT: C 24 GLN cc_start: 0.8114 (mt0) cc_final: 0.7879 (tt0) REVERT: C 129 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8142 (mmtt) REVERT: C 373 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.6893 (t80) REVERT: D 214 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8483 (tp40) REVERT: D 216 GLU cc_start: 0.7629 (mp0) cc_final: 0.7252 (mp0) REVERT: D 326 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7679 (tm-30) REVERT: E 11 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7972 (tttt) REVERT: E 45 ARG cc_start: 0.8793 (ttm110) cc_final: 0.8548 (ttp80) REVERT: E 270 LEU cc_start: 0.8429 (mt) cc_final: 0.8195 (mp) REVERT: E 354 LEU cc_start: 0.8532 (tp) cc_final: 0.8203 (tp) REVERT: E 415 ASN cc_start: 0.8336 (m-40) cc_final: 0.8075 (m-40) REVERT: F 45 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8535 (ttp80) REVERT: F 202 SER cc_start: 0.8267 (m) cc_final: 0.8016 (p) REVERT: F 207 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7572 (p0) REVERT: F 326 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7593 (tm-30) outliers start: 64 outliers final: 27 residues processed: 522 average time/residue: 0.6881 time to fit residues: 400.3833 Evaluate side-chains 524 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 492 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 155 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 254 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 52 GLN C 343 ASN C 345 GLN D 24 GLN D 343 ASN E 24 GLN E 52 GLN E 137 ASN F 52 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.136347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118362 restraints weight = 25470.186| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.79 r_work: 0.3355 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.140 Angle : 0.469 5.550 27735 Z= 0.256 Chirality : 0.037 0.152 3126 Planarity : 0.003 0.032 3474 Dihedral : 9.872 80.378 3174 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.20 % Allowed : 19.09 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2532 helix: 2.02 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.89 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.019 0.001 TYR D 257 PHE 0.015 0.001 PHE F 220 TRP 0.007 0.001 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00307 (20424) covalent geometry : angle 0.46883 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.06360 ( 1182) hydrogen bonds : angle 3.75014 ( 3456) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 500 time to evaluate : 0.742 Fit side-chains REVERT: A 102 PHE cc_start: 0.8618 (p90) cc_final: 0.8340 (p90) REVERT: A 151 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7730 (mt-10) REVERT: B 65 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7477 (tpt170) REVERT: B 117 ASP cc_start: 0.7952 (m-30) cc_final: 0.7566 (m-30) REVERT: B 136 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7724 (ttmm) REVERT: B 226 GLU cc_start: 0.7995 (tp30) cc_final: 0.7687 (tp30) REVERT: B 373 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7305 (t80) REVERT: C 11 LYS cc_start: 0.8167 (ptmt) cc_final: 0.7931 (ptmt) REVERT: C 24 GLN cc_start: 0.8103 (mt0) cc_final: 0.7872 (tt0) REVERT: C 226 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: C 373 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6955 (t80) REVERT: D 214 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8497 (tp40) REVERT: D 216 GLU cc_start: 0.7698 (mp0) cc_final: 0.7288 (mp0) REVERT: D 326 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 11 LYS cc_start: 0.8270 (ptmt) cc_final: 0.8004 (tttt) REVERT: E 45 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8562 (ttp80) REVERT: E 207 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (p0) REVERT: E 270 LEU cc_start: 0.8399 (mt) cc_final: 0.8140 (mp) REVERT: E 354 LEU cc_start: 0.8458 (tp) cc_final: 0.8154 (tp) REVERT: E 415 ASN cc_start: 0.8371 (m-40) cc_final: 0.8079 (m-40) REVERT: F 45 ARG cc_start: 0.8849 (ttm170) cc_final: 0.8567 (ttp80) REVERT: F 202 SER cc_start: 0.8231 (m) cc_final: 0.7969 (p) REVERT: F 207 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7595 (p0) REVERT: F 326 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7610 (tm-30) outliers start: 62 outliers final: 39 residues processed: 523 average time/residue: 0.6958 time to fit residues: 406.0394 Evaluate side-chains 539 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 494 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 182 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 231 optimal weight: 0.3980 chunk 214 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 52 GLN B 343 ASN B 345 GLN C 343 ASN C 345 GLN D 24 GLN D 343 ASN E 52 GLN E 137 ASN F 24 GLN F 137 ASN F 343 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117174 