Starting phenix.real_space_refine on Thu Feb 5 02:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0z_64677/02_2026/9v0z_64677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0z_64677/02_2026/9v0z_64677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v0z_64677/02_2026/9v0z_64677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0z_64677/02_2026/9v0z_64677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v0z_64677/02_2026/9v0z_64677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0z_64677/02_2026/9v0z_64677.map" } resolution = 2.35 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 9160 2.51 5 N 2544 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14408 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1399 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Chain: "E" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Restraints were copied for chains: B, C, D, F, G, H Time building chain proxies: 2.35, per 1000 atoms: 0.16 Number of scatterers: 14408 At special positions: 0 Unit cell: (70.85, 89.05, 174.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2656 8.00 N 2544 7.00 C 9160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 672.8 milliseconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 49.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.724A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.210A pdb=" N ILE A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.849A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.614A pdb=" N ILE A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.790A pdb=" N ARG A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.724A pdb=" N VAL B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.210A pdb=" N ILE B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.849A pdb=" N PHE B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.615A pdb=" N ILE B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.790A pdb=" N ARG B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.723A pdb=" N VAL C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.211A pdb=" N ILE C 52 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.850A pdb=" N PHE C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.615A pdb=" N ILE C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.789A pdb=" N ARG C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.724A pdb=" N VAL D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.210A pdb=" N ILE D 52 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 removed outlier: 3.850A pdb=" N PHE D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.615A pdb=" N ILE D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.790A pdb=" N ARG D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 19 removed outlier: 3.569A pdb=" N LYS E 15 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 removed outlier: 3.661A pdb=" N LYS E 32 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 42 through 51 removed outlier: 4.398A pdb=" N LYS E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 50 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.561A pdb=" N ASP E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 62 through 72 Processing helix chain 'E' and resid 77 through 89 removed outlier: 3.816A pdb=" N LEU E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 99 Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 124 through 131 Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.538A pdb=" N ILE E 168 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 178 Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 183 through 193 removed outlier: 3.709A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.740A pdb=" N GLN E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 252 removed outlier: 3.520A pdb=" N GLN E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 3.549A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.568A pdb=" N LYS F 15 " --> pdb=" O PRO F 11 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 35 removed outlier: 3.661A pdb=" N LYS F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 42 through 51 removed outlier: 4.396A pdb=" N LYS F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR F 49 " --> pdb=" O SER F 45 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU F 50 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 58 removed outlier: 3.561A pdb=" N ASP F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 62 through 72 Processing helix chain 'F' and resid 77 through 89 removed outlier: 3.815A pdb=" N LEU F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 99 Processing helix chain 'F' and resid 101 through 109 Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 140 through 146 Processing helix chain 'F' and resid 164 through 168 removed outlier: 3.538A pdb=" N ILE F 168 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 178 Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 183 through 193 removed outlier: 3.710A pdb=" N ALA F 191 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 225 removed outlier: 3.739A pdb=" N GLN F 225 " --> pdb=" O ARG F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 252 removed outlier: 3.518A pdb=" N GLN F 252 " --> pdb=" O PRO F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.549A pdb=" N ILE F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.569A pdb=" N LYS G 15 " --> pdb=" O PRO G 11 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 35 removed outlier: 3.661A pdb=" N LYS G 32 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 42 through 51 removed outlier: 4.397A pdb=" N LYS G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 50 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 58 removed outlier: 3.561A pdb=" N ASP G 58 " --> pdb=" O PRO G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 62 through 72 Processing helix chain 'G' and resid 77 through 89 removed outlier: 3.815A pdb=" N LEU G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 124 through 131 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.538A pdb=" N ILE G 168 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 178 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 183 through 193 removed outlier: 3.710A pdb=" N ALA G 191 " --> pdb=" O GLN G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 225 removed outlier: 3.741A pdb=" N GLN G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 252 removed outlier: 3.519A pdb=" N GLN G 252 " --> pdb=" O PRO G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 278 removed outlier: 3.549A pdb=" N ILE G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA G 278 " --> pdb=" O LEU G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 19 removed outlier: 3.569A pdb=" N LYS H 15 " --> pdb=" O PRO H 11 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 35 removed outlier: 3.661A pdb=" N LYS H 32 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Proline residue: H 33 - end of helix Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.398A pdb=" N LYS H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 50 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 58 removed outlier: 3.561A pdb=" N ASP H 58 " --> pdb=" O PRO H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 62 through 72 Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.816A pdb=" N LEU H 81 " --> pdb=" O ARG H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 140 through 146 Processing helix chain 'H' and resid 164 through 168 removed outlier: 3.538A pdb=" N ILE H 168 " --> pdb=" O PRO H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 178 Processing helix chain 'H' and resid 179 through 181 No H-bonds generated for 'chain 'H' and resid 179 through 181' Processing helix chain 'H' and resid 183 through 193 removed outlier: 3.709A pdb=" N ALA H 191 " --> pdb=" O GLN H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 225 removed outlier: 3.740A pdb=" N GLN H 225 " --> pdb=" O ARG H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 252 removed outlier: 3.518A pdb=" N GLN H 252 " --> pdb=" O PRO H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 278 removed outlier: 3.547A pdb=" N ILE H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA H 278 " --> pdb=" O LEU H 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP A 5 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 31 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 7 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE A 71 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU A 77 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP A 5 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 31 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR A 7 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA A 104 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 127 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP B 5 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 31 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 7 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLU B 65 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE B 71 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU B 77 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP B 5 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 31 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 7 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLU B 65 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA B 104 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 127 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE C 71 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU C 77 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA C 104 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY C 127 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP D 5 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU D 31 " --> pdb=" O TRP D 5 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR D 7 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU D 65 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE D 71 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU D 77 " --> pdb=" O ILE D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.661A pdb=" N TRP D 5 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU D 31 " --> pdb=" O TRP D 5 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR D 7 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU D 65 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA D 104 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY D 127 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 135 through 138 removed outlier: 5.893A pdb=" N ALA E 136 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS E 157 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU E 138 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE E 115 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N THR E 114 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE E 198 " --> pdb=" O PHE E 237 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA E 239 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE E 200 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS E 236 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE E 259 " --> pdb=" O CYS E 236 