restraints weight = 25428.425| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.79 r_work: 0.3338 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20424 Z= 0.162 Angle : 0.492 5.638 27735 Z= 0.269 Chirality : 0.038 0.156 3126 Planarity : 0.003 0.030 3474 Dihedral : 9.812 79.289 3174 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.51 % Allowed : 19.40 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2532 helix: 1.94 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 65 TYR 0.021 0.001 TYR B 257 PHE 0.017 0.001 PHE F 220 TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00368 (20424) covalent geometry : angle 0.49163 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.06937 ( 1182) hydrogen bonds : angle 3.79809 ( 3456) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 506 time to evaluate : 0.751 Fit side-chains REVERT: A 102 PHE cc_start: 0.8640 (p90) cc_final: 0.8365 (p90) REVERT: A 151 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 229 LEU cc_start: 0.8364 (mt) cc_final: 0.8126 (mp) REVERT: B 65 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7506 (tpt170) REVERT: B 117 ASP cc_start: 0.7960 (m-30) cc_final: 0.7588 (m-30) REVERT: B 136 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7784 (ttmm) REVERT: B 226 GLU cc_start: 0.7993 (tp30) cc_final: 0.7691 (tp30) REVERT: B 373 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7387 (t80) REVERT: C 24 GLN cc_start: 0.8146 (mt0) cc_final: 0.7908 (tt0) REVERT: C 226 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: C 373 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7042 (t80) REVERT: D 214 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8502 (tp40) REVERT: D 216 GLU cc_start: 0.7711 (mp0) cc_final: 0.7317 (mp0) REVERT: D 280 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6642 (mtp) REVERT: D 326 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7773 (tm-30) REVERT: E 11 LYS cc_start: 0.8276 (ptmt) cc_final: 0.8004 (tttt) REVERT: E 45 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8561 (ttp80) REVERT: E 270 LEU cc_start: 0.8424 (mt) cc_final: 0.8182 (mp) REVERT: E 354 LEU cc_start: 0.8450 (tp) cc_final: 0.8136 (tp) REVERT: E 415 ASN cc_start: 0.8373 (m-40) cc_final: 0.8084 (m-40) REVERT: F 45 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8562 (ttp80) REVERT: F 326 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7641 (tm-30) outliers start: 68 outliers final: 45 residues processed: 524 average time/residue: 0.6868 time to fit residues: 401.6621 Evaluate side-chains 551 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 501 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 65 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 83 optimal weight: 0.0970 chunk 160 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 52 GLN B 343 ASN C 52 GLN D 24 GLN D 343 ASN E 48 GLN E 52 GLN E 120 ASN E 137 ASN F 24 GLN F 137 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119690 restraints weight = 25603.936| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.70 r_work: 0.3380 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.126 Angle : 0.456 5.630 27735 Z= 0.249 Chirality : 0.036 0.163 3126 Planarity : 0.003 0.028 3474 Dihedral : 9.448 73.068 3174 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.15 % Allowed : 20.02 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2532 helix: 2.07 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.89 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 65 TYR 0.017 0.001 TYR D 257 PHE 0.012 0.001 PHE F 220 TRP 0.008 0.001 TRP A 240 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00268 (20424) covalent geometry : angle 0.45567 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.05885 ( 1182) hydrogen bonds : angle 3.70012 ( 3456) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 494 time to evaluate : 0.776 Fit side-chains REVERT: A 102 PHE cc_start: 0.8614 (p90) cc_final: 0.8337 (p90) REVERT: A 151 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 250 GLU cc_start: 0.7675 (tt0) cc_final: 0.7350 (tt0) REVERT: B 45 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8013 (ttp80) REVERT: B 65 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7358 (tpt170) REVERT: B 117 ASP cc_start: 0.7932 (m-30) cc_final: 0.7548 (m-30) REVERT: B 226 GLU cc_start: 0.7942 (tp30) cc_final: 0.7663 (tp30) REVERT: B 373 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7266 (t80) REVERT: C 24 GLN cc_start: 0.8146 (mt0) cc_final: 0.7901 (tt0) REVERT: C 45 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7928 (ttp80) REVERT: C 52 GLN cc_start: 0.7951 (tp40) cc_final: 0.7644 (tp-100) REVERT: C 226 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: C 373 