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE E 238 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 135 through 138 removed outlier: 5.893A pdb=" N ALA F 136 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS F 157 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU F 138 " --> pdb=" O LYS F 157 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE F 115 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N THR F 114 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE F 198 " --> pdb=" O PHE F 237 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA F 239 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE F 200 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS F 236 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE F 259 " --> pdb=" O CYS F 236 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE F 238 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 135 through 138 removed outlier: 5.893A pdb=" N ALA G 136 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS G 157 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU G 138 " --> pdb=" O LYS G 157 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE G 115 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N THR G 114 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE G 198 " --> pdb=" O PHE G 237 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA G 239 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE G 200 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS G 236 " --> pdb=" O ASP G 257 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE G 259 " --> pdb=" O CYS G 236 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE G 238 " --> pdb=" O ILE G 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 138 removed outlier: 5.892A pdb=" N ALA H 136 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS H 157 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU H 138 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE H 115 " --> pdb=" O ILE H 156 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N THR H 114 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE H 198 " --> pdb=" O PHE H 237 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA H 239 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE H 200 " --> pdb=" O ALA H 239 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS H 236 " --> pdb=" O ASP H 257 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE H 259 " --> pdb=" O CYS H 236 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE H 238 " --> pdb=" O ILE H 259 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1596 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: 2.38 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4010 1.33 - 1.45: 2435 1.45 - 1.56: 8203 1.56 - 1.68: 0 1.68 - 1.80: 72 Bond restraints: 14720 Sorted by residual: bond pdb=" C PHE G 52 " pdb=" N GLU G 53 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.83e-02 1.25e+03 1.75e+01 bond pdb=" C PHE E 52 " pdb=" N GLU E 53 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.83e-02 1.25e+03 1.73e+01 bond pdb=" C PHE H 52 " pdb=" N GLU H 53 " ideal model delta sigma weight residual 1.331 1.214 0.117 2.83e-02 1.25e+03 1.71e+01 bond pdb=" C PHE F 52 " pdb=" N GLU F 53 " ideal model delta sigma weight residual 1.340 1.212 0.128 5.87e-02 2.90e+02 4.77e+00 bond pdb=" CB PRO F 33 " pdb=" CG PRO F 33 " ideal model delta sigma weight residual 1.492 1.393 0.099 5.00e-02 4.00e+02 3.92e+00 ... (remaining 14715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18959 2.10 - 4.20: 827 4.20 - 6.29: 109 6.29 - 8.39: 34 8.39 - 10.49: 15 Bond angle restraints: 19944 Sorted by residual: angle pdb=" C PHE D 139 " pdb=" N HIS D 140 " pdb=" CA HIS D 140 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C PHE B 139 " pdb=" N HIS B 140 " pdb=" CA HIS B 140 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C PHE A 139 " pdb=" N HIS A 140 " pdb=" CA HIS A 140 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C PHE C 139 " pdb=" N HIS C 140 " pdb=" CA HIS C 140 " ideal model delta sigma weight residual 121.54 131.98 -10.44 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C SER G 31 " pdb=" N LYS G 32 " pdb=" CA LYS G 32 " ideal model delta sigma weight residual 120.09 125.50 -5.41 1.25e+00 6.40e-01 1.87e+01 ... (remaining 19939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 8087 11.99 - 23.98: 553 23.98 - 35.97: 172 35.97 - 47.96: 44 47.96 - 59.95: 8 Dihedral angle restraints: 8864 sinusoidal: 3584 harmonic: 5280 Sorted by residual: dihedral pdb=" CA GLU D 126 " pdb=" C GLU D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual 180.00 155.22 24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLU B 126 " pdb=" C GLU B 126 " pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 8861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1301 0.045 - 0.089: 608 0.089 - 0.134: 244 0.134 - 0.178: 55 0.178 - 0.223: 12 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CB VAL D 62 " pdb=" CA VAL D 62 " pdb=" CG1 VAL D 62 " pdb=" CG2 VAL D 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL A 62 " pdb=" CA VAL A 62 " pdb=" CG1 VAL A 62 " pdb=" CG2 VAL A 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL B 62 " pdb=" CA VAL B 62 " pdb=" CG1 VAL B 62 " pdb=" CG2 VAL B 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2217 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 85 " 0.010 2.00e-02 2.50e+03 2.00e-02 6.98e+00 pdb=" CG PHE C 85 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 85 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE C 85 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 85 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 85 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 85 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 85 " -0.010 2.00e-02 2.50e+03 2.00e-02 6.97e+00 pdb=" CG PHE B 85 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 85 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 85 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 85 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 85 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 85 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 85 " -0.009 2.00e-02 2.50e+03 1.99e-02 6.90e+00 pdb=" CG PHE D 85 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE D 85 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE D 85 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 85 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE D 85 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 85 " 0.000 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4522 2.83 - 3.35: 12424 3.35 - 3.86: 23952 3.86 - 4.38: 28869 4.38 - 4.90: 48957 Nonbonded interactions: 118724 Sorted by model distance: nonbonded pdb=" OD2 ASP G 262 " pdb=" OG1 THR G 264 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP E 262 " pdb=" OG1 THR E 264 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP F 262 " pdb=" OG1 THR F 264 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP H 262 " pdb=" OG1 THR H 264 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR H 117 " pdb=" OD1 ASN H 119 " model vdw 2.313 3.040 ... (remaining 118719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.240 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:8.320 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.011 0.128 14720 Z= 0.446 Angle : 1.043 10.491 19944 Z= 0.570 Chirality : 0.060 0.223 2220 Planarity : 0.008 0.058 2600 Dihedral : 9.846 59.946 5448 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.82 (0.14), residues: 1812 helix: -4.27 (0.08), residues: 812 sheet: -0.86 (0.25), residues: 324 loop : -2.68 (0.18), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG F 234 TYR 0.024 0.004 TYR A 112 PHE 0.041 0.004 PHE C 85 TRP 0.017 0.003 TRP C 141 HIS 0.016 0.004 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.01104 (14720) covalent geometry : angle 1.04257 (19944) hydrogen bonds : bond 0.29306 ( 536) hydrogen bonds : angle 9.00332 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6545 (mt-10) REVERT: A 27 LYS cc_start: 0.8093 (ptmt) cc_final: 0.7789 (ptpp) REVERT: A 65 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6928 (tm-30) REVERT: A 107 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7798 (mtp180) REVERT: B 16 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6947 (mtm110) REVERT: B 65 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 107 ARG cc_start: 0.7715 (mtp180) cc_final: 0.7016 (mtp180) REVERT: B 124 GLU cc_start: 0.7082 (tt0) cc_final: 0.6672 (tt0) REVERT: C 32 THR cc_start: 0.7816 (p) cc_final: 0.7607 (m) REVERT: C 107 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7738 (mtp180) REVERT: C 174 ARG cc_start: 0.7733 (mtp180) cc_final: 0.7448 (mtp180) REVERT: D 65 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6881 (tm-30) REVERT: D 107 ARG cc_start: 0.7860 (mtp180) cc_final: 0.7519 (mtm180) REVERT: D 124 GLU cc_start: 0.6961 (tt0) cc_final: 0.6617 (tt0) REVERT: E 57 PHE cc_start: 0.8482 (t80) cc_final: 0.8270 (t80) REVERT: F 177 GLN cc_start: 0.7473 (tm130) cc_final: 0.7095 (tm130) REVERT: G 79 GLN cc_start: 0.6433 (mp10) cc_final: 0.6034 (mp10) REVERT: G 93 GLU cc_start: 0.7061 (mp0) cc_final: 0.6760 (mp0) REVERT: G 95 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6896 (mm-30) REVERT: G 253 GLN cc_start: 0.7144 (mp10) cc_final: 0.6944 (mp10) REVERT: H 177 GLN cc_start: 0.7501 (tm130) cc_final: 0.6996 (tm130) REVERT: H 224 SER cc_start: 0.8039 (t) cc_final: 0.7811 (p) outliers start: 0 outliers final: 1 residues processed: 436 average time/residue: 0.7855 time to fit residues: 367.0850 Evaluate side-chains 387 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN C 75 ASN E 164 GLN E 247 GLN E 260 GLN F 65 GLN F 164 GLN F 247 GLN F 260 GLN G 65 GLN G 145 GLN G 164 GLN G 225 GLN G 247 GLN G 260 GLN H 134 GLN H 164 GLN H 223 GLN H 225 GLN H 253 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.154500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134092 restraints weight = 17985.212| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.71 r_work: 0.3689 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14720 Z= 0.136 Angle : 0.634 8.109 19944 Z= 0.324 Chirality : 0.043 0.158 2220 Planarity : 0.006 0.049 2600 Dihedral : 5.975 57.748 2015 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.65 % Allowed : 8.00 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.88 (0.17), residues: 1812 helix: -2.10 (0.15), residues: 784 sheet: -0.78 (0.25), residues: 340 loop : -2.04 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 116 TYR 0.024 0.002 TYR B 112 PHE 0.012 0.002 PHE D 85 TRP 0.013 0.002 TRP B 141 HIS 0.005 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00317 (14720) covalent geometry : angle 0.63407 (19944) hydrogen bonds : bond 0.04028 ( 536) hydrogen bonds : angle 5.07953 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 383 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: E 6 LEU cc_start: 0.8133 (tp) cc_final: 0.7916 (tt) REVERT: G 93 GLU cc_start: 0.7800 (mp0) cc_final: 0.7477 (mp0) REVERT: H 177 GLN cc_start: 0.8069 (tm130) cc_final: 0.7650 (tm130) outliers start: 25 outliers final: 14 residues processed: 390 average time/residue: 0.7449 time to fit residues: 311.0646 Evaluate side-chains 