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6925 (t80) REVERT: D 214 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8487 (tp40) REVERT: D 216 GLU cc_start: 0.7661 (mp0) cc_final: 0.7282 (mp0) REVERT: D 280 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6598 (mtp) REVERT: D 326 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7723 (tm-30) REVERT: E 45 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8574 (ttp80) REVERT: E 207 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7604 (p0) REVERT: E 270 LEU cc_start: 0.8412 (mt) cc_final: 0.8171 (mp) REVERT: E 354 LEU cc_start: 0.8506 (tp) cc_final: 0.8199 (tp) REVERT: E 415 ASN cc_start: 0.8347 (m-40) cc_final: 0.8080 (m-40) REVERT: F 45 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8555 (ttp80) REVERT: F 202 SER cc_start: 0.8106 (t) cc_final: 0.7824 (p) REVERT: F 326 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7541 (tm-30) outliers start: 61 outliers final: 45 residues processed: 515 average time/residue: 0.6721 time to fit residues: 387.2165 Evaluate side-chains 547 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 494 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 257 TYR Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 99 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 113 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 243 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 343 ASN C 153 GLN D 24 GLN D 343 ASN E 120 ASN E 137 ASN F 137 ASN F 343 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.117709 restraints weight = 25433.344| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.78 r_work: 0.3347 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20424 Z= 0.157 Angle : 0.497 5.899 27735 Z= 0.270 Chirality : 0.038 0.166 3126 Planarity : 0.003 0.032 3474 Dihedral : 9.458 73.278 3174 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.94 % Allowed : 20.74 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2532 helix: 1.96 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 65 TYR 0.020 0.001 TYR B 257 PHE 0.016 0.001 PHE F 220 TRP 0.007 0.001 TRP A 240 HIS 0.006 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00356 (20424) covalent geometry : angle 0.49661 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.06742 ( 1182) hydrogen bonds : angle 3.77865 ( 3456) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 498 time to evaluate : 0.799 Fit side-chains REVERT: A 25 ASP cc_start: 0.7056 (m-30) cc_final: 0.6784 (m-30) REVERT: A 102 PHE cc_start: 0.8659 (p90) cc_final: 0.8381 (p90) REVERT: A 151 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 229 LEU cc_start: 0.8383 (mt) cc_final: 0.8146 (mp) REVERT: B 45 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8086 (ttp80) REVERT: B 65 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7507 (tpt170) REVERT: B 117 ASP cc_start: 0.7963 (m-30) cc_final: 0.7595 (m-30) REVERT: B 226 GLU cc_start: 0.7980 (tp30) cc_final: 0.7688 (tp30) REVERT: B 280 MET cc_start: 0.7649 (mtp) cc_final: 0.7447 (mtm) REVERT: B 373 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7338 (t80) REVERT: C 24 GLN cc_start: 0.8152 (mt0) cc_final: 0.7889 (tt0) REVERT: C 45 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7945 (ttp80) REVERT: C 226 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7146 (tt0) REVERT: C 373 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7068 (t80) REVERT: D 214 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8509 (tp40) REVERT: D 216 GLU cc_start: 0.7726 (mp0) cc_final: 0.7333 (mp0) REVERT: D 280 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6646 (mtp) REVERT: D 293 TYR cc_start: 0.7761 (t80) cc_final: 0.7539 (t80) REVERT: E 11 LYS cc_start: 0.8275 (ptmt) cc_final: 0.8006 (tttt) REVERT: E 45 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8557 (ttp80) REVERT: E 207 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7583 (p0) REVERT: E 270 LEU cc_start: 0.8417 (mt) cc_final: 0.8178 (mp) REVERT: E 354 LEU cc_start: 0.8461 (tp) cc_final: 0.8156 (tp) REVERT: E 415 ASN cc_start: 0.8387 (m-40) cc_final: 0.8133 (m-40) REVERT: F 45 ARG cc_start: 0.8838 (ttm110) cc_final: 0.8568 (ttp80) REVERT: F 326 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7635 (tm-30) outliers start: 57 outliers final: 45 residues processed: 517 average time/residue: 0.6874 time to fit residues: 397.2526 Evaluate side-chains 555 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 502 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 225 GLN Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN B 52 GLN B 343 ASN B 415 ASN D 24 GLN D 343 ASN E 137 ASN F 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.135352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117811 restraints weight = 