379 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 364 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 0.0030 chunk 89 optimal weight: 0.7980 overall best weight: 0.4508 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 252 GLN F 65 GLN F 145 GLN F 177 GLN F 247 GLN F 260 GLN G 164 GLN G 223 GLN G 225 GLN G 247 GLN G 260 GLN H 134 GLN H 223 GLN H 225 GLN H 253 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134107 restraints weight = 17832.941| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.73 r_work: 0.3677 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14720 Z= 0.114 Angle : 0.593 7.928 19944 Z= 0.300 Chirality : 0.042 0.163 2220 Planarity : 0.005 0.051 2600 Dihedral : 5.557 55.690 2015 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.11 % Allowed : 9.33 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.84 (0.18), residues: 1812 helix: -0.79 (0.17), residues: 784 sheet: -0.76 (0.25), residues: 340 loop : -1.80 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.019 0.002 TYR B 112 PHE 0.018 0.001 PHE F 70 TRP 0.012 0.001 TRP D 141 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00263 (14720) covalent geometry : angle 0.59304 (19944) hydrogen bonds : bond 0.03359 ( 536) hydrogen bonds : angle 4.68095 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 367 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: G 58 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7753 (t0) REVERT: G 93 GLU cc_start: 0.7800 (mp0) cc_final: 0.7490 (mp0) REVERT: G 95 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7612 (mm-30) REVERT: G 253 GLN cc_start: 0.7650 (mp10) cc_final: 0.7335 (mp10) REVERT: H 177 GLN cc_start: 0.8006 (tm130) cc_final: 0.7634 (tm130) REVERT: H 235 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7804 (mmm-85) outliers start: 47 outliers final: 22 residues processed: 385 average time/residue: 0.8197 time to fit residues: 336.9847 Evaluate side-chains 375 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 351 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 0.0060 chunk 126 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 145 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN G 65 GLN G 164 GLN G 223 GLN G 260 GLN H 134 GLN H 223 GLN H 225 GLN H 253 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.152891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132261 restraints weight = 17667.649| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.72 r_work: 0.3659 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14720 Z= 0.132 Angle : 0.599 8.465 19944 Z= 0.303 Chirality : 0.043 0.166 2220 Planarity : 0.005 0.052 2600 Dihedral : 5.441 53.505 2015 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.17 % Allowed : 10.78 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.25 (0.19), residues: 1812 helix: -0.15 (0.18), residues: 784 sheet: -0.66 (0.26), residues: 340 loop : -1.59 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 59 TYR 0.021 0.002 TYR B 112 PHE 0.019 0.001 PHE F 70 TRP 0.016 0.002 TRP D 141 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00317 (14720) covalent geometry : angle 0.59862 (19944) hydrogen bonds : bond 0.03299 ( 536) hydrogen bonds : angle 4.54832 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: G 68 GLU cc_start: 0.7943 (tt0) cc_final: 0.7689 (tt0) REVERT: G 93 GLU cc_start: 0.7791 (mp0) cc_final: 0.7477 (mp0) REVERT: H 95 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7322 (mm-30) REVERT: H 177 GLN cc_start: 0.8007 (tm130) cc_final: 0.7617 (tm130) outliers start: 48 outliers final: 28 residues processed: 384 average time/residue: 0.7327 time to fit residues: 301.3658 Evaluate side-chains 395 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN F 260 GLN G 65 GLN G 164 GLN G 223 GLN G 260 GLN H 134 GLN H 223 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.153477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133004 restraints weight = 17639.334| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.71 r_work: 0.3656 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14720 Z= 0.133 Angle : 0.596 8.294 19944 Z= 0.301 Chirality : 0.043 0.167 2220 Planarity : 0.005 0.053 2600 Dihedral : 5.403 53.906 2015 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.17 % Allowed : 11.84 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.95 (0.19), residues: 1812 helix: 0.18 (0.19), residues: 784 sheet: -0.62 (0.26), residues: 340 loop : -1.47 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 170 TYR 0.020 0.002 TYR B 112 PHE 0.023 0.001 PHE F 70 TRP 0.017 0.001 TRP D 141 HIS 0.004 0.001 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00322 (14720) covalent geometry : angle 0.59610 (19944) hydrogen bonds : bond 0.03175 ( 536) hydrogen bonds : angle 4.51245 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 367 time to evaluate : 0.596 Fit side-chains REVERT: B 44 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7187 (tm-30) REVERT: D 74 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6648 (mp) REVERT: E 252 GLN cc_start: 0.8155 (tp40) cc_final: 0.7925 (tp40) REVERT: G 64 GLU cc_start: 0.8130 (pm20) cc_final: 0.7671 (pm20) REVERT: G 272 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7304 (mpp-170) REVERT: H 177 GLN cc_start: 0.7995 (tm130) cc_final: 0.7576 (tm130) REVERT: H 235 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7894 (mmm160) outliers start: 48 outliers final: 28 residues processed: 381 average time/residue: 0.7374 time to fit residues: 301.4035 Evaluate side-chains 395 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 364 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 