25571.524| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.69 r_work: 0.3357 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20424 Z= 0.156 Angle : 0.498 5.910 27735 Z= 0.271 Chirality : 0.038 0.166 3126 Planarity : 0.003 0.054 3474 Dihedral : 9.384 72.291 3174 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.84 % Allowed : 21.05 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.17), residues: 2532 helix: 1.95 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.92 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 65 TYR 0.019 0.001 TYR C 257 PHE 0.015 0.001 PHE F 220 TRP 0.009 0.001 TRP A 240 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00352 (20424) covalent geometry : angle 0.49770 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.06677 ( 1182) hydrogen bonds : angle 3.78054 ( 3456) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 497 time to evaluate : 0.829 Fit side-chains REVERT: A 25 ASP cc_start: 0.7082 (m-30) cc_final: 0.6801 (m-30) REVERT: A 102 PHE cc_start: 0.8652 (p90) cc_final: 0.8374 (p90) REVERT: A 151 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 229 LEU cc_start: 0.8408 (mt) cc_final: 0.8165 (mp) REVERT: B 45 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8080 (ttp80) REVERT: B 65 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7451 (tpt170) REVERT: B 117 ASP cc_start: 0.7897 (m-30) cc_final: 0.7525 (m-30) REVERT: B 226 GLU cc_start: 0.7952 (tp30) cc_final: 0.7676 (tp30) REVERT: B 373 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7407 (t80) REVERT: C 24 GLN cc_start: 0.8175 (mt0) cc_final: 0.7916 (tt0) REVERT: C 45 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7936 (ttp80) REVERT: C 226 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: C 373 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7038 (t80) REVERT: D 214 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8509 (tp40) REVERT: D 216 GLU cc_start: 0.7692 (mp0) cc_final: 0.7333 (mp0) REVERT: D 280 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6702 (mtp) REVERT: D 293 TYR cc_start: 0.7804 (t80) cc_final: 0.7603 (t80) REVERT: E 11 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7981 (tttt) REVERT: E 45 ARG cc_start: 0.8777 (ttm110) cc_final: 0.8554 (ttp80) REVERT: E 207 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7574 (p0) REVERT: E 270 LEU cc_start: 0.8431 (mt) cc_final: 0.8197 (mp) REVERT: E 330 LEU cc_start: 0.8625 (tp) cc_final: 0.8344 (mt) REVERT: E 354 LEU cc_start: 0.8529 (tp) cc_final: 0.8223 (tp) REVERT: E 415 ASN cc_start: 0.8355 (m-40) cc_final: 0.8097 (m-40) REVERT: F 45 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8561 (ttp80) REVERT: F 326 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7638 (tm-30) outliers start: 55 outliers final: 47 residues processed: 518 average time/residue: 0.6982 time to fit residues: 403.9164 Evaluate side-chains 547 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 492 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 225 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 263 GLU Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 373 TYR Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 373 TYR Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 12 ARG Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 263 GLU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 373 TYR Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 417 ILE Chi-restraints excluded: chain F residue 427 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 0.9980 chunk 205 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 26 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 3 ASN B 343 ASN C 434 ASN D 24 GLN D 343 ASN E 137 ASN F 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.121281 restraints weight = 25676.920| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.70 r_work: 0.3409 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20424 Z= 0.113 Angle : 0.455 5.639 27735 Z= 0.249 Chirality : 0.036 0.170 3126 Planarity : 0.003 0.027 3474 Dihedral : 8.926 65.074 3174 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.58 % Allowed : 21.62 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.17), residues: 2532 helix: 2.39 (0.13), residues: 1644 sheet: None (None), residues: 0 loop : -1.44 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 65 TYR 0.016 0.001 TYR A 257 PHE 0.011 0.001 PHE E 134 TRP 0.008 0.001 TRP A 240 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00229 (20424) covalent geometry : angle 0.45549 (27732) SS BOND : angle 0.00000 ( 3) hydrogen bonds : bond 0.05284 ( 1182) hydrogen bonds : angle 3.64234 ( 3456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8397.55 seconds wall clock time: 142 minutes 59.79 seconds (8579.79 seconds total)