272 ARG Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 126 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 108 optimal weight: 0.0270 chunk 102 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN G 65 GLN G 145 GLN G 164 GLN G 219 GLN G 260 GLN H 65 GLN H 145 GLN H 247 GLN H 260 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133026 restraints weight = 17849.123| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.70 r_work: 0.3660 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14720 Z= 0.146 Angle : 0.611 8.170 19944 Z= 0.309 Chirality : 0.044 0.172 2220 Planarity : 0.005 0.053 2600 Dihedral : 5.434 54.405 2015 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.37 % Allowed : 11.44 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.76 (0.19), residues: 1812 helix: 0.40 (0.19), residues: 784 sheet: -0.60 (0.26), residues: 340 loop : -1.41 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.021 0.002 TYR B 112 PHE 0.023 0.002 PHE F 70 TRP 0.020 0.002 TRP D 141 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00356 (14720) covalent geometry : angle 0.61105 (19944) hydrogen bonds : bond 0.03286 ( 536) hydrogen bonds : angle 4.53029 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 367 time to evaluate : 0.568 Fit side-chains REVERT: B 44 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: D 16 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7666 (ttp80) REVERT: D 74 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6628 (mp) REVERT: E 252 GLN cc_start: 0.8145 (tp40) cc_final: 0.7940 (tp40) REVERT: G 68 GLU cc_start: 0.7886 (tt0) cc_final: 0.7549 (tt0) REVERT: G 253 GLN cc_start: 0.7650 (mp10) cc_final: 0.7345 (mp10) REVERT: G 272 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7346 (mpp-170) REVERT: H 177 GLN cc_start: 0.8015 (tm130) cc_final: 0.7580 (tm130) REVERT: H 235 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7855 (mmm160) outliers start: 51 outliers final: 30 residues processed: 381 average time/residue: 0.7046 time to fit residues: 287.9263 Evaluate side-chains 398 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 272 ARG Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 0.0050 chunk 176 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 ASN E 65 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN F 260 GLN G 65 GLN G 145 GLN G 260 GLN H 65 GLN H 145 GLN H 260 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.152150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132494 restraints weight = 17842.137| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.67 r_work: 0.3654 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 0.061 14720 Z= 0.162 Angle : 0.629 8.608 19944 Z= 0.319 Chirality : 0.045 0.178 2220 Planarity : 0.005 0.053 2600 Dihedral : 5.523 55.615 2015 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.57 % Allowed : 11.90 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.70 (0.19), residues: 1812 helix: 0.44 (0.19), residues: 792 sheet: -0.62 (0.26), residues: 340 loop : -1.37 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.022 0.002 TYR B 112 PHE 0.025 0.002 PHE F 70 TRP 0.024 0.002 TRP B 141 HIS 0.005 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00398 (14720) covalent geometry : angle 0.62908 (19944) hydrogen bonds : bond 0.03423 ( 536) hydrogen bonds : angle 4.58147 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 time to evaluate : 0.527 Fit side-chains REVERT: B 44 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: G 62 ARG cc_start: 0.7598 (mtm180) cc_final: 0.7371 (mtm180) REVERT: G 68 GLU cc_start: 0.7873 (tt0) cc_final: 0.7549 (tt0) REVERT: G 272 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7363 (mpp-170) REVERT: H 177 GLN cc_start: 0.7958 (tm130) cc_final: 0.7509 (tm130) outliers start: 54 outliers final: 28 residues processed: 376 average time/residue: 0.7382 time to fit residues: 297.5799 Evaluate side-chains 391 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 361 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 272 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN G 65 GLN G 260 GLN H 65 GLN H 145 GLN H 260 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.152330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.132538 restraints weight = 17783.293| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.69 r_work: 0.3655 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14720 Z= 0.154 Angle : 0.632 9.187 19944 Z= 0.319 Chirality : 0.045 0.177 2220 Planarity : 0.005 0.054 2600 Dihedral : 5.494 55.262 2015 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.78 % Allowed : 12.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 1812 helix: 0.57 (0.19), residues: 784 sheet: -0.63 (0.26), residues: 340 loop : -1.35 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.022 0.002 TYR B 112 PHE 0.027 0.002 PHE F 70 TRP 0.023 0.002 TRP B 141 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00377 (14720) covalent geometry : angle 0.63165 (19944) hydrogen bonds : bond 0.03329 ( 536) hydrogen bonds : angle 4.56128 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.566 Fit side-chains REVERT: B 44 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: B 48 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7852 (mtp85) REVERT: E 87 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8428 (mp) REVERT: G 68 GLU cc_start: 0.7910 (tt0) cc_final: 0.7554 (tt0) REVERT: G 253 GLN cc_start: 0.7680 (mp10) cc_final: 0.7388 (mp10) REVERT: G 272 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7372 (mpp-170) REVERT: H 177 GLN cc_start: 0.7953 (tm130) cc_final: 0.7515 (tm130) REVERT: H 235 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7956 (mmm160) outliers start: 42 outliers final: 26 residues processed: 376 average time/residue: 0.7537 time to fit residues: 303.9283 Evaluate side-chains 383 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 272 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN F 260 GLN G 65 GLN G 260 GLN H 65 GLN H 145 GLN H 260 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.132328 restraints weight = 17979.832| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.68 r_work: 0.3649 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14720 Z= 0.160 Angle : 0.643 9.610 19944 Z= 0.325 Chirality : 0.045 0.180 2220 Planarity : 0.005 0.053 2600 Dihedral : 5.526 55.605 2015 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.65 % Allowed : 13.62 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1812 helix: 0.62 (0.19), residues: 784 sheet: -0.63 (0.26), residues: 340 loop : -1.37 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.022 0.002 TYR B 112 PHE 0.028 0.002 PHE F 70 TRP 0.025 0.002 TRP B 141 HIS 0.005 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00393 (14720) covalent geometry : angle 0.64272 (19944) hydrogen bonds : bond 0.03400 ( 536) hydrogen bonds : angle 4.57059 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.490 Fit side-chains REVERT: B 44 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: G 68 GLU cc_start: 0.7871 (tt0) cc_final: 0.7525 (tt0) REVERT: G 253 GLN cc_start: 0.7710 (mp10) cc_final: 0.7414 (mp10) REVERT: G 272 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7372 (mpp-170) REVERT: H 177 GLN cc_start: 0.7970 (tm130) cc_final: 0.7543 (tm130) outliers start: 40 outliers final: 30 residues processed: 370 average time/residue: 0.7403 time to fit residues: 293.3553 Evaluate side-chains 379 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 347 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 272 ARG Chi-restraints excluded: chain H residue 8 GLU Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 161 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 20 optimal weight: 0.0050 chunk 35 optimal weight: 0.9980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 247 GLN F 260 GLN G 65 GLN G 260 GLN H 65 GLN H 145 GLN H 260 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.153358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133634 restraints weight = 17863.891| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.70 r_work: 0.3668 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14720 Z= 0.117 Angle : 0.616 9.457 19944 Z= 0.308 Chirality : 0.043 0.176 2220 Planarity : 0.005 0.050 2600 Dihedral : 5.244 52.702 2015 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.12 % Allowed : 14.15 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.20), residues: 1812 helix: 0.77 (0.20), residues: 780 sheet: -0.58 (0.26), residues: 340 loop : -1.28 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.019 0.002 TYR G 212 PHE 0.026 0.001 PHE F 70 TRP 0.016 0.001 TRP A 141 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00273 (14720) covalent geometry : angle 0.61612 (19944) hydrogen bonds : bond 0.02939 ( 536) hydrogen bonds : angle 4.49082 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 358 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 44 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: C 48 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7971 (mtp85) REVERT: D 16 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7712 (ttp80) REVERT: D 74 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6755 (tp) REVERT: G 68 GLU cc_start: 0.7832 (tt0) cc_final: 0.7492 (tt0) REVERT: G 253 GLN cc_start: 0.7612 (mp10) cc_final: 0.7351 (mp10) REVERT: G 272 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7192 (mpp-170) REVERT: H 177 GLN cc_start: 0.7884 (tm130) cc_final: 0.7482 (tm130) outliers start: 32 outliers final: 19 residues processed: 365 average time/residue: 0.7030 time to fit residues: 274.9945 Evaluate side-chains 377 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 355 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 272 ARG Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 64 GLU Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 0.0010 chunk 156 optimal weight: 0.0370 chunk 154 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 chunk 127 optimal weight: 1.9990 overall best weight: 0.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN E 145 GLN E 247 GLN E 260 GLN F 65 GLN F 145 GLN F 223 GLN F 247 GLN F 260 GLN G 65 GLN G 260 GLN H 65 GLN H 145 GLN H 260 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133100 restraints weight = 17937.397| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.71 r_work: 0.3658 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14720 Z= 0.132 Angle : 0.631 9.459 19944 Z= 0.315 Chirality : 0.044 0.178 2220 Planarity : 0.005 0.049 2600 Dihedral : 5.127 52.785 2012 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.92 % Allowed : 14.81 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.42 (0.20), residues: 1812 helix: 0.76 (0.19), residues: 780 sheet: -0.58 (0.26), residues: 340 loop : -1.26 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 170 TYR 0.022 0.002 TYR G 212 PHE 0.010 0.001 PHE H 25 TRP 0.019 0.002 TRP D 141 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00316 (14720) covalent geometry : angle 0.63085 (19944) hydrogen bonds : bond 0.03088 ( 536) hydrogen bonds : angle 4.51846 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7096.54 seconds wall clock time: 120 minutes 57.57 seconds (7257.57 seconds total)